pSONIC: Ploidy-aware Syntenic Orthologous Networks Identified via Collinearity
AbstractWith 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 ort...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Oxford University Press
2021-05-01
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| Series: | G3: Genes, Genomes, Genetics |
| Online Access: | https://academic.oup.com/g3journal/article-lookup/doi/10.1093/g3journal/jkab170 |
| _version_ | 1818323504716578816 |
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| author | Justin L Conover Joel Sharbrough Jonathan F Wendel |
| author_facet | Justin L Conover Joel Sharbrough Jonathan F Wendel |
| author_sort | Justin L Conover |
| collection | DOAJ |
| description | AbstractWith 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 |
| first_indexed | 2024-12-13T11:13:45Z |
| format | Article |
| id | doaj.art-f243635adf6a49f0b9c75cac29911386 |
| institution | Directory Open Access Journal |
| issn | 2160-1836 |
| language | English |
| last_indexed | 2024-12-13T11:13:45Z |
| publishDate | 2021-05-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | G3: Genes, Genomes, Genetics |
| spelling | doaj.art-f243635adf6a49f0b9c75cac299113862022-12-21T23:48:41ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362021-05-0111810.1093/g3journal/jkab170pSONIC: Ploidy-aware Syntenic Orthologous Networks Identified via CollinearityJustin L Conover0https://orcid.org/0000-0002-3558-6000Joel Sharbrough1https://orcid.org/0000-0002-3642-1662Jonathan F Wendel2https://orcid.org/0000-0003-2258-5081Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USABiology Department, Colorado State University, Fort Collins, CO 80521, USADepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USAAbstractWith 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 (Gossypieaehttps://academic.oup.com/g3journal/article-lookup/doi/10.1093/g3journal/jkab170 |
| spellingShingle | Justin L Conover Joel Sharbrough Jonathan F Wendel pSONIC: Ploidy-aware Syntenic Orthologous Networks Identified via Collinearity G3: Genes, Genomes, Genetics |
| title | pSONIC: Ploidy-aware Syntenic Orthologous Networks Identified via Collinearity |
| title_full | pSONIC: Ploidy-aware Syntenic Orthologous Networks Identified via Collinearity |
| title_fullStr | pSONIC: Ploidy-aware Syntenic Orthologous Networks Identified via Collinearity |
| title_full_unstemmed | pSONIC: Ploidy-aware Syntenic Orthologous Networks Identified via Collinearity |
| title_short | pSONIC: Ploidy-aware Syntenic Orthologous Networks Identified via Collinearity |
| title_sort | psonic ploidy aware syntenic orthologous networks identified via collinearity |
| url | https://academic.oup.com/g3journal/article-lookup/doi/10.1093/g3journal/jkab170 |
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