pSONIC: Ploidy-aware Syntenic Orthologous Networks Identified via Collinearity
Open Access
- 13 May 2021
- journal article
- research article
- Published by Oxford University Press (OUP) in G3 Genes|Genomes|Genetics
- Vol. 11 (8)
- https://doi.org/10.1093/g3journal/jkab170
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 75-90% 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% of singleton gene groups follow the expected tree topology, and that our ploidy-aware algorithm recovers 97.5% identical groups when compared to splitting the allopolyploid into its two respective subgenomes, treating each as separate “species”.Keywords
Funding Information
- National Science Foundation-Plant Genome Research Program (1829176)
- Cotton Inc (IRT1134)
- University of Colorado Boulder Research Computing Group
- National Science Foundation (ACI-1532235, ACI-1532236)
This publication has 26 references indexed in Scilit:
- MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and UsabilityMolecular Biology and Evolution, 2013
- Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibresNature, 2012
- jModelTest 2: more models, new heuristics and parallel computingNature Methods, 2012
- MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearityNucleic Acids Research, 2012
- Orthology prediction methods: A quality assessment using curated protein familiesBioEssays, 2011
- Ancestral polyploidy in seed plants and angiospermsNature, 2011
- Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with RosidsPlant Physiology, 2008
- Two Rounds of Whole Genome Duplication in the Ancestral VertebratePLoS Biology, 2005
- Inparanoid: a comprehensive database of eukaryotic orthologsNucleic Acids Research, 2004
- OrthoMCL: Identification of Ortholog Groups for Eukaryotic GenomesGenome Research, 2003