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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
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