Abstract Detail

Comparative Genomics/Transcriptomics

Pires, Joseph Chris [1], Emery, Marianne [2], Willis, Madeline [3], Hao, Yue [4], Barry, Kerrie [5], Schmutz, Jeremy [6], Lyons, Eric [7], Edger, Patrick [8], Conant, Gavin [9].

Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflict induced by hybridization.

Polyploidy is increasingly seen as a driver of both evolutionary innovation and ecologicalsuccess. One source of polyploid organisms' successes may be their origins in the mergingand mixing of genomes from two different species (e.g., allopolyploidy). Using POInT (thePolyploid Orthology Inference Tool), we model the resolution of three allopolyploidy events,one from the bakers' yeast (Saccharomyces cerevisiae), one from the thale cress (Arabidopsisthaliana) and one from grasses (including Sorghum bicolor). Analyzing a total of 21genomes, we assign to every gene a probability for having come from each parental subgenome(i.e., derived from the diploid progenitor species), yielding orthologous segmentsacross all genomes. Our model detects statistically robust evidence for the existence ofbiased fractionation in all three lineages, whereby genes from one of the two subgenomeswere more likely to be lost than those from the other subgenome. We further find that adriver of this pattern of biased losses is the co-retention of genes from the same parentalgenome that share functional interactions. The pattern of biased fractionation after the Arabidopsisand grass allopolyploid events was surprisingly constant in time, with the sameparental genome favored throughout the lineages' history. In strong contrast, the yeast allopolyploidevent shows evidence of biased fractionation only immediately after the event,with balanced gene losses more recently. The rapid loss of functionally associated genesfrom a single subgenome is difficult to reconcile with the action of genetic drift and suggeststhat selection may favor the removal of specific duplicates. Coupled to the evidence forcontinuing, functionally-associated biased fractionation after the Arabidopsis thaliana At-alpha polyploid event, wesuggest that, after allopolyploidy, there are functional conflicts between interacting genesencoded in different subgenomes that are ultimately resolved through preferential duplicateloss.

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1 - University Of Missouri, 371 Bond Life Sciences Center, 1201 Rollins Street, Columbia, MO, 65211, United States
2 - University of Missouri, Biological Sciences, Columbia, MO, USA
3 - University of Missouri, Biochemistry, MO, USA
4 - North Carolina State University, Biological Sciences, Raleigh, NC, USA
5 - Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
6 - HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
7 - University of Arizona, Plant Sciences, Tucson, AZ, USA
8 - Michigan State University, East Lansing, USA
9 - North Carolina State University, Biological Sciences, NC, USA

Keywords:
Genomics
Polyploidy
Phylogenomics
Hybridization
evolutionary genomics.

Presentation Type: Oral Paper
Session: 21, Comparative Genomics and Transcriptomics I
Location: 102/Mayo Civic Center
Date: Tuesday, July 24th, 2018
Time: 11:00 AM
Number: 21012
Abstract ID:342
Candidate for Awards:Margaret Menzel Award