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Genomic architecture underlying a major transition in social evolution [email protected] http://wurmlab.github.io 2014-11-30-Lyon

2014 11-28-lyon

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Page 1: 2014 11-28-lyon

Genomic architecture underlying a major transition in

social evolution

[email protected] http://wurmlab.github.io2014-11-30-Lyon

Page 2: 2014 11-28-lyon

© Alex Wild & others

Page 3: 2014 11-28-lyon
Page 4: 2014 11-28-lyon

© National Geographic

Atta leaf-cutter ants

Page 5: 2014 11-28-lyon

© National Geographic

Atta leaf-cutter ants

Page 6: 2014 11-28-lyon

© National Geographic

Atta leaf-cutter ants

Page 7: 2014 11-28-lyon
Page 8: 2014 11-28-lyon

Oecophylla Weaver ants

© ameisenforum.de

Page 9: 2014 11-28-lyon

© ameisenforum.de

Fourmis tisserandes

Page 10: 2014 11-28-lyon

© ameisenforum.de

Oecophylla Weaver ants

Page 11: 2014 11-28-lyon

© forestryimages.org© wynnie@flickr

Page 12: 2014 11-28-lyon

Tofilski et al 2008

Forelius pusillus

Page 13: 2014 11-28-lyon

Tofilski et al 2008

Forelius pusillus hides the nest entrance at night

Page 14: 2014 11-28-lyon

Tofilski et al 2008

Forelius pusillus hides the nest entrance at night

Page 15: 2014 11-28-lyon

Tofilski et al 2008

Forelius pusillus hides the nest entrance at night

Page 16: 2014 11-28-lyon

Tofilski et al 2008

Forelius pusillus hides the nest entrance at night

Page 17: 2014 11-28-lyon

Avant

Workers staying outside die« preventive self-sacrifice »

Tofilski et al 2008

Forelius pusillus hides the nest entrance at night

Page 18: 2014 11-28-lyon

Dorylus driver ants: ants with no home

© BBC

Page 19: 2014 11-28-lyon

Animal biomass (Brazilian rainforest)

from Fittkau & Klinge 1973

Other insects AmphibiansReptiles

Birds

Mammals

Earthworms

Spiders

Soil fauna excluding earthworms,

ants & termites

Ants & termites

Page 20: 2014 11-28-lyon

Well-studied:• behavior

• morphology

• evolutionary context

• ecology

Genetic basis?

Page 21: 2014 11-28-lyon
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www.sciencemag.org SCIENCE VOL 331 25 FEBRUARY 2011 1067

REPORTS

on

Mar

ch 1

2, 2

013

ww

w.s

cien

cem

ag.o

rgD

ownl

oade

d fro

m

Solenopsis invicta fire ants are a big problem!very well studied!

Ascunce et al 2011

Page 24: 2014 11-28-lyon

Solenopsis invicta fire ant: two social forms

•1 large queen•Independent founding•Highly territorial•Many sizes of workers

•2-100 smaller queens•Dependent founding•No inter-colony aggression•All workers similar size

Single-queen form: Multiple-queen form:

Page 25: 2014 11-28-lyon

Fire ants+

Population genetics: Allozyme screen

Ken Ross

“starch gel”+

1 2 3

L. Keller

Page 26: 2014 11-28-lyon

Allozyme screen Social form associated to Gp-9 locus

Frequency of the most

common allele

Locus!

0.3!0.4!0.5!0.6!0.7!0.8!0.9!1.0!

Single queen!Multiple queen!

Est-6!Est-4!G3pdh-1!Ca-4!Pgm-4!Ddh-1!Pro-5!

Pgm-3!

Acoh-5!

acoh-1!

Acy-1!

Pgm-1!

Aat-2!

Gp-9!

Ken Ross and colleaguesLaurent Keller and colleagues

Page 27: 2014 11-28-lyon

Single queen form Multiple queen form

Ken Ross and colleaguesLaurent Keller and colleagues

Social form completely associated to Gp-9 locus

Page 28: 2014 11-28-lyon

bbbbBB BB Bb bb

Ken Ross and colleaguesLaurent Keller and colleagues

Single queen form Multiple queen form

Social form completely associated to Gp-9 locus

Page 29: 2014 11-28-lyon

bbBB BB Bb

x

Gp-9 bb females rareKen Ross and colleagues

Laurent Keller and colleagues

Single queen form Multiple queen form

Social form completely associated to Gp-9 locus

Page 30: 2014 11-28-lyon

BB BB Bb

Ken Ross and colleaguesLaurent Keller and colleagues

Single queen form Multiple queen form

Social form completely associated to Gp-9 locus

Page 31: 2014 11-28-lyon

BB BB Bb

xKen Ross and colleagues

Laurent Keller and colleagues

Single queen form Multiple queen form

Social form completely associated to Gp-9 locus

Page 32: 2014 11-28-lyon

BB BB Bb

x xKen Ross and colleagues

Laurent Keller and colleagues

Social form completely associated to Gp-9 locus

Single queen form Multiple queen form

Page 33: 2014 11-28-lyon

BB BB Bb

x x xKen Ross and colleagues

Laurent Keller and colleagues

Single queen form Multiple queen form(>15% ) (< 5% )

Social form completely associated to Gp-9 locus

Page 34: 2014 11-28-lyon

Social form completely associated to Gp-9 locus

• Is this gene the single überregulator?

Page 35: 2014 11-28-lyon

• Is this gene the single überregulator?

Social form completely associated to Gp-9 locus

maybe 1/14th of the genome?

•Only 14 allozyme markers were used

Locus!

0.3!0.4!0.5!0.6!0.7!0.8!0.9!1.0!

Single queen!Multiple queen!

Est-6!Est-4!G3pdh-1!Ca-4!Pgm-4!Ddh-1!Pro-5!

Pgm-3!

Acoh-5!

acoh-1!

Acy-1!

Pgm-1!

Aat-2!

Gp-9!

Page 36: 2014 11-28-lyon

This changes everything.454

IlluminaSolid...

Any lab can sequence anything!

Page 37: 2014 11-28-lyon
Page 38: 2014 11-28-lyon

Are other genes linked to Gp-9?Sequenced:

•Genome

Single ♂:His brothers:

11×4×

(330bp-insert paired reads) (normal single-end reads)45× +Sequencing from haploid males (for easier assembly):

(8,000 & 20,000bp-insert paired reads)

B 20x

Genome of a Gp-9 B ♂

Page 39: 2014 11-28-lyon

★ Expansion of lipid-processing gene families (for Cuticular Hydrocarbons?)

★ 420 putative olfactory receptors (more than any other insect!)

0.05

SiOR

04648+10

SiOR01968+4

SiOR0

0899+7

SiOR02814+3

SiOR04171+6

SiO

R04609+4

SiOR00330+28

SiO

R02

694+25

SiO

R04609+20

SiOR05285+6

SiOR00330+25

SiOR04510+15

SiOR00330+18

SiOR04609+23

SiOR01

968+23

SiO

R03

952+4

SiOR0

4648+16

SiO

R05

901+2

SiO

R02

944+4

SiOR01968+5

SiOR04171+19 SiOR

04648+5

SiOR10535+3

SiOR0

1224+3

SiOR06723+2

SiOR01968+9

SiOR02883+1

SiOR0

0899+3

SiOR01629+1

SiOR04171+1

SiOR01629+11

SiOR04171+10

SiOR04171+13

SiOR02694+3

SiOR04171+20

SiO

R02694+35

SiOR04171+15

SiOR04609+7

SiOR05118+2

SiOR07

837+2

SiO

R02

694+27

SiOR01968+10

SiOR04648+17

SiOR0196

8+19

SiO

R02

694+17

SiOR04648+13

SiOR01968+6

SiOR

00899+1

2

SiOR0

5901+1

SiOR00330+20

SiO

R02

648+2

SiO

R02

659+2

SiOR01968+1

6

SiOR0

0899+11

SiO

R02974

SiOR04171+2

SiOR03952+2

SiOR06792+2

SiOR04510+4

SiOR04171+28

SiOR05285+5

SiOR05285+9

SiOR

00899+1

5

SiOR

04648+3

SiO

R02694+36

SiOR10535+1

SiO

R02

694+19

SiO

R02

694+23

SiOR02694+1

SiO

R04609+14

SiOR01122

SiOR

04648+9

SiO

R02694+34

SiOR01629+8

SiOR

04648+8

SiOR04510+8

SiOR06573

SiO

R02

944+1

SiOR00330+26

SiO

R00330+1S

iOR02

694+15

SiO

R03038

SiOR05285+7

SiOR0

0899+5

SiOR04609+10

SiO

R04609+3

SiOR04339

SiOR0

8068

SiOR

04648+6

SiOR04510+2

SiOR05285+8

SiOR01

573+4

SiOR0366

3

SiOR04171+8

SiOR01858+2

SiOR01968+2SiOR01968+1

SiOR02694+5

SiOR01968+3

SiOR06723+3

SiOR01968+15

SiOR05285+1

SiOR0

0899+4

SiOR04609+22

SiOR04171+9

SiOR02694+9

SiO

R02

648+1

SiOR06792+3

SiOR0

1573+2

SiO

R02

694+20

SiOR1

0542

SiO

R04609+15

SiOR02694+8

SiOR00330+16

SiOR0

0899+2

SiOR02694+10

SiOR04510+9

SiOR05285+3

SiOR04171+24

SiO

R04609+2

SiOR05285+11

SiOR02

694+14

SiOR01

573+1

SiOR05285+2

SiOR00613

SiOR0196

8+22

SiOR

00899+9

SiO

R06

843+2

SiO

R02694+37

SiOR0

0899+1

SiOR04609+9

SiOR05431+2

SiOR10535+2

SiOR00330+15

SiO

R02

694+18

SiOR0

1224+2

SiOR04510+11

SiOR00330+23

SiO

R02

694+29

SiOR05416

SiOR05285+10

SiOR02694+2

SiOR01629+9

SiOR05431+1

SiOR02883+2

SiOR04171+14

SiO

R08

341

SiO

R02

694+22

SiOR01

224+1

SiOR01968+12

SiOR05431+3

SiOR04510+6

SiOR02694+7

SiOR04609+5

SiO

R02

944+2

SiOR03

952+3

SiOR01968+8

SiOR04609+24

SiO

R02

694+30

SiOR01629+10

SiOR04510+14

SiOR00565

SiOR05118+3

SiO

R01321

SiO

R04609+19

SiOR00330+14

SiO

R02694+38

SiOR04609+8

SiOR04171+16

SiOR10455

SiO

R04609+16

SiO

R04609+21

SiO

R02

694+28

SiO

R02

659+1

SiOR04171+5

SiOR00330+29

SiOR01968+14

SiOR03983

SiOR00330+27

SiOR05285+4

SiOR04510+1

SiOR

00899+8

SiOR

04648+7

SiO

R04609+17

SiO

R00330+5

SiO

R02

694+21

SiOR02814+4

SiOR00330+7

SiOR01

629+3

SiOR01

968+26

SiO

R02694+31

SiOR0

4648+2

SiO

R02694+39

SiOR04171+25

SiOR06577

SiOR01

968+25

SiOR04171+21

SiOR06792+6

SiO

R04609+11

SiOR02694+11

SiOR06792+1

SiOR04171+4

SiOR01629+5

SiOR00330+21

SiOR0

4648+15

SiO

R00330+6

SiO

R02

694+16

SiOR

04648+11

SiOR

04648+4

SiO

R00330+3

SiO

R06

535

SiOR04171+7

SiOR10493

SiO

R02694+32

SiOR06792+4

SiOR04510+3

SiO

R06

890

SiOR0196

8+20

SiO

R04609+12

SiOR04171+3

SiOR01968

+18

SiOR01968+11

SiO

R04609+13

SiOR01629+12

SiOR00330+22

SiO

R02694+33

SiOR00330+13

SiOR01

573+3

SiOR04510+16

SiOR04171+12

SiOR04510+13

SiOR

05118+1

SiO

R02

944+3

SiOR04171+26

SiOR04171+17

SiOR

00899+14

SiOR04171+29

SiOR

00899+1

3

SiOR02694+13

SiOR00330+24

SiOR00330+19

SiOR04171+27

SiO

R02

694+24

SiOR04510+5

SiOR07090

SiOR03952+1

SiOR04510+10

SiOR00330+17

SiO

R02

694+26

SiO

R04609+1

SiOR0

0899+6

SiOR04648+12

SiOR02814+2

SiOR00330+11

SiOR04171+18

SiOR01968+1

7

SiOR00330+10

SiOR00330+9

SiOR0162

9+2

SiOR04171+11

SiOR04510+12

SiOR0196

8+21

SiOR00330+8

SiOR01858+1

SiOR04510+7

SiOR05431+4

SiOR02694+6

SiOR01968+13

SiO

R00330+4

SiO

R04609+18

SiOR0

0899+10

SiOR00330+12

SiOR00330+31

SiO

R06

843+1

SiOR07

837+1

SiO

R00330+2

SiOR01629+4

SiOR0

4648+1

SiOR01

968+24

SiOR04171+23

SiOR0162

9+7

SiOR0

4648+14

SiO

R06

843+3

SiOR06792+5

SiOR01968+7

SiOR01629

+6

SiOR02883+3

SiOR02694+12

SiOR

05118+4

SiOR04171+22

SiO

R01080

SiOR04609+6

SiOR02814+1

SiOR00330+30

SiOR05285+12

SiOR06723+1

SiOR02694+4

Wurm et al 2011

> 400Nasonia wasp 225honey bee 165

6510

fire antGenome of a Gp-9 B ♂

Page 40: 2014 11-28-lyon

★ Expansion of lipid-processing gene families (for Cuticular Hydrocarbons)

★ 420 putative olfactory receptors (more than any other insect!)

★ Functional DNA-methylation system

Wurm et al 2011

0.05

SiOR

04648+10

SiOR01968+4

SiOR0

0899+7

SiOR02814+3

SiOR04171+6

SiO

R04609+4

SiOR00330+28

SiO

R02

694+25

SiO

R04609+20

SiOR05285+6

SiOR00330+25

SiOR04510+15

SiOR00330+18

SiOR04609+23

SiOR01

968+23

SiO

R03

952+4

SiOR0

4648+16

SiO

R05

901+2

SiO

R02

944+4

SiOR01968+5

SiOR04171+19 SiOR

04648+5

SiOR10535+3

SiOR0

1224+3

SiOR06723+2

SiOR01968+9

SiOR02883+1

SiOR0

0899+3

SiOR01629+1

SiOR04171+1

SiOR01629+11

SiOR04171+10

SiOR04171+13

SiOR02694+3

SiOR04171+20

SiO

R02694+35

SiOR04171+15

SiOR04609+7

SiOR05118+2

SiOR07

837+2

SiO

R02

694+27

SiOR01968+10

SiOR04648+17

SiOR0196

8+19

SiO

R02

694+17

SiOR04648+13

SiOR01968+6

SiOR

00899+1

2

SiOR0

5901+1

SiOR00330+20

SiO

R02

648+2

SiO

R02

659+2

SiOR01968+1

6

SiOR0

0899+11

SiO

R02974

SiOR04171+2

SiOR03

952+2

SiOR06792+2

SiOR04510+4

SiOR04171+28

SiOR05285+5

SiOR05285+9

SiOR

00899+1

5

SiOR

04648+3

SiO

R02694+36

SiOR10535+1

SiO

R02

694+19

SiO

R02

694+23

SiOR02694+1

SiO

R04609+14

SiOR01122

SiOR

04648+9

SiO

R02694+34

SiOR01629+8

SiOR

04648+8

SiOR04510+8

SiOR06573

SiO

R02

944+1

SiOR00330+26

SiO

R00330+1S

iOR02

694+15

SiO

R03038

SiOR05285+7

SiOR0

0899+5

SiOR04609+10

SiO

R04609+3

SiOR04339

SiOR0

8068

SiOR

04648+6

SiOR04510+2

SiOR05285+8

SiOR01

573+4

SiOR0366

3

SiOR04171+8

SiOR01858+2

SiOR01968+2SiOR01968+1

SiOR02694+5

SiOR01968+3

SiOR06723+3

SiOR01968+1

5

SiOR05285+1

SiOR0

0899+4

SiOR04609+22

SiOR04171+9

SiOR02694+9

SiO

R02

648+1

SiOR06792+3

SiOR0

1573+2

SiO

R02

694+20

SiOR1

0542

SiO

R04609+15

SiOR02694+8

SiOR00330+16

SiOR0

0899+2

SiOR02694+10

SiOR04510+9

SiOR05285+3

SiOR04171+24

SiO

R04609+2

SiOR05285+11

SiOR02

694+14

SiOR01

573+1

SiOR05285+2

SiOR00613

SiOR0196

8+22

SiOR

00899+9

SiO

R06

843+2

SiO

R02694+37

SiOR0

0899+1

SiOR04609+9

SiOR05431+2

SiOR10535+2

SiOR00330+15

SiO

R02

694+18

SiOR0

1224+2

SiOR04510+11

SiOR00330+23

SiO

R02

694+29

SiOR05416

SiOR05285+10

SiOR02694+2

SiOR01629+9

SiOR05431+1

SiOR02883+2

SiOR04171+14

SiO

R08

341

SiO

R02

694+22

SiOR01

224+1

SiOR01968+12

SiOR05431+3

SiOR04510+6

SiOR02694+7

SiOR04609+5

SiO

R02

944+2

SiOR03

952+3

SiOR01968+8

SiOR04609+24

SiO

R02

694+30

SiOR01629+10

SiOR04510+14

SiOR00565

SiOR05118+3

SiO

R01321

SiO

R04609+19

SiOR00330+14

SiO

R02694+38

SiOR04609+8

SiOR04171+16

SiOR10455

SiO

R04609+16

SiO

R04609+21

SiO

R02

694+28

SiO

R02

659+1

SiOR04171+5

SiOR00330+29

SiOR01968+14

SiOR03983

SiOR00330+27

SiOR05285+4

SiOR04510+1

SiOR

00899+8

SiOR

04648+7

SiO

R04609+17

SiO

R00330+5

SiO

R02

694+21

SiOR02814+4

SiOR00330+7

SiOR01

629+3

SiOR01

968+26

SiO

R02694+31

SiOR0

4648+2

SiO

R02694+39

SiOR04171+25

SiOR06577

SiOR01

968+25

SiOR04171+21

SiOR06792+6

SiO

R04609+11

SiOR02694+11

SiOR06792+1

SiOR04171+4

SiOR01629+5

SiOR00330+21

SiOR0

4648+15

SiO

R00330+6

SiO

R02

694+16

SiOR04648+11

SiOR

04648+4

SiO

R00330+3

SiO

R06

535

SiOR04171+7

SiOR10493

SiO

R02694+32

SiOR06792+4

SiOR04510+3

SiO

R06

890

SiOR0196

8+20

SiO

R04609+12

SiOR04171+3

SiOR01968

+18

SiOR01968+11

SiO

R04609+13

SiOR01629+12

SiOR00330+22

SiO

R02694+33

SiOR00330+13

SiOR01

573+3

SiOR04510+16

SiOR04171+12

SiOR04510+13

SiOR

05118+1

SiO

R02

944+3

SiOR04171+26

SiOR04171+17

SiOR

00899+14

SiOR04171+29

SiOR

00899+1

3

SiOR02694+13

SiOR00330+24

SiOR00330+19

SiOR04171+27

SiO

R02

694+24

SiOR04510+5

SiOR07090

SiOR03952+1

SiOR04510+10

SiOR00330+17

SiO

R02

694+26

SiO

R04609+1

SiOR0

0899+6

SiOR04648+12

SiOR02814+2

SiOR00330+11

SiOR04171+18

SiOR01968+1

7

SiOR00330+10

SiOR00330+9

SiOR0162

9+2

SiOR04171+11

SiOR04510+12

SiOR0196

8+21

SiOR00330+8

SiOR01858+1

SiOR04510+7

SiOR05431+4

SiOR02694+6

SiOR01968+13

SiO

R00330+4

SiO

R04609+18

SiOR0

0899+10

SiOR00330+12

SiOR00330+31

SiO

R06

843+1

SiOR07

837+1

SiO

R00330+2

SiOR01629+4

SiOR0

4648+1

SiOR01

968+24

SiOR04171+23

SiOR0162

9+7

SiOR0

4648+14

SiO

R06

843+3

SiOR06792+5

SiOR01968+7

SiOR01629

+6

SiOR02883+3

SiOR02694+12

SiOR

05118+4

SiOR04171+22

SiO

R01080

SiOR04609+6

SiOR02814+1

SiOR00330+30

SiOR05285+12

SiOR06723+1

SiOR02694+4

fire antGenome of a Gp-9 B ♂

Page 41: 2014 11-28-lyon

★ Expansion of lipid-processing gene families (for Cuticular Hydrocarbons)

★ 420 putative olfactory receptors (more than any other insect!)

★ Functional DNA-methylation system ★Ant-specific duplication and subfunctionalization

of vitellogenin (in bees: involved in reproduction & division of labor)

Wurm et al 2011

significance of these duplication events in vitellogenins, odorperception genes, and a family of lipid-processing genes. We alsodiscuss additional features of interest in the fire ant genome rel-evant to the complex social biology of this species, including sexdetermination genes, DNA methylation genes, telomerase, andthe insulin and juvenile hormone pathways.

Vitellogenins. In contrast to other insects that mainly have only oneor two vitellogenins, the fire ant genome harbors four adjacent

copies of vitellogenin (Vg1-4) (Fig. 3A), all of which are at leastpartially supported by EST reads. A phylogenetic analysis revealsthat an ancestral vitellogenin gene first underwent duplication,followed by possibly independent duplications of each of thedaughter vitellogenins, thus giving rise to Vg1 and Vg4 and to Vg2andVg3. All of these duplications occurred after the ancestor offireants split from wasps and bees (Fig. 3B). The single vitellogeninfound inA.mellifera is amultifunctional protein (26) involved in theregulation of life span (27, 28) and division of labor (29). Quanti-tative RT-PCR shows thatVg1 andVg4 are preferentially expressedin workers and Vg2 and Vg3 in queens (Fig. 3C, SI Materials andMethods, and Table S1G). Vitellogenin expression in S. invictaworkers is surprising because they lack ovaries. Given the super-organism properties of ant societies, the expression patterns sug-gest that vitellogenins underwent neo- or subfunctionalizationafter duplication to acquire caste-specific functions.

Odor Perception. Consistent with studies in other insects, we finda single S. invicta ortholog to DmOr83b, a broadly expressed ol-factory receptor (OR) required to interact with other ORs forDrosophila and Tribolium castaneum olfaction (30–32). BeyondOR83b, OR number varies greatly between insect species. Blastsearches and GeneWise searches using an HMM profile con-structed with aligned ORs from N. vitripennis (33) and Pogono-myrmex barbatus identified more than 400 loci in the S. invictagenome with significant sequence similarity to ORs. Preliminarywork on gene model reconstruction identified 297 intact full-length proteins. Many S. invicta ORs are in tandem arrays (Fig.S2A) and derive from recent expansions. S. invicta may thus har-bor the largest identified insect OR repertoire because there are10 ORs in Pediculus humanus (34), 60 in Drosophila, 165 inA. mellifera, 225 in N. vitripennis (33), and 259 in T. castaneum(32). The large numbers of N. vitripennis and T. castaneum ORsare thought to be due to current or past difficulties in host andfood finding. As has been suggested for A. mellifera (35), the largenumber of S. invicta ORs may result from the importance ofchemical communication in ants. The odorant-binding proteins(OBPs) are another family of genes also known to play roles inchemosensation in Drosophila (36). Intriguingly, the social orga-nization of S. invicta colonies is completely associated with se-

Eum

etaz

oa

No hits 3424

Not assigned 274

Cnidaria 100

Art

hro

po

da

Ne

op

tera

Coe

lom

ata

Bila

teri

a

Nematoda 25

Deuterostomia 173

Arachnida 50

Paraneoptera 577

End

opte

rygo

ta

Hym

en

op

tera

Apoidea 7398

Chalcidoidea 3271

Ichneumonoidea 94

Diptera 404

Lepidoptera 29

Coleoptera 713

Fig. 2. Taxonomic distribution of best blastp hits of S. invicta proteins to thenonredundant (nr) protein database (E < 10−5). Results were first plottedusing MEGAN software (22) and then branches with fewer than 20 hits wereremoved, branch lengths were reduced for compactness, and tree topologywas adjusted to reflect consensus phylogenies (23, 24).

Vg1Vg4 Vg3 Vg2

2,330,000 bp 2,360,000 bpA

B CSolenopsis Vg1Solenopsis Vg4Solenopsis Vg2Solenopsis Vg3

Apis VgBombus Vg

Nasonia Vg1

Nasonia Vg2Pteromalus Vg

Encarsia VgPimpla Vg

Athalia Vg

Apocrita

Tenthedinoidea

Vespoidea

Apoidea

Aculeata

Chalcidoidea

Ichneumonoidea 0

5000

10000

15000

20000

25000 Vg3Vg2

142 389 17820 1.4 9269 0.61 40WQ WQW Q WQ

*** ***Vg1 Vg4* ***

0

100

200

300

400

500

600

Fig. 3. S. invicta vitellogenins. (A) Four vitellogenins are located within a single 40,000-bp region of the S. invicta genome. (B) Parsimony tree of known hy-menopteran vitellogenin protein sequences suggests that two rounds of vitellogenin duplication occurred after the split between ants and other hyme-nopterans including bees and wasps. (C) Quantitative RT-PCR of the four putative S. invicta vitellogenins on whole bodies of major workers (W) and matedqueens (Q) (n = 10). The y axis indicates mRNA concentrations for the different vitellogenins. Values depicted by each bar are shown below the x-axis labels.Error bars represent SEs. Expression differences between queens and workers were significant (Bonferroni-corrected two-tailed t tests: *P < 0.05, ***P < 10−10).

Wurm et al. PNAS Early Edition | 3 of 6

EVOLU

TION

0.05

SiOR

04648+10

SiOR01968+4

SiOR0

0899+7

SiOR02814+3

SiOR04171+6

SiO

R04609+4

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SiO

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SiOR04510+15

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SiOR04609+23

SiOR01

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SiO

R03

952+4

SiOR0

4648+16

SiO

R05

901+2

SiO

R02

944+4

SiOR01968+5

SiOR04171+19 SiOR

04648+5

SiOR10535+3

SiOR0

1224+3

SiOR06723+2

SiOR01968+9

SiOR02883+1

SiOR0

0899+3

SiOR01629+1

SiOR04171+1

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SiOR04171+10

SiOR04171+13

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SiOR07

837+2

SiO

R02

694+27

SiOR01968+10

SiOR04648+17

SiOR0196

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SiO

R02

694+17

SiOR04648+13

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SiOR

00899+1

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SiOR0

5901+1

SiOR00330+20

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SiOR01968+1

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SiOR0

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SiOR03

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SiO

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SiOR01629+8

SiOR

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SiOR04510+8

SiOR06573

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R02

944+1

SiOR00330+26

SiO

R00330+1S

iOR02

694+15

SiO

R03038

SiOR05285+7

SiOR0

0899+5

SiOR04609+10

SiO

R04609+3

SiOR04339

SiOR0

8068

SiOR

04648+6

SiOR04510+2

SiOR05285+8

SiOR01

573+4

SiOR0366

3

SiOR04171+8

SiOR01858+2

SiOR01968+2SiOR01968+1

SiOR02694+5

SiOR01968+3

SiOR06723+3

SiOR01968+1

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SiOR05285+1

SiOR0

0899+4

SiOR04609+22

SiOR04171+9

SiOR02694+9

SiO

R02

648+1

SiOR06792+3

SiOR0

1573+2

SiO

R02

694+20

SiOR1

0542

SiO

R04609+15

SiOR02694+8

SiOR00330+16

SiOR0

0899+2

SiOR02694+10

SiOR04510+9

SiOR05285+3

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SiO

R04609+2

SiOR05285+11

SiOR02

694+14

SiOR01

573+1

SiOR05285+2

SiOR00613

SiOR0196

8+22

SiOR

00899+9

SiO

R06

843+2

SiO

R02694+37

SiOR0

0899+1

SiOR04609+9

SiOR05431+2

SiOR10535+2

SiOR00330+15

SiO

R02

694+18

SiOR0

1224+2

SiOR04510+11

SiOR00330+23

SiO

R02

694+29

SiOR05416

SiOR05285+10

SiOR02694+2

SiOR01629+9

SiOR05431+1

SiOR02883+2

SiOR04171+14

SiO

R08

341

SiO

R02

694+22

SiOR01

224+1

SiOR01968+12

SiOR05431+3

SiOR04510+6

SiOR02694+7

SiOR04609+5

SiO

R02

944+2

SiOR03

952+3

SiOR01968+8

SiOR04609+24

SiO

R02

694+30

SiOR01629+10

SiOR04510+14

SiOR00565

SiOR05118+3

SiO

R01321

SiO

R04609+19

SiOR00330+14

SiO

R02694+38

SiOR04609+8

SiOR04171+16

SiOR10455

SiO

R04609+16

SiO

R04609+21

SiO

R02

694+28

SiO

R02

659+1

SiOR04171+5

SiOR00330+29

SiOR01968+14

SiOR03983

SiOR00330+27

SiOR05285+4

SiOR04510+1

SiOR

00899+8

SiOR

04648+7

SiO

R04609+17

SiO

R00330+5

SiO

R02

694+21

SiOR02814+4

SiOR00330+7

SiOR01

629+3

SiOR01

968+26

SiO

R02694+31

SiOR0

4648+2

SiO

R02694+39

SiOR04171+25

SiOR06577

SiOR01

968+25

SiOR04171+21

SiOR06792+6

SiO

R04609+11

SiOR02694+11

SiOR06792+1

SiOR04171+4

SiOR01629+5

SiOR00330+21

SiOR0

4648+15

SiO

R00330+6

SiO

R02

694+16

SiOR04648+11

SiOR

04648+4

SiO

R00330+3

SiO

R06

535

SiOR04171+7

SiOR10493

SiO

R02694+32

SiOR06792+4

SiOR04510+3

SiO

R06

890

SiOR0196

8+20

SiO

R04609+12

SiOR04171+3

SiOR01968

+18

SiOR01968+11

SiO

R04609+13

SiOR01629+12

SiOR00330+22

SiO

R02694+33

SiOR00330+13

SiOR01

573+3

SiOR04510+16

SiOR04171+12

SiOR04510+13

SiOR

05118+1

SiO

R02

944+3

SiOR04171+26

SiOR04171+17

SiOR

00899+14

SiOR04171+29

SiOR

00899+1

3

SiOR02694+13

SiOR00330+24

SiOR00330+19

SiOR04171+27

SiO

R02

694+24

SiOR04510+5

SiOR07090

SiOR03952+1

SiOR04510+10

SiOR00330+17

SiO

R02

694+26

SiO

R04609+1

SiOR0

0899+6

SiOR04648+12

SiOR02814+2

SiOR00330+11

SiOR04171+18

SiOR01968+1

7

SiOR00330+10

SiOR00330+9

SiOR0162

9+2

SiOR04171+11

SiOR04510+12

SiOR0196

8+21

SiOR00330+8

SiOR01858+1

SiOR04510+7

SiOR05431+4

SiOR02694+6

SiOR01968+13

SiO

R00330+4

SiO

R04609+18

SiOR0

0899+10

SiOR00330+12

SiOR00330+31

SiO

R06

843+1

SiOR07

837+1

SiO

R00330+2

SiOR01629+4

SiOR0

4648+1

SiOR01

968+24

SiOR04171+23

SiOR0162

9+7

SiOR0

4648+14

SiO

R06

843+3

SiOR06792+5

SiOR01968+7

SiOR01629

+6

SiOR02883+3

SiOR02694+12

SiOR

05118+4

SiOR04171+22

SiO

R01080

SiOR04609+6

SiOR02814+1

SiOR00330+30

SiOR05285+12

SiOR06723+1

SiOR02694+4

fire antGenome of a Gp-9 B ♂

Wurm et al 2011

Page 42: 2014 11-28-lyon

Social form completely associated to Gp-9 locus

BB BB Bb

x x x

Single queen form Multiple queen form(>15% ) (< 5% )

Are other genes linked to Gp-9?

Page 43: 2014 11-28-lyon

Sequenced:•Genome of a Gp-9 B ♂•Genome of a Gp-9 b ♂

“Next Generation Genotyping.”RAD sequencing

Are other genes linked to Gp-9?

Page 44: 2014 11-28-lyon

“Next Generation Genotyping.”

Bb

unfertilised eggs

haploid ♂

Gp-9 B Gp-9 b Gp-9 B Gp-9 b Gp-9 b Gp-9 B

RAD sequencing

38 B♂ & 38 b♂

Page 45: 2014 11-28-lyon

EcoR1 EcoR1 EcoR1

Gp-9 B

RAD sequencing of haploid ♂ for SNP discovery & genotyping

Page 46: 2014 11-28-lyon

EcoR1 EcoR1 EcoR1

AACTG

AACTG

AACTG

AACTG

Gp-9 B

RAD sequencing of haploid ♂ for SNP discovery & genotyping

Gp-9 B

Page 47: 2014 11-28-lyon

AACTGGp-9 B

Gp-9 B

GGCCT

Gp-9 B

Gp-9 B

AAGGTGp-9 B

Gp-9 B

CCAGTGp-9 b

Gp-9 b

TAAATGp-9 b

Gp-9 b

GGAATGp-9 b

Gp-9 b

38 Gp-9 B males

38 Gp-9 b males

RAD sequencing of haploid ♂ for SNP discovery & genotyping

Page 48: 2014 11-28-lyon

Identify polymorphismindividual x locus

genotype table

RADseq: sequencing the same 0.01% of the genome in many individuals

A B C D E FL1 A C A A C CL2 G G T - T GL3 - A G A - GL4 C - - G G CL5 T T C T C -L6 G A A - - G

2419

loci

38 B� & 38 b�

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20+

Amount of variance explained per principal component

Principal Component

% V

aria

nce

Exp

lain

ed

05

1015

2025

30

12.7%

6.1% 5.4% 4.8% 4.7% 3.9% 3.5% 3.2% 3.1% 2.9% 2.8% 2.6% 2.4% 2.3% 2.2% 2.0% 1.9% 1.7% 1.6%

30.2%

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20+

Amount of variance explained per principal component

Principal Component

% V

aria

nce

Exp

lain

ed

05

1015

2025

30

PCA: Principal Component Analysis

Page 49: 2014 11-28-lyon

pc: 2 % variance: 6.073

pc: 3

%

var

ianc

e: 5

.441

-0.2

-0.1

0.0

0.1

0.2

-0.2 -0.1 0.0 0.1 0.2pc: 2 % variance: 6.073

pc: 3

%

var

ianc

e: 5

.441

-0.2

-0.1

0.0

0.1

0.2

-0.2 -0.1 0.0 0.1 0.2

Principal Components: PC2 vs PC3

Gp-9 B �Gp-9 b �

Page 50: 2014 11-28-lyon

pc: 1 % variance: 12.666

pc: 2

%

var

ianc

e: 6

.073

-0.2

-0.1

0.0

0.1

0.2

-0.10 -0.05 0.00 0.05 0.10 0.15

Principal Components: PC1 vs PC2

pc: 1 % variance: 12.666

pc: 2

%

var

ianc

e: 6

.073

-0.2

-0.1

0.0

0.1

0.2

-0.10 -0.05 0.00 0.05 0.10 0.15

Gp-9 B ♂Gp-9 b ♂

Page 51: 2014 11-28-lyon

Confirmed in 8 additional families (sons of Bb queens) with RAD (3 families) and PCR (5 families). BBqueens: normal recombination throughout (RAD 3 families) ⟹ Gp-9 is not a “recombination cold-spot”

brc_m013_0001..brc_m013_0005brc_m013_0006..brc_m013_0014brc_m013_0015..brc_m013_0017brc_m013_0018brc_m013_0019..brc_m013_0020brc_m013_0021..brc_m013_0029brc_m013_0030..brc_m013_0031brc_m013_0032..brc_m013_0034brc_m013_0035..brc_m013_0036brc_m013_0037..brc_m013_0038brc_m013_0039..brc_m013_0043brc_m013_0044brc_m013_0045brc_m013_0046..brc_m013_0048brc_m013_0049brc_m013_0050..brc_m013_0051brc_m013_0052..brc_m013_0056brc_m013_0057..brc_m013_0061

brc_m013_0062..brc_m013_0075brc_m013_0076..brc_m013_0078brc_m013_0079..brc_m013_0081

brc_m013_0082..brc_m013_0088

brc_m013_0089..brc_m013_0092

brc_m013_0093..brc_m013_0096brc_m013_0097brc_m013_0098..brc_m013_0113brc_m013_0114..brc_m013_0119brc_m013_0120..brc_m013_0130brc_m013_0131brc_m013_0132..brc_m013_0134brc_m013_0135..brc_m013_0136brc_m013_0137..brc_m013_0139brc_m013_0140..brc_m013_0142brc_m013_0143brc_m013_0144..brc_m013_0146brc_m013_0147..brc_m013_0154brc_m013_0155

brc_m013_0156brc_m013_0157..brc_m013_0180brc_m013_0181brc_m013_0182brc_m013_0183..brc_m013_0188brc_m013_0189..brc_m013_0208brc_m013_0209brc_m013_0210..brc_m013_0211brc_m013_0212..brc_m013_0215brc_m013_0216brc_m013_0217brc_m013_0218..brc_m013_0224brc_m013_0225..brc_m013_0228brc_m013_0229..brc_m013_0237brc_m013_0238..brc_m013_0245

brc_m013_0246..brc_m013_0270

brc_m013_0271..brc_m013_0274brc_m013_0275brc_m013_0276..brc_m013_0278

brc_m013_0279

brc_m013_0280

brc_m013_0281..brc_m013_0294

brc_m013_0295..brc_m013_0303brc_m013_0304brc_m013_0305..brc_m013_0307brc_m013_0308brc_m013_0309..brc_m013_0314brc_m013_0315..brc_m013_0317brc_m013_0318..brc_m013_0320brc_m013_0321..brc_m013_0326brc_m013_0327brc_m013_0328brc_m013_0329..brc_m013_0330brc_m013_0331..brc_m013_0333brc_m013_0334..brc_m013_0339brc_m013_0340brc_m013_0341..brc_m013_0343brc_m013_0344brc_m013_0345..brc_m013_0349brc_m013_0350

brc_m013_0351..brc_m013_0354brc_m013_0355brc_m013_0356brc_m013_0357..brc_m013_0361brc_m013_0362..brc_m013_0376brc_m013_0377..brc_m013_0390brc_m013_0391..brc_m013_0393brc_m013_0394..brc_m013_0400brc_m013_0401..brc_m013_0439brc_m013_0440..brc_m013_0478brc_m013_0479..brc_m013_0480

0

20

40

60

80

100

120

140

160

180

LG1brc_m013_0481brc_m013_0482..brc_m013_0484brc_m013_0485..brc_m013_0488brc_m013_0489..brc_m013_0502brc_m013_0503brc_m013_0504..brc_m013_0519brc_m013_0520..brc_m013_0532brc_m013_0533..brc_m013_0534brc_m013_0535..brc_m013_0537brc_m013_0538..brc_m013_0540brc_m013_0541..brc_m013_0543brc_m013_0544..brc_m013_0545brc_m013_0546..brc_m013_0549

brc_m013_0550..brc_m013_0554

brc_m013_0555..brc_m013_0560

brc_m013_0561..brc_m013_0562brc_m013_0563..brc_m013_0565

brc_m013_0566brc_m013_0567brc_m013_0568..brc_m013_0570brc_m013_0571..brc_m013_0573

brc_m013_0574..brc_m013_0575brc_m013_0576..brc_m013_0578brc_m013_0579..brc_m013_0580brc_m013_0581brc_m013_0582..brc_m013_0584brc_m013_0585brc_m013_0586brc_m013_0587brc_m013_0588..brc_m013_0591brc_m013_0592brc_m013_0593brc_m013_0594..brc_m013_0612brc_m013_0613..brc_m013_0614brc_m013_0615..brc_m013_0632brc_m013_0633brc_m013_0634..brc_m013_0648brc_m013_0649..brc_m013_0655brc_m013_0656brc_m013_0657..brc_m013_0694brc_m013_0695..brc_m013_0703brc_m013_0704brc_m013_0705brc_m013_0706..brc_m013_0707brc_m013_0708brc_m013_0709..brc_m013_0711brc_m013_0712..brc_m013_0715brc_m013_0716..brc_m013_0721brc_m013_0722brc_m013_0723brc_m013_0724..brc_m013_0728brc_m013_0729brc_m013_0730brc_m013_0731brc_m013_0732..brc_m013_0735brc_m013_0736..brc_m013_0769brc_m013_0770..brc_m013_0771brc_m013_0772..brc_m013_0773brc_m013_0774..brc_m013_0775brc_m013_0776..brc_m013_0782brc_m013_0783brc_m013_0784..brc_m013_0795brc_m013_0796..brc_m013_0798brc_m013_0799..brc_m013_0801brc_m013_0802..brc_m013_0805brc_m013_0806..brc_m013_0809brc_m013_0810..brc_m013_0811brc_m013_0812..brc_m013_0824brc_m013_0825..brc_m013_0826brc_m013_0827..brc_m013_0829brc_m013_0830..brc_m013_0831brc_m013_0832..brc_m013_0842brc_m013_0843..brc_m013_0854brc_m013_0855..brc_m013_0861brc_m013_0862brc_m013_0863..brc_m013_0864brc_m013_0865..brc_m013_0867brc_m013_0868..brc_m013_0883brc_m013_0884..brc_m013_0893brc_m013_0894brc_m013_0895..brc_m013_0897brc_m013_0898..brc_m013_0906brc_m013_0907..brc_m013_0910brc_m013_0911..brc_m013_0925brc_m013_0926..brc_m013_0928brc_m013_0929..brc_m013_0931

0

20

40

60

80

100

120

140

LG2brc_m013_0932..brc_m013_0941brc_m013_0942..brc_m013_0943brc_m013_0944..brc_m013_0945brc_m013_0946..brc_m013_0949brc_m013_0950..brc_m013_0952

brc_m013_0953..brc_m013_0975

brc_m013_0976..brc_m013_1019brc_m013_1020brc_m013_1021brc_m013_1022..brc_m013_1061brc_m013_1062brc_m013_1063

brc_m013_1064..brc_m013_1065

brc_m013_1066..brc_m013_1068brc_m013_1069brc_m013_1070

brc_m013_1071..brc_m013_1074

brc_m013_1075

brc_m013_1076..brc_m013_1081

brc_m013_1082..brc_m013_1086brc_m013_1087..brc_m013_1088brc_m013_1089..brc_m013_1098brc_m013_1099..brc_m013_1106brc_m013_1107..brc_m013_1116brc_m013_1117brc_m013_1118..brc_m013_1121brc_m013_1122..brc_m013_1127brc_m013_1128brc_m013_1129..brc_m013_1136brc_m013_1137..brc_m013_1138brc_m013_1139..brc_m013_1141brc_m013_1142..brc_m013_1144brc_m013_1145..brc_m013_1156brc_m013_1157brc_m013_1158..brc_m013_1170brc_m013_1171..brc_m013_1181brc_m013_1182..brc_m013_1185brc_m013_1186brc_m013_1187..brc_m013_1205brc_m013_1206..brc_m013_1218brc_m013_1219..brc_m013_1220brc_m013_1221..brc_m013_1224brc_m013_1225..brc_m013_1228brc_m013_1229brc_m013_1230..brc_m013_1236brc_m013_1237brc_m013_1238..brc_m013_1247brc_m013_1248..brc_m013_1251

brc_m013_1252brc_m013_1253..brc_m013_1268brc_m013_1269..brc_m013_1270brc_m013_1271..brc_m013_1273brc_m013_1274brc_m013_1275..brc_m013_1280brc_m013_1281

brc_m013_1282..brc_m013_1286brc_m013_1287..brc_m013_1298brc_m013_1299..brc_m013_1307brc_m013_1308brc_m013_1309..brc_m013_1313brc_m013_1314..brc_m013_1317brc_m013_1318..brc_m013_1319brc_m013_1320..brc_m013_1326brc_m013_1327..brc_m013_1340brc_m013_1341..brc_m013_1362brc_m013_1363..brc_m013_1385

0

20

40

60

80

100

120

140

LG3brc_m013_1386..brc_m013_1388brc_m013_1389..brc_m013_1398brc_m013_1399..brc_m013_1406brc_m013_1407..brc_m013_1411brc_m013_1412..brc_m013_1413brc_m013_1414..brc_m013_1416

brc_m013_1417brc_m013_1418..brc_m013_1420brc_m013_1421..brc_m013_1424brc_m013_1425..brc_m013_1432brc_m013_1433..brc_m013_1442brc_m013_1443brc_m013_1444..brc_m013_1450brc_m013_1451brc_m013_1452brc_m013_1453..brc_m013_1455brc_m013_1456..brc_m013_1467brc_m013_1468..brc_m013_1469brc_m013_1470brc_m013_1471..brc_m013_1474brc_m013_1475brc_m013_1476brc_m013_1477brc_m013_1478..brc_m013_1482brc_m013_1483

brc_m013_1484brc_m013_1485..brc_m013_1487brc_m013_1488..brc_m013_1490

brc_m013_1491brc_m013_1492..brc_m013_1494brc_m013_1495..brc_m013_1496

brc_m013_1497..brc_m013_1500brc_m013_1501brc_m013_1502..brc_m013_1513brc_m013_1514..brc_m013_1562brc_m013_1563..brc_m013_1565brc_m013_1566..brc_m013_1567

brc_m013_1568..brc_m013_1580brc_m013_1581..brc_m013_1587brc_m013_1588..brc_m013_1591brc_m013_1592..brc_m013_1593brc_m013_1594..brc_m013_1604brc_m013_1605..brc_m013_1607brc_m013_1608..brc_m013_1609brc_m013_1610..brc_m013_1611brc_m013_1612..brc_m013_1616brc_m013_1617..brc_m013_1618brc_m013_1619..brc_m013_1620brc_m013_1621..brc_m013_1629brc_m013_1630..brc_m013_1633brc_m013_1634..brc_m013_1638brc_m013_1639..brc_m013_1647brc_m013_1648..brc_m013_1649brc_m013_1650..brc_m013_1656brc_m013_1657..brc_m013_1665brc_m013_1666..brc_m013_1672brc_m013_1673..brc_m013_1674brc_m013_1675..brc_m013_1678brc_m013_1679..brc_m013_1682brc_m013_1683brc_m013_1684brc_m013_1685..brc_m013_1686brc_m013_1687..brc_m013_1700brc_m013_1701..brc_m013_1702brc_m013_1703brc_m013_1704..brc_m013_1707brc_m013_1708..brc_m013_1709brc_m013_1710..brc_m013_1714brc_m013_1715..brc_m013_1728brc_m013_1729..brc_m013_1742

0

20

40

60

80

100

120

140

LG4brc_m013_1743..brc_m013_1750

brc_m013_1751..brc_m013_1766brc_m013_1767brc_m013_1768

brc_m013_1769..brc_m013_1772

brc_m013_1773..brc_m013_1779brc_m013_1780brc_m013_1781brc_m013_1782..brc_m013_1783brc_m013_1784brc_m013_1785..brc_m013_1786

brc_m013_1787

brc_m013_1788brc_m013_1789..brc_m013_1790brc_m013_1791..brc_m013_1793brc_m013_1794..brc_m013_1797brc_m013_1798..brc_m013_1800brc_m013_1801..brc_m013_1804brc_m013_1805brc_m013_1806..brc_m013_1808brc_m013_1809brc_m013_1810..brc_m013_1813brc_m013_1814..brc_m013_1818brc_m013_1819..brc_m013_1820brc_m013_1821..brc_m013_1822brc_m013_1823..brc_m013_1824brc_m013_1825brc_m013_1826..brc_m013_1840brc_m013_1841..brc_m013_1842brc_m013_1843brc_m013_1844..brc_m013_1848brc_m013_1849brc_m013_1850brc_m013_1851..brc_m013_1853brc_m013_1854..brc_m013_1858brc_m013_1859..brc_m013_1866brc_m013_1867..brc_m013_1868brc_m013_1869brc_m013_1870..brc_m013_1874brc_m013_1875..brc_m013_1876brc_m013_1877..brc_m013_1878brc_m013_1879..brc_m013_1883brc_m013_1884brc_m013_1885brc_m013_1886..brc_m013_1888brc_m013_1889..brc_m013_1895brc_m013_1896..brc_m013_1899brc_m013_1900..brc_m013_1913brc_m013_1914brc_m013_1915..brc_m013_1922brc_m013_1923brc_m013_1924..brc_m013_1928brc_m013_1929..brc_m013_1942brc_m013_1943..brc_m013_1946brc_m013_1947..brc_m013_1948brc_m013_1949brc_m013_1950..brc_m013_1953brc_m013_1954..brc_m013_1955brc_m013_1956brc_m013_1957..brc_m013_1963brc_m013_1964..brc_m013_1966brc_m013_1967..brc_m013_1968brc_m013_1969..brc_m013_1970brc_m013_1971brc_m013_1972brc_m013_1973..brc_m013_1980brc_m013_1981..brc_m013_1983brc_m013_1984..brc_m013_1990brc_m013_1991..brc_m013_1993brc_m013_1994..brc_m013_1996brc_m013_1997..brc_m013_2009

0

20

40

60

80

100

120

LG5brc_m013_2010..brc_m013_2028

brc_m013_2029..brc_m013_2038brc_m013_2039

brc_m013_2040..brc_m013_2041brc_m013_2042..brc_m013_2047brc_m013_2048..brc_m013_2050brc_m013_2051..brc_m013_2053brc_m013_2054..brc_m013_2062brc_m013_2063brc_m013_2064..brc_m013_2065brc_m013_2066..brc_m013_2067brc_m013_2068brc_m013_2069..brc_m013_2071brc_m013_2072..brc_m013_2081brc_m013_2082

brc_m013_2083brc_m013_2084brc_m013_2085..brc_m013_2099brc_m013_2100brc_m013_2101..brc_m013_2102brc_m013_2103..brc_m013_2107brc_m013_2108brc_m013_2109..brc_m013_2112

brc_m013_2113..brc_m013_2114brc_m013_2115..brc_m013_2123brc_m013_2124..brc_m013_2131brc_m013_2132brc_m013_2133brc_m013_2134..brc_m013_2136

brc_m013_2137

brc_m013_2138..brc_m013_2139

brc_m013_2140..brc_m013_2142brc_m013_2143..brc_m013_2150brc_m013_2151..brc_m013_2152brc_m013_2153..brc_m013_2161brc_m013_2162..brc_m013_2163

brc_m013_2164..brc_m013_2165brc_m013_2166..brc_m013_2170brc_m013_2171..brc_m013_2172brc_m013_2173brc_m013_2174..brc_m013_2182brc_m013_2183..brc_m013_2186brc_m013_2187..brc_m013_2190brc_m013_2191..brc_m013_2193brc_m013_2194brc_m013_2195..brc_m013_2201brc_m013_2202..brc_m013_2203brc_m013_2204..brc_m013_2220brc_m013_2221..brc_m013_2232brc_m013_2233..brc_m013_2239brc_m013_2240..brc_m013_2261brc_m013_2262..brc_m013_2267brc_m013_2268..brc_m013_2269brc_m013_2270..brc_m013_2271brc_m013_2272..brc_m013_2282brc_m013_2283..brc_m013_2284brc_m013_2285..brc_m013_2299brc_m013_2300..brc_m013_2301brc_m013_2302..brc_m013_2305brc_m013_2306..brc_m013_2307brc_m013_2308..brc_m013_2330brc_m013_2331..brc_m013_2337brc_m013_2338..brc_m013_2352

0

20

40

60

80

100

120

LG6brc_m013_2353..brc_m013_2365brc_m013_2366..brc_m013_2369

brc_m013_2370..brc_m013_2372brc_m013_2373..brc_m013_2378brc_m013_2379..brc_m013_2386brc_m013_2387brc_m013_2388..brc_m013_2394brc_m013_2395..brc_m013_2397brc_m013_2398brc_m013_2399brc_m013_2400brc_m013_2401brc_m013_2402..brc_m013_2407brc_m013_2408..brc_m013_2411brc_m013_2412..brc_m013_2416brc_m013_2417brc_m013_2418brc_m013_2419..brc_m013_2436brc_m013_2437..brc_m013_2441brc_m013_2442brc_m013_2443..brc_m013_2444brc_m013_2445brc_m013_2446..brc_m013_2453brc_m013_2454brc_m013_2455..brc_m013_2460brc_m013_2461brc_m013_2462..brc_m013_2470brc_m013_2471..brc_m013_2474brc_m013_2475..brc_m013_2482brc_m013_2483brc_m013_2484..brc_m013_2487brc_m013_2488brc_m013_2489..brc_m013_2492brc_m013_2493..brc_m013_2496brc_m013_2497brc_m013_2498..brc_m013_2504brc_m013_2505brc_m013_2506..brc_m013_2510brc_m013_2511..brc_m013_2523brc_m013_2524..brc_m013_2531brc_m013_2532..brc_m013_2536brc_m013_2537..brc_m013_2555brc_m013_2556..brc_m013_2571brc_m013_2572..brc_m013_2573brc_m013_2574..brc_m013_2579brc_m013_2580..brc_m013_2581brc_m013_2582..brc_m013_2587brc_m013_2588brc_m013_2589..brc_m013_2594

brc_m013_2595

brc_m013_2596..brc_m013_2597brc_m013_2598..brc_m013_2604brc_m013_2605brc_m013_2606..brc_m013_2616brc_m013_2617..brc_m013_2619brc_m013_2620..brc_m013_2623

brc_m013_2624brc_m013_2625..brc_m013_2626brc_m013_2627..brc_m013_2628

brc_m013_2629..brc_m013_2630

0

20

40

60

80

100

LG7brc_m013_2631..brc_m013_2632brc_m013_2633brc_m013_2634..brc_m013_2635brc_m013_2636..brc_m013_2642brc_m013_2643..brc_m013_2657brc_m013_2658..brc_m013_2659brc_m013_2660..brc_m013_2661brc_m013_2662

brc_m013_2663

brc_m013_2664brc_m013_2665..brc_m013_2666

brc_m013_2667..brc_m013_2668brc_m013_2669..brc_m013_2670brc_m013_2671..brc_m013_2680brc_m013_2681..brc_m013_2682brc_m013_2683brc_m013_2684..brc_m013_2685brc_m013_2686..brc_m013_2694

brc_m013_2695..brc_m013_2698brc_m013_2699..brc_m013_2713

brc_m013_2714..brc_m013_2725brc_m013_2726..brc_m013_2727brc_m013_2728..brc_m013_2731brc_m013_2732brc_m013_2733..brc_m013_2753brc_m013_2754..brc_m013_2758brc_m013_2759..brc_m013_2763brc_m013_2764..brc_m013_2779brc_m013_2780brc_m013_2781brc_m013_2782..brc_m013_2784brc_m013_2785..brc_m013_2787brc_m013_2788..brc_m013_2791brc_m013_2792..brc_m013_2797brc_m013_2798..brc_m013_2799brc_m013_2800brc_m013_2801..brc_m013_2804brc_m013_2805..brc_m013_2809

brc_m013_2810..brc_m013_2811

brc_m013_2812..brc_m013_2813brc_m013_2814..brc_m013_2817brc_m013_2818..brc_m013_2827brc_m013_2828brc_m013_2829..brc_m013_2832brc_m013_2833brc_m013_2834..brc_m013_2840brc_m013_2841..brc_m013_2846brc_m013_2847brc_m013_2848..brc_m013_2852brc_m013_2853brc_m013_2854..brc_m013_2856brc_m013_2857..brc_m013_2862brc_m013_2863..brc_m013_2868brc_m013_2869..brc_m013_2874brc_m013_2875..brc_m013_2896

0

20

40

60

80

100

LG8

brc_m013_2897..brc_m013_2920brc_m013_2921..brc_m013_2928brc_m013_2929..brc_m013_2931brc_m013_2932

brc_m013_2933

brc_m013_2934..brc_m013_2935brc_m013_2936brc_m013_2937..brc_m013_2943brc_m013_2944brc_m013_2945..brc_m013_2946brc_m013_2947brc_m013_2948brc_m013_2949..brc_m013_2950brc_m013_2951..brc_m013_2957brc_m013_2958..brc_m013_2961brc_m013_2962..brc_m013_2970brc_m013_2971..brc_m013_2980brc_m013_2981..brc_m013_2992brc_m013_2993..brc_m013_2996brc_m013_2997..brc_m013_2998brc_m013_2999..brc_m013_3000brc_m013_3001brc_m013_3002..brc_m013_3003brc_m013_3004brc_m013_3005brc_m013_3006..brc_m013_3010brc_m013_3011..brc_m013_3014brc_m013_3015brc_m013_3016..brc_m013_3019brc_m013_3020brc_m013_3021..brc_m013_3030brc_m013_3031..brc_m013_3032brc_m013_3033..brc_m013_3034brc_m013_3035..brc_m013_3036brc_m013_3037..brc_m013_3045brc_m013_3046..brc_m013_3052brc_m013_3053brc_m013_3054..brc_m013_3061brc_m013_3062..brc_m013_3066brc_m013_3067..brc_m013_3068brc_m013_3069..brc_m013_3076brc_m013_3077..brc_m013_3084brc_m013_3085..brc_m013_3087brc_m013_3088..brc_m013_3089brc_m013_3090..brc_m013_3096brc_m013_3097..brc_m013_3100brc_m013_3101..brc_m013_3104brc_m013_3105brc_m013_3106..brc_m013_3112brc_m013_3113..brc_m013_3122brc_m013_3123..brc_m013_3124brc_m013_3125..brc_m013_3127brc_m013_3128..brc_m013_3145brc_m013_3146..brc_m013_3159brc_m013_3160..brc_m013_3172

0

20

40

60

80

100

LG9brc_m013_3173..brc_m013_3175brc_m013_3176..brc_m013_3180brc_m013_3181..brc_m013_3189brc_m013_3190..brc_m013_3198brc_m013_3199brc_m013_3200..brc_m013_3201brc_m013_3202..brc_m013_3203brc_m013_3204brc_m013_3205..brc_m013_3206brc_m013_3207..brc_m013_3211brc_m013_3212..brc_m013_3214brc_m013_3215..brc_m013_3227brc_m013_3228..brc_m013_3230brc_m013_3231..brc_m013_3235brc_m013_3236..brc_m013_3238brc_m013_3239..brc_m013_3242brc_m013_3243..brc_m013_3244brc_m013_3245brc_m013_3246..brc_m013_3247brc_m013_3248..brc_m013_3249brc_m013_3250..brc_m013_3252brc_m013_3253..brc_m013_3257brc_m013_3258brc_m013_3259brc_m013_3260..brc_m013_3261brc_m013_3262..brc_m013_3263brc_m013_3264brc_m013_3265..brc_m013_3269brc_m013_3270..brc_m013_3274brc_m013_3275..brc_m013_3276brc_m013_3277..brc_m013_3281brc_m013_3282..brc_m013_3284brc_m013_3285brc_m013_3286..brc_m013_3289brc_m013_3290..brc_m013_3296brc_m013_3297brc_m013_3298..brc_m013_3300brc_m013_3301..brc_m013_3302brc_m013_3303..brc_m013_3305brc_m013_3306..brc_m013_3308brc_m013_3309..brc_m013_3314brc_m013_3315..brc_m013_3317brc_m013_3318..brc_m013_3329brc_m013_3330..brc_m013_3331brc_m013_3332..brc_m013_3338brc_m013_3339..brc_m013_3340brc_m013_3341..brc_m013_3344brc_m013_3345..brc_m013_3349brc_m013_3350..brc_m013_3357brc_m013_3358..brc_m013_3359brc_m013_3360brc_m013_3361..brc_m013_3368brc_m013_3369..brc_m013_3372brc_m013_3373..brc_m013_3376brc_m013_3377brc_m013_3378..brc_m013_3386brc_m013_3387..brc_m013_3388brc_m013_3389..brc_m013_3395brc_m013_3396..brc_m013_3399

0

20

40

60

80

LG10brc_m013_3400..brc_m013_3411brc_m013_3412brc_m013_3413..brc_m013_3424brc_m013_3425brc_m013_3426brc_m013_3427..brc_m013_3429

brc_m013_3430

brc_m013_3431..brc_m013_3432brc_m013_3433..brc_m013_3435brc_m013_3436brc_m013_3437..brc_m013_3439

brc_m013_3440..brc_m013_3441brc_m013_3442

brc_m013_3443..brc_m013_3445brc_m013_3446..brc_m013_3447brc_m013_3448..brc_m013_3449brc_m013_3450..brc_m013_3454brc_m013_3455brc_m013_3456..brc_m013_3462brc_m013_3463..brc_m013_3464brc_m013_3465brc_m013_3466..brc_m013_3467brc_m013_3468..brc_m013_3472brc_m013_3473brc_m013_3474..brc_m013_3476brc_m013_3477..brc_m013_3487brc_m013_3488brc_m013_3489..brc_m013_3491brc_m013_3492..brc_m013_3500brc_m013_3501..brc_m013_3512brc_m013_3513..brc_m013_3514brc_m013_3515..brc_m013_3524brc_m013_3525..brc_m013_3527brc_m013_3528..brc_m013_3531brc_m013_3532..brc_m013_3547brc_m013_3548..brc_m013_3557brc_m013_3558..brc_m013_3566brc_m013_3567..brc_m013_3568brc_m013_3569..brc_m013_3570brc_m013_3571..brc_m013_3574brc_m013_3575..brc_m013_3582brc_m013_3583..brc_m013_3592brc_m013_3593..brc_m013_3605brc_m013_3606..brc_m013_3616brc_m013_3617..brc_m013_3618brc_m013_3619..brc_m013_3622brc_m013_3623..brc_m013_3624brc_m013_3625..brc_m013_3628brc_m013_3629..brc_m013_3635

0

20

40

60

80

LG11

brc_m013_3636..brc_m013_3661brc_m013_3662..brc_m013_3665

brc_m013_3666..brc_m013_3667brc_m013_3668brc_m013_3669..brc_m013_3671

brc_m013_3672

brc_m013_3673..brc_m013_3674brc_m013_3675..brc_m013_3682

brc_m013_3683..brc_m013_3685

brc_m013_3686..brc_m013_3688

brc_m013_3689..brc_m013_3693

brc_m013_3694..brc_m013_3698brc_m013_3699

brc_m013_3700brc_m013_3701..brc_m013_3702brc_m013_3703..brc_m013_3704brc_m013_3705..brc_m013_3712brc_m013_3713brc_m013_3714..brc_m013_3716brc_m013_3717..brc_m013_3724brc_m013_3725..brc_m013_3730brc_m013_3731..brc_m013_3752brc_m013_3753..brc_m013_3758brc_m013_3759..brc_m013_3789brc_m013_3790..brc_m013_3801brc_m013_3802..brc_m013_3814brc_m013_3815..brc_m013_3818brc_m013_3819..brc_m013_3822brc_m013_3823..brc_m013_3826brc_m013_3827..brc_m013_3832brc_m013_3833..brc_m013_3837brc_m013_3838brc_m013_3839..brc_m013_3841brc_m013_3842..brc_m013_3847

brc_m013_3848..brc_m013_3853brc_m013_3854..brc_m013_3858brc_m013_3859..brc_m013_3868brc_m013_3869..brc_m013_3871brc_m013_3872..brc_m013_3901brc_m013_3902brc_m013_3903..brc_m013_3909brc_m013_3910brc_m013_3911..brc_m013_3926brc_m013_3927..brc_m013_3931brc_m013_3932..brc_m013_3948

0

20

40

60

80

LG12

brc_m013_3949..brc_m013_3952brc_m013_3953..brc_m013_3958brc_m013_3959..brc_m013_3970brc_m013_3971

brc_m013_3972..brc_m013_3975brc_m013_3976

brc_m013_3977..brc_m013_3985

brc_m013_3986brc_m013_3987..brc_m013_3994brc_m013_3995..brc_m013_3997brc_m013_3998..brc_m013_4004

brc_m013_4005..brc_m013_4006brc_m013_4007..brc_m013_4008brc_m013_4009..brc_m013_4010brc_m013_4011..brc_m013_4013brc_m013_4014brc_m013_4015brc_m013_4016..brc_m013_4019brc_m013_4020..brc_m013_4021brc_m013_4022..brc_m013_4025brc_m013_4026..brc_m013_4032brc_m013_4033..brc_m013_4036brc_m013_4037..brc_m013_4041brc_m013_4042..brc_m013_4043

brc_m013_4044..brc_m013_4046brc_m013_4047..brc_m013_4056brc_m013_4057brc_m013_4058..brc_m013_4063brc_m013_4064..brc_m013_4071brc_m013_4072..brc_m013_4075brc_m013_4076brc_m013_4077brc_m013_4078..brc_m013_4085brc_m013_4086..brc_m013_4089brc_m013_4090..brc_m013_4091brc_m013_4092..brc_m013_4093brc_m013_4094..brc_m013_4095brc_m013_4096..brc_m013_4114brc_m013_4115..brc_m013_4117brc_m013_4118..brc_m013_4131brc_m013_4132..brc_m013_4133brc_m013_4134..brc_m013_4146

0

20

40

60

80

LG13

brc_m013_4147..brc_m013_4150brc_m013_4151..brc_m013_4167

brc_m013_4168brc_m013_4169

brc_m013_4170brc_m013_4171..brc_m013_4172brc_m013_4173..brc_m013_4175brc_m013_4176brc_m013_4177..brc_m013_4178brc_m013_4179..brc_m013_4183brc_m013_4184..brc_m013_4185brc_m013_4186..brc_m013_4187brc_m013_4188..brc_m013_4191brc_m013_4192brc_m013_4193..brc_m013_4194brc_m013_4195..brc_m013_4206brc_m013_4207..brc_m013_4210brc_m013_4211..brc_m013_4213brc_m013_4214brc_m013_4215..brc_m013_4217brc_m013_4218..brc_m013_4221brc_m013_4222..brc_m013_4223brc_m013_4224..brc_m013_4231brc_m013_4232..brc_m013_4234brc_m013_4235..brc_m013_4239brc_m013_4240..brc_m013_4246brc_m013_4247..brc_m013_4248brc_m013_4249..brc_m013_4258brc_m013_4259..brc_m013_4260brc_m013_4261..brc_m013_4269brc_m013_4270..brc_m013_4271brc_m013_4272..brc_m013_4278brc_m013_4279..brc_m013_4280brc_m013_4281..brc_m013_4284brc_m013_4285brc_m013_4286..brc_m013_4288brc_m013_4289..brc_m013_4294brc_m013_4295..brc_m013_4296brc_m013_4297..brc_m013_4301brc_m013_4302..brc_m013_4313brc_m013_4314..brc_m013_4320brc_m013_4321..brc_m013_4322brc_m013_4323..brc_m013_4345brc_m013_4346..brc_m013_4351

0

20

40

60

LG14brc_m013_4352..brc_m013_4366brc_m013_4367brc_m013_4368brc_m013_4369..brc_m013_4373brc_m013_4374..brc_m013_4381brc_m013_4382..brc_m013_4383brc_m013_4384..brc_m013_4385brc_m013_4386brc_m013_4387..brc_m013_4388brc_m013_4389brc_m013_4390..brc_m013_4404brc_m013_4405brc_m013_4406..brc_m013_4409brc_m013_4410..brc_m013_4411brc_m013_4412..brc_m013_4418brc_m013_4419..brc_m013_4434brc_m013_4435..brc_m013_4442brc_m013_4443..brc_m013_4448brc_m013_4449..brc_m013_4451brc_m013_4452..brc_m013_4461brc_m013_4462..brc_m013_4471brc_m013_4472..brc_m013_4475brc_m013_4476..brc_m013_4477brc_m013_4478brc_m013_4479brc_m013_4480..brc_m013_4485brc_m013_4486brc_m013_4487..brc_m013_4491brc_m013_4492brc_m013_4493brc_m013_4494..brc_m013_4495brc_m013_4496..brc_m013_4501brc_m013_4502..brc_m013_4510brc_m013_4511..brc_m013_4531brc_m013_4532brc_m013_4533..brc_m013_4534brc_m013_4535..brc_m013_4541brc_m013_4542..brc_m013_4543brc_m013_4544..brc_m013_4545brc_m013_4546..brc_m013_4548brc_m013_4549..brc_m013_4551brc_m013_4552..brc_m013_4555brc_m013_4556..brc_m013_4561

0

20

40

60

LG15

brc_m013_4562..brc_m013_4577brc_m013_4578..brc_m013_4594brc_m013_4595..brc_m013_4599brc_m013_4600..brc_m013_4625brc_m013_4626..brc_m013_4638brc_m013_4639..brc_m013_4642brc_m013_4643..brc_m013_4644brc_m013_4645..brc_m013_4650brc_m013_4651..brc_m013_4663brc_m013_4664..brc_m013_4668brc_m013_4669..brc_m013_4670brc_m013_4671..brc_m013_4674brc_m013_4675..brc_m013_4679brc_m013_4680..brc_m013_4681brc_m013_4682brc_m013_4683..brc_m013_4688brc_m013_4689..brc_m013_4692brc_m013_4693..brc_m013_4695brc_m013_4696..brc_m013_4701brc_m013_4702brc_m013_4703..brc_m013_4712brc_m013_4713..brc_m013_4717brc_m013_4718..brc_m013_4720brc_m013_4721brc_m013_4722..brc_m013_4726brc_m013_4727..brc_m013_4728brc_m013_4729..brc_m013_4742brc_m013_4743brc_m013_4744..brc_m013_4746brc_m013_4747brc_m013_4748..brc_m013_4749brc_m013_4750..brc_m013_4752

brc_m013_4753..brc_m013_4756brc_m013_4757..brc_m013_4759brc_m013_4760..brc_m013_4762brc_m013_4763brc_m013_4764..brc_m013_4766brc_m013_4767..brc_m013_4769brc_m013_4770brc_m013_4771..brc_m013_4774brc_m013_4775..brc_m013_4776brc_m013_4777..brc_m013_4778brc_m013_4779..brc_m013_4780brc_m013_4781..brc_m013_4793brc_m013_4794brc_m013_4795..brc_m013_4798brc_m013_4799..brc_m013_4802brc_m013_4803..brc_m013_4806brc_m013_4807brc_m013_4808..brc_m013_4814brc_m013_4815..brc_m013_4819brc_m013_4820brc_m013_4821brc_m013_4822..brc_m013_4823brc_m013_4824brc_m013_4825..brc_m013_4855brc_m013_4856..brc_m013_4858brc_m013_4859..brc_m013_4863brc_m013_4864..brc_m013_4865brc_m013_4866..brc_m013_4875brc_m013_4876..brc_m013_4881brc_m013_4882..brc_m013_4891brc_m013_4892..brc_m013_4895brc_m013_4896..brc_m013_4911brc_m013_4912..brc_m013_4938brc_m013_4939brc_m013_4940..brc_m013_4957brc_m013_4958..brc_m013_4959brc_m013_4960..brc_m013_4972brc_m013_4973..brc_m013_4981brc_m013_4982..brc_m013_4983

0

20

40

60

80

100

120

LGSB

Gp-9

Figure 1a b

Si_gnF.scaffold00779_nt2778431.7

Si_gnF.scaffold00779_nt1255229Si_gnF.scaffold02684_nt10884.2

Si_gnF.scaffold00779_nt1633919Si_gnF.scaffold00779_nt17842486.5

Si_gnF.scaffold00779_nt3746833Si_gnF.scaffold00779_nt374687927.3Si_gnF.scaffold00779_nt382158728.5

Si_gnF.scaffold00779_nt417489034.2

Si_gnF.scaffold09607_nt698300Si_gnF.scaffold09607_nt69848340.2

Si_gnF.scaffold09758_nt22273252.8

Si_gnF.scaffold05266_nt63430678.4Si_gnF.scaffold05266_nt65952779.7

Si_gnF.scaffold05266_nt733643Si_gnF.scaffold05266_nt75364482.8

Si_gnF.scaffold07090_nt71001087.6

Si_gnF.scaffold07090_nt105177192.7

Si_gnF.scaffold00255_nt314067Si_gnF.scaffold00255_nt40777897.5

Si_gnF.scaffold03404_nt128925Si_gnF.scaffold03404_nt228606Si_gnF.scaffold03404_nt241461

104.4

Si_gnF.scaffold00413_nt676115107.3

Si_gnF.scaffold00413_nt1035856109.6Si_gnF.scaffold01573_nt108462110.8Si_gnF.scaffold01573_nt447618112.1Si_gnF.scaffold00899_nt377419Si_gnF.scaffold00899_nt686574114.4Si_gnF.scaffold00899_nt236146Si_gnF.scaffold00899_nt332715Si_gnF.scaffold00899_nt335756

115.8

Si_gnF.scaffold00469_nt794118.0Si_gnF.scaffold00690_nt229012Si_gnF.scaffold00690_nt415290119.3

Si_gnF.scaffold06914_nt297673125.1

Si_gnF.scaffold01957_nt412242Si_gnF.scaffold02848_nt41846127.6

LGS Bfrom M013

Si_gnF.scaffold00779_nt2778430.0Si_gnF.scaffold00779_nt1255229Si_gnF.scaffold02684_nt10881.2

Si_gnF.scaffold00779_nt1633919Si_gnF.scaffold00779_nt17842486.7

Si_gnF.scaffold00779_nt3746833Si_gnF.scaffold00779_nt3746879Si_gnF.scaffold00779_nt3821587

22.2

Si_gnF.scaffold00779_nt417489029.2

Si_gnF.scaffold09607_nt698300Si_gnF.scaffold09607_nt69848361.9

Si_gnF.scaffold01573_nt10846280.7Si_gnF.scaffold00255_nt314067Si_gnF.scaffold00255_nt407778Si_gnF.scaffold00413_nt1035856Si_gnF.scaffold00413_nt676115Si_gnF.scaffold00469_nt794Si_gnF.scaffold00690_nt229012Si_gnF.scaffold00690_nt415290Si_gnF.scaffold00899_nt236146Si_gnF.scaffold00899_nt332715Si_gnF.scaffold00899_nt335756Si_gnF.scaffold00899_nt377419Si_gnF.scaffold00899_nt686574Si_gnF.scaffold01573_nt447618Si_gnF.scaffold01957_nt412242Si_gnF.scaffold03404_nt128925Si_gnF.scaffold03404_nt228606Si_gnF.scaffold03404_nt241461Si_gnF.scaffold05266_nt634306Si_gnF.scaffold05266_nt659527Si_gnF.scaffold05266_nt733643Si_gnF.scaffold05266_nt753644Si_gnF.scaffold06914_nt297673Si_gnF.scaffold07090_nt1051771Si_gnF.scaffold07090_nt710010Si_gnF.scaffold09758_nt222732

81.8

Si_gnF.scaffold02848_nt4184690.5

LGS B/bfrom P034

Gp-9

Total285 non-recombiningmarkersbrc_m013_0001..brc_m013_0005

brc_m013_0006..brc_m013_0014brc_m013_0015..brc_m013_0017brc_m013_0018brc_m013_0019..brc_m013_0020brc_m013_0021..brc_m013_0029brc_m013_0030..brc_m013_0031brc_m013_0032..brc_m013_0034brc_m013_0035..brc_m013_0036brc_m013_0037..brc_m013_0038brc_m013_0039..brc_m013_0043brc_m013_0044brc_m013_0045brc_m013_0046..brc_m013_0048brc_m013_0049brc_m013_0050..brc_m013_0051brc_m013_0052..brc_m013_0056brc_m013_0057..brc_m013_0061

brc_m013_0062..brc_m013_0075brc_m013_0076..brc_m013_0078brc_m013_0079..brc_m013_0081

brc_m013_0082..brc_m013_0088

brc_m013_0089..brc_m013_0092

brc_m013_0093..brc_m013_0096brc_m013_0097brc_m013_0098..brc_m013_0113brc_m013_0114..brc_m013_0119brc_m013_0120..brc_m013_0130brc_m013_0131brc_m013_0132..brc_m013_0134brc_m013_0135..brc_m013_0136brc_m013_0137..brc_m013_0139brc_m013_0140..brc_m013_0142brc_m013_0143brc_m013_0144..brc_m013_0146brc_m013_0147..brc_m013_0154brc_m013_0155

brc_m013_0156brc_m013_0157..brc_m013_0180brc_m013_0181brc_m013_0182brc_m013_0183..brc_m013_0188brc_m013_0189..brc_m013_0208brc_m013_0209brc_m013_0210..brc_m013_0211brc_m013_0212..brc_m013_0215brc_m013_0216brc_m013_0217brc_m013_0218..brc_m013_0224brc_m013_0225..brc_m013_0228brc_m013_0229..brc_m013_0237brc_m013_0238..brc_m013_0245

brc_m013_0246..brc_m013_0270

brc_m013_0271..brc_m013_0274brc_m013_0275brc_m013_0276..brc_m013_0278

brc_m013_0279

brc_m013_0280

brc_m013_0281..brc_m013_0294

brc_m013_0295..brc_m013_0303brc_m013_0304brc_m013_0305..brc_m013_0307brc_m013_0308brc_m013_0309..brc_m013_0314brc_m013_0315..brc_m013_0317brc_m013_0318..brc_m013_0320brc_m013_0321..brc_m013_0326brc_m013_0327brc_m013_0328brc_m013_0329..brc_m013_0330brc_m013_0331..brc_m013_0333brc_m013_0334..brc_m013_0339brc_m013_0340brc_m013_0341..brc_m013_0343brc_m013_0344brc_m013_0345..brc_m013_0349brc_m013_0350

brc_m013_0351..brc_m013_0354brc_m013_0355brc_m013_0356brc_m013_0357..brc_m013_0361brc_m013_0362..brc_m013_0376brc_m013_0377..brc_m013_0390brc_m013_0391..brc_m013_0393brc_m013_0394..brc_m013_0400brc_m013_0401..brc_m013_0439brc_m013_0440..brc_m013_0478brc_m013_0479..brc_m013_0480

0

20

40

60

80

100

120

140

160

180

LG1brc_m013_0481brc_m013_0482..brc_m013_0484brc_m013_0485..brc_m013_0488brc_m013_0489..brc_m013_0502brc_m013_0503brc_m013_0504..brc_m013_0519brc_m013_0520..brc_m013_0532brc_m013_0533..brc_m013_0534brc_m013_0535..brc_m013_0537brc_m013_0538..brc_m013_0540brc_m013_0541..brc_m013_0543brc_m013_0544..brc_m013_0545brc_m013_0546..brc_m013_0549

brc_m013_0550..brc_m013_0554

brc_m013_0555..brc_m013_0560

brc_m013_0561..brc_m013_0562brc_m013_0563..brc_m013_0565

brc_m013_0566brc_m013_0567brc_m013_0568..brc_m013_0570brc_m013_0571..brc_m013_0573

brc_m013_0574..brc_m013_0575brc_m013_0576..brc_m013_0578brc_m013_0579..brc_m013_0580brc_m013_0581brc_m013_0582..brc_m013_0584brc_m013_0585brc_m013_0586brc_m013_0587brc_m013_0588..brc_m013_0591brc_m013_0592brc_m013_0593brc_m013_0594..brc_m013_0612brc_m013_0613..brc_m013_0614brc_m013_0615..brc_m013_0632brc_m013_0633brc_m013_0634..brc_m013_0648brc_m013_0649..brc_m013_0655brc_m013_0656brc_m013_0657..brc_m013_0694brc_m013_0695..brc_m013_0703brc_m013_0704brc_m013_0705brc_m013_0706..brc_m013_0707brc_m013_0708brc_m013_0709..brc_m013_0711brc_m013_0712..brc_m013_0715brc_m013_0716..brc_m013_0721brc_m013_0722brc_m013_0723brc_m013_0724..brc_m013_0728brc_m013_0729brc_m013_0730brc_m013_0731brc_m013_0732..brc_m013_0735brc_m013_0736..brc_m013_0769brc_m013_0770..brc_m013_0771brc_m013_0772..brc_m013_0773brc_m013_0774..brc_m013_0775brc_m013_0776..brc_m013_0782brc_m013_0783brc_m013_0784..brc_m013_0795brc_m013_0796..brc_m013_0798brc_m013_0799..brc_m013_0801brc_m013_0802..brc_m013_0805brc_m013_0806..brc_m013_0809brc_m013_0810..brc_m013_0811brc_m013_0812..brc_m013_0824brc_m013_0825..brc_m013_0826brc_m013_0827..brc_m013_0829brc_m013_0830..brc_m013_0831brc_m013_0832..brc_m013_0842brc_m013_0843..brc_m013_0854brc_m013_0855..brc_m013_0861brc_m013_0862brc_m013_0863..brc_m013_0864brc_m013_0865..brc_m013_0867brc_m013_0868..brc_m013_0883brc_m013_0884..brc_m013_0893brc_m013_0894brc_m013_0895..brc_m013_0897brc_m013_0898..brc_m013_0906brc_m013_0907..brc_m013_0910brc_m013_0911..brc_m013_0925brc_m013_0926..brc_m013_0928brc_m013_0929..brc_m013_0931

0

20

40

60

80

100

120

140

LG2brc_m013_0932..brc_m013_0941brc_m013_0942..brc_m013_0943brc_m013_0944..brc_m013_0945brc_m013_0946..brc_m013_0949brc_m013_0950..brc_m013_0952

brc_m013_0953..brc_m013_0975

brc_m013_0976..brc_m013_1019brc_m013_1020brc_m013_1021brc_m013_1022..brc_m013_1061brc_m013_1062brc_m013_1063

brc_m013_1064..brc_m013_1065

brc_m013_1066..brc_m013_1068brc_m013_1069brc_m013_1070

brc_m013_1071..brc_m013_1074

brc_m013_1075

brc_m013_1076..brc_m013_1081

brc_m013_1082..brc_m013_1086brc_m013_1087..brc_m013_1088brc_m013_1089..brc_m013_1098brc_m013_1099..brc_m013_1106brc_m013_1107..brc_m013_1116brc_m013_1117brc_m013_1118..brc_m013_1121brc_m013_1122..brc_m013_1127brc_m013_1128brc_m013_1129..brc_m013_1136brc_m013_1137..brc_m013_1138brc_m013_1139..brc_m013_1141brc_m013_1142..brc_m013_1144brc_m013_1145..brc_m013_1156brc_m013_1157brc_m013_1158..brc_m013_1170brc_m013_1171..brc_m013_1181brc_m013_1182..brc_m013_1185brc_m013_1186brc_m013_1187..brc_m013_1205brc_m013_1206..brc_m013_1218brc_m013_1219..brc_m013_1220brc_m013_1221..brc_m013_1224brc_m013_1225..brc_m013_1228brc_m013_1229brc_m013_1230..brc_m013_1236brc_m013_1237brc_m013_1238..brc_m013_1247brc_m013_1248..brc_m013_1251

brc_m013_1252brc_m013_1253..brc_m013_1268brc_m013_1269..brc_m013_1270brc_m013_1271..brc_m013_1273brc_m013_1274brc_m013_1275..brc_m013_1280brc_m013_1281

brc_m013_1282..brc_m013_1286brc_m013_1287..brc_m013_1298brc_m013_1299..brc_m013_1307brc_m013_1308brc_m013_1309..brc_m013_1313brc_m013_1314..brc_m013_1317brc_m013_1318..brc_m013_1319brc_m013_1320..brc_m013_1326brc_m013_1327..brc_m013_1340brc_m013_1341..brc_m013_1362brc_m013_1363..brc_m013_1385

0

20

40

60

80

100

120

140

LG3brc_m013_1386..brc_m013_1388brc_m013_1389..brc_m013_1398brc_m013_1399..brc_m013_1406brc_m013_1407..brc_m013_1411brc_m013_1412..brc_m013_1413brc_m013_1414..brc_m013_1416

brc_m013_1417brc_m013_1418..brc_m013_1420brc_m013_1421..brc_m013_1424brc_m013_1425..brc_m013_1432brc_m013_1433..brc_m013_1442brc_m013_1443brc_m013_1444..brc_m013_1450brc_m013_1451brc_m013_1452brc_m013_1453..brc_m013_1455brc_m013_1456..brc_m013_1467brc_m013_1468..brc_m013_1469brc_m013_1470brc_m013_1471..brc_m013_1474brc_m013_1475brc_m013_1476brc_m013_1477brc_m013_1478..brc_m013_1482brc_m013_1483

brc_m013_1484brc_m013_1485..brc_m013_1487brc_m013_1488..brc_m013_1490

brc_m013_1491brc_m013_1492..brc_m013_1494brc_m013_1495..brc_m013_1496

brc_m013_1497..brc_m013_1500brc_m013_1501brc_m013_1502..brc_m013_1513brc_m013_1514..brc_m013_1562brc_m013_1563..brc_m013_1565brc_m013_1566..brc_m013_1567

brc_m013_1568..brc_m013_1580brc_m013_1581..brc_m013_1587brc_m013_1588..brc_m013_1591brc_m013_1592..brc_m013_1593brc_m013_1594..brc_m013_1604brc_m013_1605..brc_m013_1607brc_m013_1608..brc_m013_1609brc_m013_1610..brc_m013_1611brc_m013_1612..brc_m013_1616brc_m013_1617..brc_m013_1618brc_m013_1619..brc_m013_1620brc_m013_1621..brc_m013_1629brc_m013_1630..brc_m013_1633brc_m013_1634..brc_m013_1638brc_m013_1639..brc_m013_1647brc_m013_1648..brc_m013_1649brc_m013_1650..brc_m013_1656brc_m013_1657..brc_m013_1665brc_m013_1666..brc_m013_1672brc_m013_1673..brc_m013_1674brc_m013_1675..brc_m013_1678brc_m013_1679..brc_m013_1682brc_m013_1683brc_m013_1684brc_m013_1685..brc_m013_1686brc_m013_1687..brc_m013_1700brc_m013_1701..brc_m013_1702brc_m013_1703brc_m013_1704..brc_m013_1707brc_m013_1708..brc_m013_1709brc_m013_1710..brc_m013_1714brc_m013_1715..brc_m013_1728brc_m013_1729..brc_m013_1742

0

20

40

60

80

100

120

140

LG4brc_m013_1743..brc_m013_1750

brc_m013_1751..brc_m013_1766brc_m013_1767brc_m013_1768

brc_m013_1769..brc_m013_1772

brc_m013_1773..brc_m013_1779brc_m013_1780brc_m013_1781brc_m013_1782..brc_m013_1783brc_m013_1784brc_m013_1785..brc_m013_1786

brc_m013_1787

brc_m013_1788brc_m013_1789..brc_m013_1790brc_m013_1791..brc_m013_1793brc_m013_1794..brc_m013_1797brc_m013_1798..brc_m013_1800brc_m013_1801..brc_m013_1804brc_m013_1805brc_m013_1806..brc_m013_1808brc_m013_1809brc_m013_1810..brc_m013_1813brc_m013_1814..brc_m013_1818brc_m013_1819..brc_m013_1820brc_m013_1821..brc_m013_1822brc_m013_1823..brc_m013_1824brc_m013_1825brc_m013_1826..brc_m013_1840brc_m013_1841..brc_m013_1842brc_m013_1843brc_m013_1844..brc_m013_1848brc_m013_1849brc_m013_1850brc_m013_1851..brc_m013_1853brc_m013_1854..brc_m013_1858brc_m013_1859..brc_m013_1866brc_m013_1867..brc_m013_1868brc_m013_1869brc_m013_1870..brc_m013_1874brc_m013_1875..brc_m013_1876brc_m013_1877..brc_m013_1878brc_m013_1879..brc_m013_1883brc_m013_1884brc_m013_1885brc_m013_1886..brc_m013_1888brc_m013_1889..brc_m013_1895brc_m013_1896..brc_m013_1899brc_m013_1900..brc_m013_1913brc_m013_1914brc_m013_1915..brc_m013_1922brc_m013_1923brc_m013_1924..brc_m013_1928brc_m013_1929..brc_m013_1942brc_m013_1943..brc_m013_1946brc_m013_1947..brc_m013_1948brc_m013_1949brc_m013_1950..brc_m013_1953brc_m013_1954..brc_m013_1955brc_m013_1956brc_m013_1957..brc_m013_1963brc_m013_1964..brc_m013_1966brc_m013_1967..brc_m013_1968brc_m013_1969..brc_m013_1970brc_m013_1971brc_m013_1972brc_m013_1973..brc_m013_1980brc_m013_1981..brc_m013_1983brc_m013_1984..brc_m013_1990brc_m013_1991..brc_m013_1993brc_m013_1994..brc_m013_1996brc_m013_1997..brc_m013_2009

0

20

40

60

80

100

120

LG5brc_m013_2010..brc_m013_2028

brc_m013_2029..brc_m013_2038brc_m013_2039

brc_m013_2040..brc_m013_2041brc_m013_2042..brc_m013_2047brc_m013_2048..brc_m013_2050brc_m013_2051..brc_m013_2053brc_m013_2054..brc_m013_2062brc_m013_2063brc_m013_2064..brc_m013_2065brc_m013_2066..brc_m013_2067brc_m013_2068brc_m013_2069..brc_m013_2071brc_m013_2072..brc_m013_2081brc_m013_2082

brc_m013_2083brc_m013_2084brc_m013_2085..brc_m013_2099brc_m013_2100brc_m013_2101..brc_m013_2102brc_m013_2103..brc_m013_2107brc_m013_2108brc_m013_2109..brc_m013_2112

brc_m013_2113..brc_m013_2114brc_m013_2115..brc_m013_2123brc_m013_2124..brc_m013_2131brc_m013_2132brc_m013_2133brc_m013_2134..brc_m013_2136

brc_m013_2137

brc_m013_2138..brc_m013_2139

brc_m013_2140..brc_m013_2142brc_m013_2143..brc_m013_2150brc_m013_2151..brc_m013_2152brc_m013_2153..brc_m013_2161brc_m013_2162..brc_m013_2163

brc_m013_2164..brc_m013_2165brc_m013_2166..brc_m013_2170brc_m013_2171..brc_m013_2172brc_m013_2173brc_m013_2174..brc_m013_2182brc_m013_2183..brc_m013_2186brc_m013_2187..brc_m013_2190brc_m013_2191..brc_m013_2193brc_m013_2194brc_m013_2195..brc_m013_2201brc_m013_2202..brc_m013_2203brc_m013_2204..brc_m013_2220brc_m013_2221..brc_m013_2232brc_m013_2233..brc_m013_2239brc_m013_2240..brc_m013_2261brc_m013_2262..brc_m013_2267brc_m013_2268..brc_m013_2269brc_m013_2270..brc_m013_2271brc_m013_2272..brc_m013_2282brc_m013_2283..brc_m013_2284brc_m013_2285..brc_m013_2299brc_m013_2300..brc_m013_2301brc_m013_2302..brc_m013_2305brc_m013_2306..brc_m013_2307brc_m013_2308..brc_m013_2330brc_m013_2331..brc_m013_2337brc_m013_2338..brc_m013_2352

0

20

40

60

80

100

120

LG6brc_m013_2353..brc_m013_2365brc_m013_2366..brc_m013_2369

brc_m013_2370..brc_m013_2372brc_m013_2373..brc_m013_2378brc_m013_2379..brc_m013_2386brc_m013_2387brc_m013_2388..brc_m013_2394brc_m013_2395..brc_m013_2397brc_m013_2398brc_m013_2399brc_m013_2400brc_m013_2401brc_m013_2402..brc_m013_2407brc_m013_2408..brc_m013_2411brc_m013_2412..brc_m013_2416brc_m013_2417brc_m013_2418brc_m013_2419..brc_m013_2436brc_m013_2437..brc_m013_2441brc_m013_2442brc_m013_2443..brc_m013_2444brc_m013_2445brc_m013_2446..brc_m013_2453brc_m013_2454brc_m013_2455..brc_m013_2460brc_m013_2461brc_m013_2462..brc_m013_2470brc_m013_2471..brc_m013_2474brc_m013_2475..brc_m013_2482brc_m013_2483brc_m013_2484..brc_m013_2487brc_m013_2488brc_m013_2489..brc_m013_2492brc_m013_2493..brc_m013_2496brc_m013_2497brc_m013_2498..brc_m013_2504brc_m013_2505brc_m013_2506..brc_m013_2510brc_m013_2511..brc_m013_2523brc_m013_2524..brc_m013_2531brc_m013_2532..brc_m013_2536brc_m013_2537..brc_m013_2555brc_m013_2556..brc_m013_2571brc_m013_2572..brc_m013_2573brc_m013_2574..brc_m013_2579brc_m013_2580..brc_m013_2581brc_m013_2582..brc_m013_2587brc_m013_2588brc_m013_2589..brc_m013_2594

brc_m013_2595

brc_m013_2596..brc_m013_2597brc_m013_2598..brc_m013_2604brc_m013_2605brc_m013_2606..brc_m013_2616brc_m013_2617..brc_m013_2619brc_m013_2620..brc_m013_2623

brc_m013_2624brc_m013_2625..brc_m013_2626brc_m013_2627..brc_m013_2628

brc_m013_2629..brc_m013_2630

0

20

40

60

80

100

LG7brc_m013_2631..brc_m013_2632brc_m013_2633brc_m013_2634..brc_m013_2635brc_m013_2636..brc_m013_2642brc_m013_2643..brc_m013_2657brc_m013_2658..brc_m013_2659brc_m013_2660..brc_m013_2661brc_m013_2662

brc_m013_2663

brc_m013_2664brc_m013_2665..brc_m013_2666

brc_m013_2667..brc_m013_2668brc_m013_2669..brc_m013_2670brc_m013_2671..brc_m013_2680brc_m013_2681..brc_m013_2682brc_m013_2683brc_m013_2684..brc_m013_2685brc_m013_2686..brc_m013_2694

brc_m013_2695..brc_m013_2698brc_m013_2699..brc_m013_2713

brc_m013_2714..brc_m013_2725brc_m013_2726..brc_m013_2727brc_m013_2728..brc_m013_2731brc_m013_2732brc_m013_2733..brc_m013_2753brc_m013_2754..brc_m013_2758brc_m013_2759..brc_m013_2763brc_m013_2764..brc_m013_2779brc_m013_2780brc_m013_2781brc_m013_2782..brc_m013_2784brc_m013_2785..brc_m013_2787brc_m013_2788..brc_m013_2791brc_m013_2792..brc_m013_2797brc_m013_2798..brc_m013_2799brc_m013_2800brc_m013_2801..brc_m013_2804brc_m013_2805..brc_m013_2809

brc_m013_2810..brc_m013_2811

brc_m013_2812..brc_m013_2813brc_m013_2814..brc_m013_2817brc_m013_2818..brc_m013_2827brc_m013_2828brc_m013_2829..brc_m013_2832brc_m013_2833brc_m013_2834..brc_m013_2840brc_m013_2841..brc_m013_2846brc_m013_2847brc_m013_2848..brc_m013_2852brc_m013_2853brc_m013_2854..brc_m013_2856brc_m013_2857..brc_m013_2862brc_m013_2863..brc_m013_2868brc_m013_2869..brc_m013_2874brc_m013_2875..brc_m013_2896

0

20

40

60

80

100

LG8

brc_m013_2897..brc_m013_2920brc_m013_2921..brc_m013_2928brc_m013_2929..brc_m013_2931brc_m013_2932

brc_m013_2933

brc_m013_2934..brc_m013_2935brc_m013_2936brc_m013_2937..brc_m013_2943brc_m013_2944brc_m013_2945..brc_m013_2946brc_m013_2947brc_m013_2948brc_m013_2949..brc_m013_2950brc_m013_2951..brc_m013_2957brc_m013_2958..brc_m013_2961brc_m013_2962..brc_m013_2970brc_m013_2971..brc_m013_2980brc_m013_2981..brc_m013_2992brc_m013_2993..brc_m013_2996brc_m013_2997..brc_m013_2998brc_m013_2999..brc_m013_3000brc_m013_3001brc_m013_3002..brc_m013_3003brc_m013_3004brc_m013_3005brc_m013_3006..brc_m013_3010brc_m013_3011..brc_m013_3014brc_m013_3015brc_m013_3016..brc_m013_3019brc_m013_3020brc_m013_3021..brc_m013_3030brc_m013_3031..brc_m013_3032brc_m013_3033..brc_m013_3034brc_m013_3035..brc_m013_3036brc_m013_3037..brc_m013_3045brc_m013_3046..brc_m013_3052brc_m013_3053brc_m013_3054..brc_m013_3061brc_m013_3062..brc_m013_3066brc_m013_3067..brc_m013_3068brc_m013_3069..brc_m013_3076brc_m013_3077..brc_m013_3084brc_m013_3085..brc_m013_3087brc_m013_3088..brc_m013_3089brc_m013_3090..brc_m013_3096brc_m013_3097..brc_m013_3100brc_m013_3101..brc_m013_3104brc_m013_3105brc_m013_3106..brc_m013_3112brc_m013_3113..brc_m013_3122brc_m013_3123..brc_m013_3124brc_m013_3125..brc_m013_3127brc_m013_3128..brc_m013_3145brc_m013_3146..brc_m013_3159brc_m013_3160..brc_m013_3172

0

20

40

60

80

100

LG9brc_m013_3173..brc_m013_3175brc_m013_3176..brc_m013_3180brc_m013_3181..brc_m013_3189brc_m013_3190..brc_m013_3198brc_m013_3199brc_m013_3200..brc_m013_3201brc_m013_3202..brc_m013_3203brc_m013_3204brc_m013_3205..brc_m013_3206brc_m013_3207..brc_m013_3211brc_m013_3212..brc_m013_3214brc_m013_3215..brc_m013_3227brc_m013_3228..brc_m013_3230brc_m013_3231..brc_m013_3235brc_m013_3236..brc_m013_3238brc_m013_3239..brc_m013_3242brc_m013_3243..brc_m013_3244brc_m013_3245brc_m013_3246..brc_m013_3247brc_m013_3248..brc_m013_3249brc_m013_3250..brc_m013_3252brc_m013_3253..brc_m013_3257brc_m013_3258brc_m013_3259brc_m013_3260..brc_m013_3261brc_m013_3262..brc_m013_3263brc_m013_3264brc_m013_3265..brc_m013_3269brc_m013_3270..brc_m013_3274brc_m013_3275..brc_m013_3276brc_m013_3277..brc_m013_3281brc_m013_3282..brc_m013_3284brc_m013_3285brc_m013_3286..brc_m013_3289brc_m013_3290..brc_m013_3296brc_m013_3297brc_m013_3298..brc_m013_3300brc_m013_3301..brc_m013_3302brc_m013_3303..brc_m013_3305brc_m013_3306..brc_m013_3308brc_m013_3309..brc_m013_3314brc_m013_3315..brc_m013_3317brc_m013_3318..brc_m013_3329brc_m013_3330..brc_m013_3331brc_m013_3332..brc_m013_3338brc_m013_3339..brc_m013_3340brc_m013_3341..brc_m013_3344brc_m013_3345..brc_m013_3349brc_m013_3350..brc_m013_3357brc_m013_3358..brc_m013_3359brc_m013_3360brc_m013_3361..brc_m013_3368brc_m013_3369..brc_m013_3372brc_m013_3373..brc_m013_3376brc_m013_3377brc_m013_3378..brc_m013_3386brc_m013_3387..brc_m013_3388brc_m013_3389..brc_m013_3395brc_m013_3396..brc_m013_3399

0

20

40

60

80

LG10brc_m013_3400..brc_m013_3411brc_m013_3412brc_m013_3413..brc_m013_3424brc_m013_3425brc_m013_3426brc_m013_3427..brc_m013_3429

brc_m013_3430

brc_m013_3431..brc_m013_3432brc_m013_3433..brc_m013_3435brc_m013_3436brc_m013_3437..brc_m013_3439

brc_m013_3440..brc_m013_3441brc_m013_3442

brc_m013_3443..brc_m013_3445brc_m013_3446..brc_m013_3447brc_m013_3448..brc_m013_3449brc_m013_3450..brc_m013_3454brc_m013_3455brc_m013_3456..brc_m013_3462brc_m013_3463..brc_m013_3464brc_m013_3465brc_m013_3466..brc_m013_3467brc_m013_3468..brc_m013_3472brc_m013_3473brc_m013_3474..brc_m013_3476brc_m013_3477..brc_m013_3487brc_m013_3488brc_m013_3489..brc_m013_3491brc_m013_3492..brc_m013_3500brc_m013_3501..brc_m013_3512brc_m013_3513..brc_m013_3514brc_m013_3515..brc_m013_3524brc_m013_3525..brc_m013_3527brc_m013_3528..brc_m013_3531brc_m013_3532..brc_m013_3547brc_m013_3548..brc_m013_3557brc_m013_3558..brc_m013_3566brc_m013_3567..brc_m013_3568brc_m013_3569..brc_m013_3570brc_m013_3571..brc_m013_3574brc_m013_3575..brc_m013_3582brc_m013_3583..brc_m013_3592brc_m013_3593..brc_m013_3605brc_m013_3606..brc_m013_3616brc_m013_3617..brc_m013_3618brc_m013_3619..brc_m013_3622brc_m013_3623..brc_m013_3624brc_m013_3625..brc_m013_3628brc_m013_3629..brc_m013_3635

0

20

40

60

80

LG11

brc_m013_3636..brc_m013_3661brc_m013_3662..brc_m013_3665

brc_m013_3666..brc_m013_3667brc_m013_3668brc_m013_3669..brc_m013_3671

brc_m013_3672

brc_m013_3673..brc_m013_3674brc_m013_3675..brc_m013_3682

brc_m013_3683..brc_m013_3685

brc_m013_3686..brc_m013_3688

brc_m013_3689..brc_m013_3693

brc_m013_3694..brc_m013_3698brc_m013_3699

brc_m013_3700brc_m013_3701..brc_m013_3702brc_m013_3703..brc_m013_3704brc_m013_3705..brc_m013_3712brc_m013_3713brc_m013_3714..brc_m013_3716brc_m013_3717..brc_m013_3724brc_m013_3725..brc_m013_3730brc_m013_3731..brc_m013_3752brc_m013_3753..brc_m013_3758brc_m013_3759..brc_m013_3789brc_m013_3790..brc_m013_3801brc_m013_3802..brc_m013_3814brc_m013_3815..brc_m013_3818brc_m013_3819..brc_m013_3822brc_m013_3823..brc_m013_3826brc_m013_3827..brc_m013_3832brc_m013_3833..brc_m013_3837brc_m013_3838brc_m013_3839..brc_m013_3841brc_m013_3842..brc_m013_3847

brc_m013_3848..brc_m013_3853brc_m013_3854..brc_m013_3858brc_m013_3859..brc_m013_3868brc_m013_3869..brc_m013_3871brc_m013_3872..brc_m013_3901brc_m013_3902brc_m013_3903..brc_m013_3909brc_m013_3910brc_m013_3911..brc_m013_3926brc_m013_3927..brc_m013_3931brc_m013_3932..brc_m013_3948

0

20

40

60

80

LG12

brc_m013_3949..brc_m013_3952brc_m013_3953..brc_m013_3958brc_m013_3959..brc_m013_3970brc_m013_3971

brc_m013_3972..brc_m013_3975brc_m013_3976

brc_m013_3977..brc_m013_3985

brc_m013_3986brc_m013_3987..brc_m013_3994brc_m013_3995..brc_m013_3997brc_m013_3998..brc_m013_4004

brc_m013_4005..brc_m013_4006brc_m013_4007..brc_m013_4008brc_m013_4009..brc_m013_4010brc_m013_4011..brc_m013_4013brc_m013_4014brc_m013_4015brc_m013_4016..brc_m013_4019brc_m013_4020..brc_m013_4021brc_m013_4022..brc_m013_4025brc_m013_4026..brc_m013_4032brc_m013_4033..brc_m013_4036brc_m013_4037..brc_m013_4041brc_m013_4042..brc_m013_4043

brc_m013_4044..brc_m013_4046brc_m013_4047..brc_m013_4056brc_m013_4057brc_m013_4058..brc_m013_4063brc_m013_4064..brc_m013_4071brc_m013_4072..brc_m013_4075brc_m013_4076brc_m013_4077brc_m013_4078..brc_m013_4085brc_m013_4086..brc_m013_4089brc_m013_4090..brc_m013_4091brc_m013_4092..brc_m013_4093brc_m013_4094..brc_m013_4095brc_m013_4096..brc_m013_4114brc_m013_4115..brc_m013_4117brc_m013_4118..brc_m013_4131brc_m013_4132..brc_m013_4133brc_m013_4134..brc_m013_4146

0

20

40

60

80

LG13

brc_m013_4147..brc_m013_4150brc_m013_4151..brc_m013_4167

brc_m013_4168brc_m013_4169

brc_m013_4170brc_m013_4171..brc_m013_4172brc_m013_4173..brc_m013_4175brc_m013_4176brc_m013_4177..brc_m013_4178brc_m013_4179..brc_m013_4183brc_m013_4184..brc_m013_4185brc_m013_4186..brc_m013_4187brc_m013_4188..brc_m013_4191brc_m013_4192brc_m013_4193..brc_m013_4194brc_m013_4195..brc_m013_4206brc_m013_4207..brc_m013_4210brc_m013_4211..brc_m013_4213brc_m013_4214brc_m013_4215..brc_m013_4217brc_m013_4218..brc_m013_4221brc_m013_4222..brc_m013_4223brc_m013_4224..brc_m013_4231brc_m013_4232..brc_m013_4234brc_m013_4235..brc_m013_4239brc_m013_4240..brc_m013_4246brc_m013_4247..brc_m013_4248brc_m013_4249..brc_m013_4258brc_m013_4259..brc_m013_4260brc_m013_4261..brc_m013_4269brc_m013_4270..brc_m013_4271brc_m013_4272..brc_m013_4278brc_m013_4279..brc_m013_4280brc_m013_4281..brc_m013_4284brc_m013_4285brc_m013_4286..brc_m013_4288brc_m013_4289..brc_m013_4294brc_m013_4295..brc_m013_4296brc_m013_4297..brc_m013_4301brc_m013_4302..brc_m013_4313brc_m013_4314..brc_m013_4320brc_m013_4321..brc_m013_4322brc_m013_4323..brc_m013_4345brc_m013_4346..brc_m013_4351

0

20

40

60

LG14brc_m013_4352..brc_m013_4366brc_m013_4367brc_m013_4368brc_m013_4369..brc_m013_4373brc_m013_4374..brc_m013_4381brc_m013_4382..brc_m013_4383brc_m013_4384..brc_m013_4385brc_m013_4386brc_m013_4387..brc_m013_4388brc_m013_4389brc_m013_4390..brc_m013_4404brc_m013_4405brc_m013_4406..brc_m013_4409brc_m013_4410..brc_m013_4411brc_m013_4412..brc_m013_4418brc_m013_4419..brc_m013_4434brc_m013_4435..brc_m013_4442brc_m013_4443..brc_m013_4448brc_m013_4449..brc_m013_4451brc_m013_4452..brc_m013_4461brc_m013_4462..brc_m013_4471brc_m013_4472..brc_m013_4475brc_m013_4476..brc_m013_4477brc_m013_4478brc_m013_4479brc_m013_4480..brc_m013_4485brc_m013_4486brc_m013_4487..brc_m013_4491brc_m013_4492brc_m013_4493brc_m013_4494..brc_m013_4495brc_m013_4496..brc_m013_4501brc_m013_4502..brc_m013_4510brc_m013_4511..brc_m013_4531brc_m013_4532brc_m013_4533..brc_m013_4534brc_m013_4535..brc_m013_4541brc_m013_4542..brc_m013_4543brc_m013_4544..brc_m013_4545brc_m013_4546..brc_m013_4548brc_m013_4549..brc_m013_4551brc_m013_4552..brc_m013_4555brc_m013_4556..brc_m013_4561

0

20

40

60

LG15

brc_m013_4562..brc_m013_4577brc_m013_4578..brc_m013_4594brc_m013_4595..brc_m013_4599brc_m013_4600..brc_m013_4625brc_m013_4626..brc_m013_4638brc_m013_4639..brc_m013_4642brc_m013_4643..brc_m013_4644brc_m013_4645..brc_m013_4650brc_m013_4651..brc_m013_4663brc_m013_4664..brc_m013_4668brc_m013_4669..brc_m013_4670brc_m013_4671..brc_m013_4674brc_m013_4675..brc_m013_4679brc_m013_4680..brc_m013_4681brc_m013_4682brc_m013_4683..brc_m013_4688brc_m013_4689..brc_m013_4692brc_m013_4693..brc_m013_4695brc_m013_4696..brc_m013_4701brc_m013_4702brc_m013_4703..brc_m013_4712brc_m013_4713..brc_m013_4717brc_m013_4718..brc_m013_4720brc_m013_4721brc_m013_4722..brc_m013_4726brc_m013_4727..brc_m013_4728brc_m013_4729..brc_m013_4742brc_m013_4743brc_m013_4744..brc_m013_4746brc_m013_4747brc_m013_4748..brc_m013_4749brc_m013_4750..brc_m013_4752

brc_m013_4753..brc_m013_4756brc_m013_4757..brc_m013_4759brc_m013_4760..brc_m013_4762brc_m013_4763brc_m013_4764..brc_m013_4766brc_m013_4767..brc_m013_4769brc_m013_4770brc_m013_4771..brc_m013_4774brc_m013_4775..brc_m013_4776brc_m013_4777..brc_m013_4778brc_m013_4779..brc_m013_4780brc_m013_4781..brc_m013_4793brc_m013_4794brc_m013_4795..brc_m013_4798brc_m013_4799..brc_m013_4802brc_m013_4803..brc_m013_4806brc_m013_4807brc_m013_4808..brc_m013_4814brc_m013_4815..brc_m013_4819brc_m013_4820brc_m013_4821brc_m013_4822..brc_m013_4823brc_m013_4824brc_m013_4825..brc_m013_4855brc_m013_4856..brc_m013_4858brc_m013_4859..brc_m013_4863brc_m013_4864..brc_m013_4865brc_m013_4866..brc_m013_4875brc_m013_4876..brc_m013_4881brc_m013_4882..brc_m013_4891brc_m013_4892..brc_m013_4895brc_m013_4896..brc_m013_4911brc_m013_4912..brc_m013_4938brc_m013_4939brc_m013_4940..brc_m013_4957brc_m013_4958..brc_m013_4959brc_m013_4960..brc_m013_4972brc_m013_4973..brc_m013_4981brc_m013_4982..brc_m013_4983

0

20

40

60

80

100

120

LGSB

Gp-9

Figure 1a b

Si_gnF.scaffold00779_nt2778431.7

Si_gnF.scaffold00779_nt1255229Si_gnF.scaffold02684_nt10884.2

Si_gnF.scaffold00779_nt1633919Si_gnF.scaffold00779_nt17842486.5

Si_gnF.scaffold00779_nt3746833Si_gnF.scaffold00779_nt374687927.3Si_gnF.scaffold00779_nt382158728.5

Si_gnF.scaffold00779_nt417489034.2

Si_gnF.scaffold09607_nt698300Si_gnF.scaffold09607_nt69848340.2

Si_gnF.scaffold09758_nt22273252.8

Si_gnF.scaffold05266_nt63430678.4Si_gnF.scaffold05266_nt65952779.7

Si_gnF.scaffold05266_nt733643Si_gnF.scaffold05266_nt75364482.8

Si_gnF.scaffold07090_nt71001087.6

Si_gnF.scaffold07090_nt105177192.7

Si_gnF.scaffold00255_nt314067Si_gnF.scaffold00255_nt40777897.5

Si_gnF.scaffold03404_nt128925Si_gnF.scaffold03404_nt228606Si_gnF.scaffold03404_nt241461

104.4

Si_gnF.scaffold00413_nt676115107.3

Si_gnF.scaffold00413_nt1035856109.6Si_gnF.scaffold01573_nt108462110.8Si_gnF.scaffold01573_nt447618112.1Si_gnF.scaffold00899_nt377419Si_gnF.scaffold00899_nt686574114.4Si_gnF.scaffold00899_nt236146Si_gnF.scaffold00899_nt332715Si_gnF.scaffold00899_nt335756

115.8

Si_gnF.scaffold00469_nt794118.0Si_gnF.scaffold00690_nt229012Si_gnF.scaffold00690_nt415290119.3

Si_gnF.scaffold06914_nt297673125.1

Si_gnF.scaffold01957_nt412242Si_gnF.scaffold02848_nt41846127.6

LGS Bfrom M013

Si_gnF.scaffold00779_nt2778430.0Si_gnF.scaffold00779_nt1255229Si_gnF.scaffold02684_nt10881.2

Si_gnF.scaffold00779_nt1633919Si_gnF.scaffold00779_nt17842486.7

Si_gnF.scaffold00779_nt3746833Si_gnF.scaffold00779_nt3746879Si_gnF.scaffold00779_nt3821587

22.2

Si_gnF.scaffold00779_nt417489029.2

Si_gnF.scaffold09607_nt698300Si_gnF.scaffold09607_nt69848361.9

Si_gnF.scaffold01573_nt10846280.7Si_gnF.scaffold00255_nt314067Si_gnF.scaffold00255_nt407778Si_gnF.scaffold00413_nt1035856Si_gnF.scaffold00413_nt676115Si_gnF.scaffold00469_nt794Si_gnF.scaffold00690_nt229012Si_gnF.scaffold00690_nt415290Si_gnF.scaffold00899_nt236146Si_gnF.scaffold00899_nt332715Si_gnF.scaffold00899_nt335756Si_gnF.scaffold00899_nt377419Si_gnF.scaffold00899_nt686574Si_gnF.scaffold01573_nt447618Si_gnF.scaffold01957_nt412242Si_gnF.scaffold03404_nt128925Si_gnF.scaffold03404_nt228606Si_gnF.scaffold03404_nt241461Si_gnF.scaffold05266_nt634306Si_gnF.scaffold05266_nt659527Si_gnF.scaffold05266_nt733643Si_gnF.scaffold05266_nt753644Si_gnF.scaffold06914_nt297673Si_gnF.scaffold07090_nt1051771Si_gnF.scaffold07090_nt710010Si_gnF.scaffold09758_nt222732

81.8

Si_gnF.scaffold02848_nt4184690.5

LGS B/bfrom P034

Gp-9

Total285 non-recombiningmarkers

No recombination between B and b over ⅔ of a chromosme!

4% of genome linked to Gp-9

Page 52: 2014 11-28-lyon

Sex chromosomes

X Y

Gp-9 B

Gp-9 b

SB Sb

“Social chromosomes”

?

Why non-recombining?

Page 53: 2014 11-28-lyon

Small portion (200,000bp) of social chromosome

Structural differences between B and blikely inhibit recombination

SB

Sb

Page 54: 2014 11-28-lyon

Sb SB Gp-9B

genetic map

E3

E17

A22

Gp-9 B male Gp-9 b male Figure 2 a

b Diploid Gp-9 Bb

Sb SB Gp-9B

genetic map

E3

E17

A22

Gp-9 B male Gp-9 b male Figure 2 a

b Diploid Gp-9 Bb

Sb SB Gp-9B

genetic map

E3

E17

A22

Gp-9 B male Gp-9 b male Figure 2 a

b Diploid Gp-9 Bb

Sb SB Gp-9B

genetic map

E3

E17

A22

Gp-9 B male Gp-9 b male Figure 2 a

b Diploid Gp-9 Bb

Flourescence in situ Hybridization

John Wang @ Taipei

Structural differences between B and blikely inhibit recombination

Page 55: 2014 11-28-lyon

Gp-9 B

Gp-9 b

SB Sb

“Social chromosomes”

Likely several rearrangments

Page 56: 2014 11-28-lyon

X

X X Y

Likely several rearrangements

•Prediction:

SBSB SB Sb

Single queen colony Multiple queen colony

Differences between SB and Sb?•genes?

Region contains 800 genes! only small differences⟹ Prediction: directional (antagonistic?) selection?

Sb is degenerating?

Page 57: 2014 11-28-lyon

SB

Sb

• More, larger repetitive DNA in Sb compared to SB• larger introns in Sb• larger intergenic regions in Sb• assembly worse (smaller scaffolds) in Sb

• increased dN/dS

[b] vs. [c]: p < 10-4

[a] vs. [c]: p < 10-7

Gp-9B male Gp-9b male

Region:

Genome assembly:

Normally recombiningregions from all 16

linkage groups

Normally recombiningregions from all 16

linkage groups

Sb region without recombination

in Gp-9 Bb queens

SB region without recombination

in Gp-9 Bb queens

Sca

ffold

leng

th (b

p)

0

1,000,000

2,000,000

3,000,000

4,000,000

5,000,000

6,000,000

[a] [a], [b] [a] [c]

SB Sb

Sb is degenerating?

Page 58: 2014 11-28-lyon

X

X X Y

Likely several rearrangements

•Prediction:

SBSB SB Sb

Single queen colony Multiple queen colony

Differences between SB and Sb?•genes?

Region contains 800 genes! only small differences⟹ Prediction: directional (antagonistic?) selection?

Sb is degenerating?•Probably ♂ haploidy: strong purifying selection ⟹ slower degeneration

Page 59: 2014 11-28-lyon

Formica selysi

Purcell et al 2014Convergent social chromosome architecture

J Meunier

Single queen form Multiple queen form

Alpine silver antCommon ancestor with fire ant: 130 MYA

Page 60: 2014 11-28-lyon

≠ social chromosomes

Purcell et al 2014

Solenopsis invicta social chromosome

Formica selysi social

chromosome

Page 61: 2014 11-28-lyon

Social chromosomes also for other major social transitions?

Page 62: 2014 11-28-lyon

Summary

Fire ant Solenopsis invicta queen number determined by Gp-9 genotypes: •only BB workers ➔ single BB queen•with Bb workers ➔ multiple Bb queens

Genome sequencing + RAD Genotyping >500 individuals•Gp-9 marks ~4% of genome ➔ social chromosomes:

SB is like X; Sb is like YStructural differences between SB and Sb ➔ no recombination

Ants are cool.

Formica selysi: Convergent evolution of social chromosomes

Page 63: 2014 11-28-lyon

genome evolution social evolutionGenerally

Single- vs. Multiple queennessin fire antsin similar independent species

•one or many loci?•one or many genes?•convergence?

Social parasitism

Strengths of selection in social evolution

concepts & mechanisms

Candidate gene studiesVitellogeninSex determination genes

Tools for genomics work on emerging model organisms

Molecular response to social upheaval

Caste differentiation (Medically relevant)

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Four tools

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suck less. Four tools that

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Four tools

suck less. (hopefully)

Four tools that

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1. SequenceServer

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“Can you BLAST this for me?”

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“Can you BLAST this for me?”

Antgenomes.org SequenceServer BLAST made easy

(well, we’re trying...)

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http://www.sequenceserver.com/

(requires a BLAST+ install)

Do you have BLAST-formatted databases? If not: sequenceserver format-databases /path/to/fastas

1. Installinggem install sequenceserver

# ~/.sequenceserver.conf bin: ~/ncbi-blast-2.2.25+/bin/ database: /Users/me/blast_databases/

2. Configure.

sequenceserver ### Launched SequenceServer at: http://0.0.0.0:4567

3. Launch.

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2. Bionode

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ExamplesBASH

JavaScript

bionode.io (online shell)

bionode-ncbi urls assembly Solenopsis invicta | grep genomic.fna

http://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000188075.1_Si_gnG/ GCA_000188075.1_Si_gnG_genomic.fna.gz

bionode-ncbi download sra arthropoda | bionode-sra

bionode-ncbi download gff bacteria

var ncbi = require('bionode-ncbi') ncbi.urls('assembly', 'Solenopsis invicta'), gotData) function gotData(urls) { var genome = urls[0].genomic.fna download(genome) })

#"Get"descriptions"for"papers"related"to"SRA"search!

bionode!ncbi!search!sra!Solenopsis!invicta!|!!!!!!!!!!tool3stream!extractProperty!uid!|!!!!!!!!!!bionode!ncbi!link!sra!pubmed!|!!!!!!!!!!tool3stream!extractProperty!destUID!|! !!!!!!!!bionode!ncbi!search!pubmed!

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Difficulty writing scalable, reproducible andcomplex bioinformatic pipelines.Solution: Node.js everywhereStreams var ncbi = require('bionode-ncbi') var tool = require('tool-stream') var through = require('through2') var fork1 = through.obj() var fork2 = through.obj()

ncbi .search('sra', 'Solenopsis invicta') .pipe(fork1) .pipe(dat.reads)

fork1 .pipe(tool.extractProperty('expxml.Biosample.id')) .pipe(ncbi.search('biosample')) .pipe(dat.samples)

fork1 .pipe(tool.extractProperty('uid')) .pipe(ncbi.link('sra', 'pubmed'))

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Working with Gene predictions

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Gene predictionDozens of software algorithms: dozens of predictions

20% failure rate: •missing pieces•extra pieces•incorrect merging•incorrect splitting

Visual inspection... and manual fixing required.

1 gene = 5 minutes to 3 days

Yand

ell &

Enc

e 20

13 N

RG

GTCTACAATGCGATTGTAAAATAGCACGAgAGGTGCATATGATGAACGACTATGTTCCACAACCACAGCTCATATATAACATGATTTtGTTTGCCGAATTCATACACGCATTACAACACACATTGAATTCAATAATAATATCAAATTCACATTCAAAGCTTTCAAGTTAGACAAAAGTTTTAATGCCGTTTTtACCTGTTTTtGAAAAGGTAATTTTCTTTAGATATATTATGTTGAATaTTAGGGTTTTTATAAAGAATGTGTATATTGUTTACAATATAAAAGACACAATTGCAAACTAGCATGATTGTAAACAATTGCTAAACGGATCAATATAAATTAAAATTGTAATATTAAGTATCAAACCGATAATTTTTATTTATTGTTCATTGTTTGTTCTTTATTTTGTTATTTGTAAATAATGAAA

Evidence

Evidence

Consensus:

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3. GeneValidator

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Monica Dragan

Ismail Moghul

https://github.com/monicadragan/GeneValidatorhttps://github.com/IsmailM/GeneValidatorApp

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Monica Draganhttps://github.com/monicadragan/GeneValidatorhttps://github.com/IsmailM/GeneValidatorApp

Ismail Moghul

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GeneValidator

Run on:

�whole geneset: identify most problematic predictions

�alternative models for a gene (choose best)

�individual genes (while manually curating)

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4. Afra: Crowdsourcing gene model curation

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Gene predictionDozens of software algorithms: dozens of predictions

20% failure rate: •missing pieces•extra pieces•incorrect merging•incorrect splitting

Visual inspection... and manual fixing required. 1 gene = 20 minutes to 3 days15,000 genes * 20 species = impossible. Ya

ndell

& E

nce

2013

NRG

GTCTACAATGCGATTGTAAAATAGCACGAgAGGTGCATATGATGAACGACTATGTTCCACAACCACAGCTCATATATAACATGATTTtGTTTGCCGAATTCATACACGCATTACAACACACATTGAATTCAATAATAATATCAAATTCACATTCAAAGCTTTCAAGTTAGACAAAAGTTTTAATGCCGTTTTtACCTGTTTTtGAAAAGGTAATTTTCTTTAGATATATACAGTTTGTAATaTTAGGTATTTTATAAACAGTGTGTATATTTCTTACAATATAAAAGACACAATTGCAAACTAGCATGATTGTAAACAATTGCTAAACGGATCAATATAAATTAAAATTGTAATATTAAGTATCAAACCGATAATTTTTATTTATTGTTCATTGTTTGTTCTTTATTTTGTTATTTGTAAATAATGAAA

Evidence

Evidence

Consensus:

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Afra: Crowdsourcing gene model curation

Challenges• Recruiting & retaining contributors

• Ensuring qualityBegin

Needs curation

Create initial tasks

Being curated

Curate

Being curated

Curate

Being curated

Curate

Submit Submit Submit

Auto-check

Done

Inconsistent: create

“review” task

Consistent: create next required task

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Timelines• Rolled out to:

• 8 MSc students

• 20 3rd year students

• Need to improve tutorials/guidance/documentation

• Roll out to 200 first years (few months)

• Expand

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Summary

Fire ant Solenopsis invicta queen number determined by Gp-9 genotypes: •only BB workers ➔ single BB queen•with Bb workers ➔ multiple Bb queens

Genome sequencing + RAD Genotyping >500 individuals•Gp-9 marks ~4% of genome ➔ social chromosomes:

SB is like X; Sb is like YStructural differences between SB and Sb ➔ no recombination

Ants are cool.

Formica selysi: Convergent evolution of social chromosomesA few tools for genomics: • http://sequenceserver.com (easy custom BLAST server)• http://bionode.io (Agile data & analysis workflows)• http://afra.sbcs.qmul.ac.uk (Crowdsourcing gene feature curation)• http://genevalidator.sbcs.qmul.ac.uk Identifying gene prediction

problems

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Ecology & Evolution & Vital-IT @ LausanneOrganismal Biology & Psych @ Queen Mary

QMUL lab (R Pracana, B Vieira, E Stolle, A Priyam, I Moghul et al) Laurent Keller lab (J WANG, D SHOEMAKER,O RIBA-GROGNUZ, M Nipitwattanaphon)

http://wurmlab.github.io

M Corona, S Nygaard, BG Hunt, KK Ingram, L Falquet, M Nipitwattanaphon, D Gotzek, MB Dijkstra, J Oettler, F Comtesse, CJ Shih, WJ Wu, CC Yang, J Thomas, E Beaudoing, S Pradervand, V Flegel, ED Cook, R Fabbretti, H Stockinger, L Long, WG Farmerie, J Oakey, JJ Boomsma, P Pamilo, SV Yi, J Heinze, MAD Goodisman, L Farinelli, K Harshman, N

Hulo, L Cerutti, Ioannis Xenarios

Michel Chapuisat, Jess Purcell, Alan Breslford, Nicolas Perrin