Analysis of subgenome structure and evolution in allopolyploid plants

Matteo Schiavinato4th year PhD student

Institute of Computational BiologyAG Himmelbauer

BOKU

Background

Plants and ploidy

Genome ploidy > 2n excess of genetic material

Polyploidy evolutionary mechanism

e.g. flowering plants at K-T boundary (~65 MyA)

Many cultivated crops are polyploid

e.g. tobacco, cotton, wheat, quinoa, coffee, strawberry, ...

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Auto-polyploidy

Whole-genome duplication

Sudden increase in ploidy

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Allo-polyploidy

Two genomes from different species

maternal and paternal subgenomes

subgenome dominance

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biased fractionation

subgenomic intermixing gene / genome repurposing

Subgenome separation

■ FISH

Fluorescent probesfrom parental genomes

Detect fluorescence on hybrid genome

■ Genomicsequencing

Sequence parental genomes

Map parental reads on hybrid genome

■ Phylogenomics

Phylogenetic trees with hybrid and candidate parents

Assign chromosomes from gene homology

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“

Can we observe subgenomic intermixingfrom read mapping?

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Mapping-based separation (N. tabacum)

Reads from parent A Reads from parent B

Subgenome BSubgenome A

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Failure with mapping (N. benthamiana)

Reads from parent A Reads from parent B

IntermixedIntermixed

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Other hybrids?

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Subgenomic intermixingassessment

Coverage-based

metrics

Coverage in windows

of 500 kbp

J = 0 (min)

J ~ 0.5

J ~ 0.9 (max = 1)

In collaboration with:

Alexandrina Bodrug

Results

All analysed species

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Arachis hypogaea and

Arachis monticola

domesticated and wild peanut

Gossypium hirsutum

cotton

Chenopodium quinoa

quinoa

Triticum turgidum ssp. dicoccoides

and ssp. durum

wild and domesticated emmer wheat

Brassica napus (rapeseed)

and Brassica juncea (mustard)

Nicotiana benthamiana

(Australian tobacco) and

Nicotiana tabacum

(smoking tobacco)

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Two test cases

Wild and domesticated peanut• effect of domestication• 10,000 evolutionary years (short time)

Quinoa vs Nicotiana benthamiana (Australian tobacco)• effect of environment• 5 million evolutionary years (long time)

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Cultivated peanut

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Wild peanut

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Quinoa

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Australian tobacco

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Summary

Subgenome evolution several forces

Subgenome separation hindered by intermixing

Our pipeline assess subgenomic intermixing state Manticore

Manuscript in preparation!

AG HimmelbauerInstitute of Computational BiologyUniversity of Natural Resources and Life Sciences (BOKU), VIENNA (AT)

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AcknowledgementsAlexandrina BodrugBOKU, VIENNA (AT)

MeMatteo Schiavinato - BOKU, VIENNA (AT)

@schmat_90