Project Detail

Diversification and stabilization of allotetraploid species with identical genomic composition

Name: Diversification and stabilization of allotetraploid species with identical genomic composition
Researchers: Belyayev Alexander (member of research team)
Trávníček Pavel (member of research team)
Mahelka Václav (member of research team)
Mandák Bohumil (member of research team)
Number: LUAUS23118
Realization from: 2023
Realization to: 2026
Summary: The allotetraploid species of the Chenopodium album agg. with CCDD genomic composition (those originating from the same parental combination) are a good example of allopolyploids to study the aforementioned tasks. Traditionally four species are recognized within this group based on morphology, i.e. C. betaceum Andrz (distributed in Eurasia), C. glaucophyllum Aellen (North America), C. novopokrovskyanum (Aellen) Uotila (Central and Western Asia) and C. striatiforme J. Murr (Europe). While their paternal lineage D is represented by an extant diploid species currently growing in central and eastern Asia (C. acuminatum Willd.), the diploid donor of the C subgenome is probably extinct. These species are widespread and morphologically well differentiated indicating a low level of interspecific gene flow despite frequent sympatric occurrence. Therefore, they represent a good model group to study the diversification and adaptation of allotetraploid species with the same combination of subgenomes. Recently the genomes of several Chenopodium species were assembled, including a high-quality chromosome level assembly of C. formosanum, a hexaploid species with BBCCDD subgenomes, that shares the CCDD subgenomes with our focal group. In our study, we will use the assembly as a reference to perform a whole genome re-sequencing for a high number of CCDD individuals. Using the multiple resequenced genomes we will target phylogenomic, population genomic and structural genomic analyses on the CC and DD subgenomes separately. We will infer the evolutionary history for the group of closely related, but morphologically and geographically well differentiated, CCDD tetraploid species from the C. betaceum alliance. Particularly, we will investigate: (1) whether the recognized taxa are the result of multiple independent allopolyploidization events or diversification of a single allotetraploid ancestor and establish an universal, multiple evidence based procedure for differentiation between these two evolutionary scenarios, that could be used for other organisms, too. And (2) if there are any subgenome-specific signatures of selection underlying both the genomic diversification and its maintenance in the recognized Chenopodium taxa. Further (3) we will select two individuals representing the most divergent taxa and reconstruct a chromosome level genome assembly for both of them. Using this approach we will identify whether structural variation, both large (chromosome-level rearrangements: insertions, deletions or inversions) and small (insertions/deletions affecting single genes) scale, could contributed to the diversification and stabilization of the species in addition to the variation at SNP level.

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