Abstract Detail



Comparative Genomics/Transcriptomics

Hao, Yue  [1], Colle, Marivi [2], Edger, Patrick [3], Pires, Joseph [4], Conant, Gavin [5].

Statistically modeling preferentially gene retention after the paleopolyploidy events in the tribe Brassiceae.

As the most important tribe within the family Brassicaceae, the tribe Brassiceae contains many economically valuable crops such as cabbage, collard greens, kale, broccoli, cauliflower, Chinese cabbage, turnip and mustard. The tribe Brassiceae shares an ancient whole genome triplication (WGT), and plants in this tribe demonstrate high morphological diversity within each species. Thus it a fascinating system to study the effect of polyploidy on evolutionary innovation. Polyploidy often occurs by the hybridization of related but not identical lineages, and previous studies have identified a tendency for one of these parental lineages to lose fewer genes after polyploidy than the other (known as biased fractionation). We have developed a phylogenomic pipeline call POInT (Polyploidy Orthology Inference Tool) that allows us to trace this history of gene loss across a set of modern genomes that all descend from the same polyploid ancestor. Using it, we have phylogenetically modeled the resolution of the Brassica triplication, confirming that it resulted in modern species with three distinguishable subgenomes. By phasing the gene loss patterns post-WGT, we are able to describe the relative rate of gene loss that is intrinsic to the three subgenomes and to show that each subgenome has a statistically distinguishable rate of such losses. We also show that the pattern of losses immediately after the WGT is distinct from later losses, likely as a result of the proposed two-step nature of the WGT.


1 - North Carolina State University, Bioinformatics Research Center, 335 Ricks Hall, 1 Lampe Dr, Raleigh, NC, 27695, USA
2 - Michigan State University, Department of Plant, Soil and Microbial Sciences, 578 Wilson Road, Room 105, East Lansing, MI, 48824, USA
3 - Michigan State University, Department of Horticulture, 1066 Bogue St, Room A334, East Lansing, MI, 48824, USA
4 - University of Missouri - Columbia, Division of Biological Sciences, 371b Bond Life Sciences Center, 1201 Rollins Street, Columbia, MO, 65211, USA
5 - North Carolina State University, Department of Biological Sciences, 356 Ricks Hall, 1 Lampe Dr, Raleigh, NC, 27695, USA

Keywords:
polyploidy
biased fractionation
Brassica.

Presentation Type: Oral Paper
Number: 0009
Abstract ID:530
Candidate for Awards:Margaret Menzel Award


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