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Arachis hypogaea – 2n=4x=40In situ hybridization of two BACs including repeatsContrasting distribution of their major repeat familie
audia Guerra Araujo et al in prep 2011, EMBRAPA, Brazil
Darwin 1859The only figure in “The origin of species”
Patel, Badakshi, HH, Davey et al 2011 Annals of Botany in press
Cell fusion hybrid of two tetraploid tobacco species
Resistance to Peronosporainherited in cell fusion hybrid (right) from one parent
Brassica rapa (AA)
Brassica nigra (BB)
Brassicajuncea (AABB)
Brassica napus (AACC)
Brassicacarinata (BBCC)
Brassica oleracea (CC)2n=20
2n=362n=34
2n=16
2n=382n=18
8
The Brassica genus is monophyletic, from single common ancestor.What has changed in the DNA sequences?
B. napus (AACC, 2n=4x=38) – hybridized with C-genome CACTA element redB. oleracea (CC, 2n=2x=18) B. rapa (AA, 2n=2x=20)
Alix et al. The CACTA transposon Bot1 played a major role in Brassica genome divergence and gene proliferation. Plant Journal
AJ 245479
AC 189496
AC 189446
AC 189655
AC 189480
B ot1-1
B ot1-2
B ot1-3
large insertion specific of Bot1-1
Bo6L1-151010bp
large insertion in common between Bot1-2 and Bot1-3
Rearrangementspecific of Bot1-3
B. napus
B. rapa
B. oleracea
AJ 245479
AC 189496
AC 189446AC 189446
AC 189655AC 189655
AC 189480AC 189480
B ot1-1B ot1-1
B ot1-2B ot1-2
B ot1-3B ot1-3
large insertion specific of Bot1-1
Bo6L1-151010bp
large insertion in common between Bot1-2 and Bot1-3
Rearrangementspecific of Bot1-3
B. napus
B. rapa
B. oleracea
…
Dotplot comparisons at scale of 10,000s bpTwo Musa chromosomes are >95% homologous with gapsFaisal Nouroz 2012
2011/09/01 12
Dotter plot of Brassica oleracea var. alboglabra clone BoB028L01 x Brassica rapa subsp. pekinensis clone KBrB073F16 with transposable elements.
Brassica oleracea (C genome) sequence
Bra
ssic
a ra
pa (A
gen
ome)
seq
uenc
eDot-plots of genomic sequence from homoeologous pairs of BACs
An inversion
Region of low homology
Region of high homology between A and C sequence
Transposed (moved) sequence
500bp Insertion-gap pair: present in A
4kb Insertion-gap pair: present in C genome
gi 195970379 vs. gi 199580153
Microsatellitekb
Sequence level at scale of 100s to 1000s of bp – analysis by dotplot
9-bp TSD (TATCCTATT)6-bp TIR and 66-bp imperfect sub-TIR
551-bp BART1 TE
TSD TIR TIR TSD
2011/09/01 14
TATCCTATTGCGCAATTGTCAATAATAGCACTTTTTGAAGTTTATGTCTCAAAATAGCACTAGAAGGAGAAAGTCACAAAAATGATATTCATTAAAGGGTAAAATATCTCTTATATCCTTGGTTTAAAATTAAATAAACAAACAAAAATAAATAAAAATAAATAAAAAAAATGAAAAAAAAGAAATTTTTTTTATAGTTTCAGATTATATGTTTTCAGATTCGATTTTTTTTTTATTTTTTTATTTTTTTCGAAATTTTTTTTTTATTTTTTTTCAAATTTTCTTTTTATAATTTAAAAATACTTTTTGAAACTGTTTTTTTAATTTTTATTTTTTATTTTAGTATTTATTTTTTATAAAATTTTAAACCCTAATTCCTAAACCCCCACCCCTTAACTCTAAACCCTAAGGTTTGGATTAATTAACCCAATGGATATAAGTGTATATTTACCTCTTTAATGAAACCTATTTTTGTGACTTTGAATCTTGAGTGCTACTTTGGGAACAAAAACTTGGTTTGGTGCTATCCTAGTCTTTTTCTCTATCCTATT
TACCACCCTTCTTTGTTCAATACTTTTTACAGTTTTTGGAAAGGACATGTTTCTTCTATCATCACTTAATGGTTATATATGTATGAGAAGTTTGAAAGAGATTACACTGTTTTGGAATATTAAAAAAAAAAGATATTACAAGATCTGATTTTGTTTGTATTTTAAAATTCTACCAAATCTCTCCTCAAAATCTTGGTCAAAGTCCAAAAATCCAAATATCTCAGTTAAATTCCACCAAATATGAAATCCTAAAACTTTTCCAAAATAGTTCAATAAGCCCTTAGTGTTTGGTG
AAGTGAATGGATGCTCGCATTAGTTACTATGAGCCGATTCTCGCTCTTGCGAAAGCTAAAGAGGAAAAGGCCTTCGCATTGCAGAAGAGCTGGCTGCCAGCGAGCAAGAGGTTTTCAATATTGGCTTGTGGAAAATTTGTTGCCACTTTTGCTTTACTAAGGAATGAAATAATACTTGTTTTTTTTTTTCATGGTTAATATTAGAAGATATAATTTCCTTTGAAGTTAGATTACGTTTCTTTATGTCGACGAAGTGAAGAAATATTGTCTTGTTTATGGTTCCTTCTAGTCCCAACCTTTTTTCAAGAAGGTACAGTACGTGTCAGGATTTATATGGATATACACA
Brassica rapa with inserted 542bp sequence not present in B. oleracea. 9bp TSD (red letters and arroand TIR (blue). Flanking primers used in PCR (next slide) as blue arrows on sequenceFaisal Nouroz 2011
………………..……………….
1 246 TSD TIR 542-bp TE TIR TSD 790 1000
Rapa185F Rapa177RRapa8002Rapa141F
B. rapa (47186-48200)B. oleracea (66,350-66750)
B. rapa (AA) B. juncea (AABB)
………………..……………….
B. napus (AACC)
………………..……………….
………………..……………….
………………..……………….=A =T =C =G
B. nigra (BB)
B. oleracea (CC)
B. carinata (BBCC)
B. oleracea (GK97361)
Hexaploid Brassica (carinata x rapa)
Schematic representation of insertion in Brassica rapa and other Brassica genomes. Green, red, blue and
black boxes showing DNA motifs.
700 bp hAT
Microsatellite
715 bp hAT
1016 bp in LINE
258 MITE
402 bp hAT
237 bp Mariner Like
Inversion
914 bp LINE
2781 bp MuDR Like
505 bp Unknown
1655 bp in B.rapa
380 in B.rapa
670 bp hAT
819 bp Unknown
524 bp SINE
216 bp SINE
1189 bp Mariner Like
3869 bp TE
1080 bp LINE
242, 644 & 274 bp SINEs
Brassica oleracea (C genome; EU642504.1)
Bra
ssic
a ra
pa(A
gen
ome;
A
C18
9298
.1)
TEs in B. oleracea
1284 bp Unknown
ancestral
Low-copy number High-copy number Low-copy number High-copy number
Low-copy number High-copy number
High copy spp: homogenized, amplification from a limited number of master copies
Low copy spp: much variation
S.vav42!248
0.1
Afacer1T.mono106/42!133pt1T.mono106/42!155pt1
Ae.umb106/208!1911Ae.umb106/208!1810Ae.umb106/208!2012
S.vav147!259pt1Pet w 25/208!088Pet w 25/208!077
S.vav106/208!215pt1S.vav106/208!204pt2
S.vav106/208!215pt2S.vav25/208!182
S.mon42!136Pet 22594 25/42!3324
Pet 22594 25/42!3425CS/325/208!1820
S.vav25/208!193T.tau25/147!2524pt2
CS/325/147!2322pt2L.moll25/42!156
Pet w25/147!123CS/325/208!1719
CS/325/147!2120Pet w25/147!3231
Ae.umb25/147!124Ae.umb25/208!168
L.moll25/42!167119Repeat2
Pet w 25/208!099S.mon147!1811
S.vav106/208!204pt1119Repeat3
S.vav147!2711pt1S.mon25/147!081
T.mono25/208!1212
S.vav42!237pt1S.vav42!237pt2
T.tau25/147!2625T.tau25/147!2726
Ae.umb25/208!157T.tau25/208!1517
T.tau106/42!177Ae.umb25/42!091
L.moll25/42!189CS/325/208!1618
T.tau25/147!2524pt1CS/325/147!2322pt1
Pet 22594 25/208!2325Pet 22594 25/147!1918
Pet 22594 25/208!2426T.tau25/208!1315
T.tau25/208!1416Ae.umb25/147!135
Ae.umb25/147!146Ae.umb25/208!179
7491000
996
1000
725
985
564
1000
580
646
942
616882
998
981
623
537915
578
120bp repeat unit family
in Triticum, Aegilops and
Secale species
119Repeat1
Homology between sequences
70-100% in Triticum/Aegilopsand Secale species
Pet 2259425!315
Colour blockrepresents species
High copy,
High diversity
T.tauschii (D genome)
S. cereale (R genome)
Triticum aestivum 2n=6x=42
DAPI pSc119.2 dpTa1
High copy number – low diversity in each of 3 genomes
Correlation between genetic relationships and similarity of dpTa1
hybridization
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
Coefficient of parentage
Prop
orti
on o
f ch
rom
osom
e ar
ms
with
id
enti
cal i
n si
tu s
igna
l
Chromosomal
location of
DBC-150
repeats
Micro- or dot chromosomes
Kuhn (Belo Horizonte, Brazil) et al. Chromosome Research
Interspersion of pBuM and DBC-150
pBuM DBC-150
High interspersion
Low interspersion
Non-homologous repeats
D. gouveai D. antoneita D. seriema
ancestral
A B C D
High-copy number High-copy number High-copy number High-copy number
E F
Low-copy number Low-copy number
New species-specific variants
From species level to populations …
High copy numberlong and continuous homogeneous arrays
Low copy number interspersed and discontinuous arrays
Total = 119 repeats
NJ tree
High copy species
Low copy species
Alpha/beta repeat variation
Kuhn et al. 2011 in press Mol Biol Evol
A
B
C
A’
B’
C’
XL1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
CEN
26 27 29 30 31
C
3228 33 34
3L61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 82 83 84 85 86 87 89 90 91 92 93 94 95 96 97 98 99
3R81 88 100
47 48 50 5249 51 53 54 55 56 57 58
2L21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
2R
35 36 37 38 39 4041 42 43 44 45 46
CEN
CEN
C
C
XL
XR
XR
2L 2R
3L 3R
?
1.688 tandem repeats in Drosophila melanogaster
Large arrays n heterochromatin of chromosomes 2, 3 and XShort arrays are found in the euchromatin
Het (2)Het (3)Het (X)Eu (2)Eu (3)Eu (X)
30F
2RHet25A-B
22A-C
2L-Het
21D
21E-F
25C-D
59D 59C-D57A26D-F
27C
25D-E
24D
96A9
6C
D
96F
98B
3L-H
et
(B2)
3L-H
et
(B1)
XL-Het12E-F
2B (B1)
2B (B2)
12D-E 12B-C
12B-C 13E
8E
3C
12F-13A
12F-13A
Homogenization of arrays: differential for hetero- and eu-chromatin
Proportion of 1.688 arrays in three genomic landscape classeseuchromatic arrays are close to, genes or within intronsArray size could be selectively constrained by a role as gene regulators
0%10%20%30%40%50%60%70%80%90%
100%
Chr. 2 (16) Chr. 3 (7) Chr. X (29)
Transcription
Flanked by genes
Desert
Kuhn et al. 2011 in press Mol Biol Evol
Kim, HH, Cho et al. 2011 Science Signaling
Circadian Clock regulationafter Leloup & Goldbeter
cf Andrew Millarin Arabidopsis
X X
Y
Y
Z
Z
Many of the repetitive sequences are retrotransposons and DNA transposonsSome are microsatellite motifsSome are satellites – including the most rapidly evolving sequences
rapid evolution in copy number, location and sequence, with diverse turnover mechanisms
often mark the major differences between closely related species
it is hard to analyse by next generation or whole-genome sequencing methods
Th. intermedium Anti 5meC
Th. intermedium DNA Anti 5meC
Niaz Ali, Trude Schwarzacher – Poster 59
Wsm-1: only highly effective source of resistance to WSMV
Greybosch et al. 2009
0
0.5
1
1.5
2
2.5
3
3.5
4
1961 1970 1980 1990 2000 2007
Maize Rice
Wheat Human
Area
United Nations Millennium Development Goals- MDGs
• Goal 1 – Eradicate extreme poverty and hunger
•Goal 2 – Achieve universal primary education
• Goal 3 – Promote gender equity and empower women
• Goal 4 – Reduce child mortality
• Goal 5 – Improve maternal health
• Goal 6- Combat HIV/AIDS, malaria and other diseases
• Goal 7 - Ensure environmental sustainability
• Goal 8 - Develop a global partnership for development
Pat [email protected] pw/user: ‘visitor’
Social media: #ICC18 andPathh1 on TwitterReports: AoBBlog.com and Storify.com/pathh1