PSONIC: Ploidy-aware Syntenic Orthologous Networks Identified via Collinearity.

ABSTRACT: With the rapid rise in availability of high-quality genomes for closely related species, methods for orthology inference that incorporate synteny are increasingly useful. Polyploidy perturbs the 1:1 expected frequencies of orthologs between two species, complicating the identification of orthologs. Here we present a method of ortholog inference, Ploidy-aware Syntenic Orthologous Networks Identified via Collinearity (pSONIC). We demonstrate the utility of pSONIC using four species in the cotton tribe (Gossypieae), including one allopolyploid, and place between 75% and 90% of genes from each species into nearly 32,000 orthologous groups, 97% of which consist of at most singletons or tandemly duplicated genes-58.8% more than comparable methods that do not incorporate synteny. We show that 99%

SUBMITTER: Conover JL 

PROVIDER: S-EPMC8496325 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature