Domestication, polyploidy and genomics of crops #PAGXXV Heslop-Harrison

Domestication, polyploidy and genomics of crops (and weeds)Pat Heslop-Harrison &Trude SchwarzacherLeicester, UK

[email protected]

www.molcyt.com

www.molcyt.org

Twitter Pathh1 .Crop Evolution Genomics & Future Agricultural Productivity PAGXXV 14 January 201720 min talk

http://www.molcyt.com/

Outputs

–Crops(Chemical energy)

– Food– Feed– Fuel– Fibre

– Flowers– Pharmaceuticals

– Fun2

Inputs

–Light

–Heat

–Water

–Gasses

–Nutrients

–Light

–Heat

–Water

–Gasses

–Nutrients

(Ecosystem services)

Outputs

–CROPS

– Chemical energy

Domestication, Polyploidy and Genomics of Crops

• CROPS: where one species controls the growth and reproduction of another

Domestication, Polyploidy and Genomics of Crops

• Most species domesticated 10,000 years ago (cereals, legumes/pulses, brassicas, fruits, cows/sheep/pigs, silkworm/bees)

• Few species more recently (rabbits, fish, trees, biofuel crops)

• A few dropped out of production

• First steps: productive, reproduce easily, disease-free, edible/tasty, harvestable …

• With critical technology of people: not obvious

Heslop-Harrison & Schwarzacher Domestication genomics in Arie Altman www.tinyurl.com/domest and review of rabbits www.tinyurl.com/rabdom

http://www.tinyurl.com/domest

http://www.tinyurl.com/rabdom

Pinus sylvestrisScots pine

Argemone mexicana

Japanese knotweed – invasive in EuropeFallopia (and Fallopia x Muehlenbeckia hybrids)

Larrea tridentaCreosote bush

Domestication, polyploidy and genomics of crops and weeds

• CROPS: where one species controls the growth and reproduction of another

• WEEDS

• Many animals collect food to see them through the winter, build nests in anticipation of reproduction

• A few plants kill off all others nearby

• Ants (Formicidae) farm plants, animals and fungi

• Humans only for 20% of their history – and still exploiting environment unsustainably!

Organelle sequencesfrom chloroplasts or

mitochondria

Sequences from viruses

Transgenes introduced with molecular biology

methods

Genes, regulatory and non-coding low-copy sequences

Dispersed repeats

Repetitive DNA sequences

Nuclear Genome

Tandem repeatsSatellite sequences

DNA transposonsRetrotransposons

Centromericrepeats

Structural components of chromosomes

Telomericrepeats

Simple sequence repeats or

microsatellites

Repeated genes

Subtelomericrepeats

45S and 5S rRNA genes

Blocks of tandem repeats at discrete chromosomal loci

DNA sequence components of the nuclear genomeAfter Biscotti et al. Chromosome Research 2015

Other genes

Transposable elements

Autonomous/ non-autonomous

Dispersed repeats that we don’t know

about – except each is significant proportion

of genome

Genomic Components: properties

• Tandem Repeats

• Simple Sequence Repeats

• Dispersed Repeats

• Functional Repeats

• Retroelements

• Genes

Typical Fraction

10%

5%

10%

15%

50%

10%


• Genome size

• Critical parameter for genome studies – first sequenced genomes chosen to be small ... Large genomes only tackled 25 years on

• But is it critical for species …

• No: you can’t ‘look’ at a species and make any suggestion about it’s genome size …

Nothing special about crop genomes?Crop Genome size 2n Ploidy Food

Rice 400 Mb 24 2 Triploid endosperm

Wheat 17,000 Mbp 42 6 Triploid endosperm

Maize 950 Mbp 10 4 (palaeo-tetraploid) Triploid endosperm

Rapeseed B.

napus

1125 Mbp 38 4 Cotyledon oil/protein

Sugar beet 758 Mbp 18 2 Modified root

Cassava 770 Mbp 36 2 Tuber

Soybean 1,100 Mbp 40 4 Seed cotyledon

Oil palm 3,400 Mbp 32 2 Fruit mesocarp

Banana 500 Mbp 33 3 Fruit mesocarp

Heslop-Harrison & Schwarzacher 2012. Tinyurl.com/domest


• Polyploidy is also critical part of genomes …

• No: you can’t ‘look’ at a species and make any suggestion about it’s ploidy …

D’Hont et al. Nature 2012

doi:10.1038/nature11241

D’Hont et al.

Nature 2012

doi:10.1038/na

ture11241

Whole-genome duplication events.


• Ancient polyploidy (detected by sequencing)

• Modern polyploidy (detected by cytogenetics)

• Advantages: more control, genes free to mutate, ?larger cells/organs

• Disadvantages: meiosis challenging, buffering of changes, more DNA to replicate

Repetitive DNA in dandelion3 microspecies 22, 12 & 12 Gb2n=3x=24 apomicticRubar Salih & Lubos Majesky

k-mer analysis

For a 16-mer length, there are 2 billion canonical 16-mers (416/2), and the average 16-mer occurs 10 times in the 22Gb of sequence data.

The overall distribution of these informs us about how repetitive the genome is, and the frequency of different repetitive elements.

k-mer analysisThe most abundant 16-mers in the 150bp genome reads:7bp telomere sequence (TTTAGGG/CCCTAAA) added ends of each chromosome

occurs a total of 7M times, much higher than the expectation of 140.

From 128-merGT10kbCoverage Depth = 7

AF(11)_S983_009Blue: DAPI fluorescence.Green: telomere primer HC_89bpRed: 5S rDNA

In asexual dandelion microspecies

Rubar M. Salih

Genome evolution and biodiversity

•Actively evolving repetitive sequences in the genome•Differences seen between microspecies in repeats•Structural and mobile components of genome identified•Chloroplast sequence gives phylogeny and robust markers for diversity (PLoS One in press Dec 2016)

So questions are

1) where is this sequence located in the genome? and 2) are there any differences between the microspecies in its abundance?

We can see this is a Ty1-Copia element because the retroelements coding domains are in the order

RNaseHReverse TranscriptaseIntegrase

LTRs divergentMore (solo LTRs)

RepeatExplorer: Graph-based clustering of related sequences, program/approach byNovák P, Neumann P, Pech J, Steinhaisl J, Macas J. RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics. 2013 Mar 15;29(6):792-3.

Widely dispersed

distribution of a copia

retroelementfamily over all chromosomes of Taraxacum

Retrotransposons in Taraxacum

2n=3x=24NOR sats shown

Distribution from RepeatExplorer

O978

the top 10 in terms of genome% and nature of sequence - for each of the three spp.

#

TxS3 TxA978 TxO978

Repeat masker Genome % Repeat masker Genome % Repeat masker Genome %

1 Low complexity 1.60 Low complexity 0.965 Simple repeat 1.400

2 Low complexity 1.26 Low complexity 0.818 LTR.Gypsy 1.250

3 LTR.Gypsy 1.22 LTR.Gypsy 0.807 Simple repeat 1.200

4 LTR.Gypsy 1.17 Low complexity 0.796 Low complexity 0.963

5 Low_complexity 1.09 Low complexity 0.788 LTR.Gypsy 0.845

6 LTR.Copia 1.04 Low complexity 0.771 Low complexity 0.820

7 LTR.Gypsy 0.995 LTR.Gypsy 0.730 LTR.Gypsy 0.793

8 Low_complexity 0.982 Low complexity 0.713 Low complexity 0.781

9 LTR.Gypsy 0.940 LTR.Gypsy 0.682 LTR.Gypsy 0.741

10 LTR.Copia 0.841 Low complexity 0.671 Low complexity 0.724

S3

A978Petunia

Relative counts of various k-mers in three Taraxacummicrospecies

Rubar Salih et al. in prep

Dispersed on chromosomes in all microspecies: but differences

AA1_AK07_171D_45S B_010

AC1_O996_171 D_KsHC B_003AC11_S933_171 D_KsHC B_004

0.075%

Low complexity

Assembled to genome of:

A:

S:

O:

Sequence CL80 double-dots on 14 chromosomes (not 16 -not 2 genomes worth) - is it a centromeric repeat?

LTR.Copia (2hits, 0.103%)

Low complexity (5hits, 0.0895%)

Genome proportion = 0.2480%

Assembled to genome:

A =

S =

O =

AE (3)_A978_A dig_pta794_001

AE (4)_O976_A dig_pta794_002AE (2)_S3_A dig_Pta794 bio_002

Unknown or ChloroplastLow Complexity

Mixed RepeatLTR Degenerate

LTR GypsyLTR Copia

DNA TransposonsLINES

LTR CaulimovirusSimple Repeat

rRNATandem Repeat

Telomere

Gen

om

e p

rop

ort

ion

(%

)

Cluster (number)

I I I I I I I I1 50 100 150 200 250 300 351

Telomere

Tandem Repeat

rRNA

Simple Repeat

LTR Caulimovirus

LINES

DNA Transposons

LTR Copia

LTR Gypsy

LTR Degenerate

Mixed Repeat

Low Complexity

Unknown or Chloroplast

Retroelements and tandem repeats in Petunia Supplementary Ms 2. Bombarely et al. Petunia genome sequenceNature Plants 2: article number 16074.

Telomere

Tandem Repeat

rRNA

Simple Repeat

LTR Caulimovirus

LINES

DNA Transposons

LTR Copia

LTR Gypsy

LTR Degenerate

Mixed Repeat

Low Complexity

Unknown or Chloroplast


mitochondria



methods


Dispersed repeats


Nuclear Genome



Centromericrepeats


Telomericrepeats


microsatellites

Repeated genes

Subtelomericrepeats




Other genes





of genome

Japanese knotweed – invasive in watercourses in EuropeFallopia (and Fallopia x Muehlenbeckia hybrids)

Repeat Explorer analysis raw reads of F. japonica and M. australis. Top clusters represented 50% of the reads in F. japonica and 39.5% of reads in M. australis.F. japonica has a higher proportion of dispersed repeats than M. australis.

Fallopia x Muehlenbeckia hybrid : Differential probes identified by k-mer and RepeatExplorerGreen is Fallopia-specific; Red is equal in both genomesDesjardins, Bailey, Wang, Schwarzacher, Heslop-Harrison. 2017 in prep

Desjardins, Bailey, Wang, Schwarzacher, Heslop-Harrison. 2017 in prep.

Panicum sensu stricto c. 100 species; x=9Evolution of Panicum miliaceum Proso millet

P. miliaceum 2n=4x=36

P. capillare2n=2x=18

P. repens2n=4x=36

also 2n=18 to 54

P. sumatrense2n=2x=18 or 4x=36

Global North-temperate

Low genetic diverstiy

Weedy forms

P. virgatum2n=4x=36 or 2x=18

? ? ? ? ??

• Hunt , HH et al. 2014. Reticulate evolution in Panicum (Poaceae): the origin of tetraploid broomcorn millet, P. miliaceum. J Exp Bot. 2014

Chromosome and genome engineering

Cell fusionhybrid of two4x tetraploidtobaccospecies

Patel, Badakshi, HH, Davey et al 2011 Annals of Botany

Nicotianahybrid4x + 4x

cell fusions

Each of 4chromosome

sets hasdistinctiverepetitiveDNA when

probed withgenomic DNA

Patel et alAnn Bot 2011

Cell fusionhybrid of two4x tetraploidtobaccospecies

Four genomesdifferentiallylabelled

Patel, Badakshi, HH, Davey et al 2011 Annals Botany

Wheat evolution and hybridsTriticum uratu

2n=2x=14AA

EinkornTriticum monococcum

2n=2x=14AA

Bread wheatTriticumaestivum2n=6x=42AABBDD

Durum/SpaghettiTriticum turgidum ssp durum

2n=4x=28AABB

Triticum dicoccoides2n=4x=28AABB

Aegilops speltoidesrelative

2n=2x=14BB Triticum tauschii

(Aegilops squarrosa)2n=2x=14

DD

TriticalexTriticosecale

2n=6x=42AABBRR

RyeSecale cereale

2n=2x=14RR

Centromere dynamics and timing of chromosome synapsis (6x wheat)Adel Sepsi, Higgins, Heslop‐Harrison, Schwarzacher. CENH3 morphogenesis reveals dynamic centromere

associations during synaptonemal complex formation and the progression through male meiosis in hexaploid wheat. Plant Journal. 2016 Sep 1.

Sepsi et al. Plant Journal 2016

(b) Centromere depolarisation and SC formation during Zygotene

Interphase Leptotene Zygotene Late ZygoteneTelomere bouquet

Homologue chromosome pairs Centromeres ZYP1

Early Zygotene

1 2 3

Subtelomeric synapsis Interstitial alignment Interstitial elongation

(a) Centromere, telomere and chromosome arm dynamics in meiotic prophase I.

Sepsi et al. Plant Journal 2016

• How do genomes evolve?–Gene mutation very rarely

• (human: 10−8/site/generation)

–Chromosome evolution

–Polyploidy and genome duplication

–Repetitive sequences: mobility & copy number• (10−4/generation in µsat)

–Recombination

–Epigenetic aspects: centromeres & expression

Repetitive sequences

• Many families and various types

• Abundant

• Rapidly evolving … or conserved

– Copy number and sequence

• May be near-genome specific, even chromosome-specific

• Various genome/chromosomal locations


mitochondria



methods


Dispersed repeats


Nuclear Genome



Centromericrepeats


Telomericrepeats


microsatellites

Repeated genes

Subtelomericrepeats




Other genes





of genome

mitochondria



methods


Dispersed repeats


Nuclear Genome



Centromericrepeats


Telomericrepeats


microsatellites

Repeated genes

Subtelomericrepeats



Real? Passively Amplified DNA sequences: PADsOr: Transposable element derivatives (LTRs etc)?

Other genes



Dispersed repeats that we don’t know about –

except each is significant proportion

of genome

Domestication, polyploidy and genomics of crops (and weeds)Pat Heslop-Harrison &Trude Schwarzacherand collaboratorsLeicester, UK

[email protected]

www.molcyt.com

www.molcyt.org

Twitter Pathh1 .


From Chromosome to Nucleus

Pat Heslop-Harrison [email protected] www.molcyt.com

mailto:[email protected]


• About half of all higher plant species are recognizable as polyploids, a major feature of genome architecture where there are more than two sets of chromosomes. Advantages include multiple copies of each gene with different regulation, so essentially fixing heterosis; larger cell size; and the opportunity for mutation without lethality. Disadvantages include twice as much DNA to replicate; incorrect control of multiple gene copies in interacting genomes; chromosome instability at mitosis; and the challenges of ensuring chromosome pairing and regular meiotic segregation in seed crops, in breeding hybrid materials, or else combining sterility with parthenocarpy in fruit crops. Given these substantial contrasts, it is perhaps surprising that the top three cereal crops are wheat (a modern hexaploid 2n=6x=42), rice (diploid, 2n=2x=14), and maize (palaeotetraploid, 2n= 2 or 4 x =20), suggesting neither advantages nor disadvantages are overwhelming. I will consider the balance of positives and negatives over evolutionary and crop-breeding timescales. In the second part of my talk, I will consider how knowledge of polyploid behaviour and knowledge of ancestors can be exploited, discussing our work with polyploids, both well-known (wheat, Brassica, banana) and less known (proso millet, ornamentals and saffron crocus). Further details and references will be at www.molcyt.com. Email phh(a)molcyt.com

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Domestication, polyploidy and genomics of crops #PAGXXV Heslop-Harrison