Compositae‐ParaLoss‐1272: A complementary sunflower‐specific probe set reduces paralogs in phylogenomic analyses of complex systems
Abstract Premise A family‐specific probe set for sunflowers, Compositae‐1061, enables family‐wide phylogenomic studies and investigations at lower taxonomic levels, but may lack resolution at genus to species levels, especially in groups complicated by polyploidy and hybridization. Methods We develo...
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| Format: | Article |
| Language: | English |
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Wiley
2024-01-01
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| Series: | Applications in Plant Sciences |
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| Online Access: | https://doi.org/10.1002/aps3.11568 |
| _version_ | 1797304142372274176 |
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| author | Erika R. Moore‐Pollard Daniel S. Jones Jennifer R. Mandel |
| author_facet | Erika R. Moore‐Pollard Daniel S. Jones Jennifer R. Mandel |
| author_sort | Erika R. Moore‐Pollard |
| collection | DOAJ |
| description | Abstract Premise A family‐specific probe set for sunflowers, Compositae‐1061, enables family‐wide phylogenomic studies and investigations at lower taxonomic levels, but may lack resolution at genus to species levels, especially in groups complicated by polyploidy and hybridization. Methods We developed a Hyb‐Seq probe set, Compositae‐ParaLoss‐1272, that targets orthologous loci in Asteraceae. We tested its efficiency across the family by simulating target enrichment sequencing in silico. Additionally, we tested its effectiveness at lower taxonomic levels in the historically complex genus Packera. We performed Hyb‐Seq with Compositae‐ParaLoss‐1272 for 19 Packera taxa that were previously studied using Compositae‐1061. The resulting sequences from each probe set, plus a combination of both, were used to generate phylogenies, compare topologies, and assess node support. Results We report that Compositae‐ParaLoss‐1272 captured loci across all tested Asteraceae members, had less gene tree discordance, and retained longer loci than Compositae‐1061. Most notably, Compositae‐ParaLoss‐1272 recovered substantially fewer paralogous sequences than Compositae‐1061, with only ~5% of the recovered loci reporting as paralogous, compared to ~59% with Compositae‐1061. Discussion Given the complexity of plant evolutionary histories, assigning orthology for phylogenomic analyses will continue to be challenging. However, we anticipate Compositae‐ParaLoss‐1272 will provide improved resolution and utility for studies of complex groups and lower taxonomic levels in the sunflower family. |
| first_indexed | 2024-03-08T00:04:10Z |
| format | Article |
| id | doaj.art-76b9e4e055954045ad4dbac7f45359d7 |
| institution | Directory Open Access Journal |
| issn | 2168-0450 |
| language | English |
| last_indexed | 2024-03-08T00:04:10Z |
| publishDate | 2024-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Applications in Plant Sciences |
| spelling | doaj.art-76b9e4e055954045ad4dbac7f45359d72024-02-17T10:50:29ZengWileyApplications in Plant Sciences2168-04502024-01-01121n/an/a10.1002/aps3.11568Compositae‐ParaLoss‐1272: A complementary sunflower‐specific probe set reduces paralogs in phylogenomic analyses of complex systemsErika R. Moore‐Pollard0Daniel S. Jones1Jennifer R. Mandel2Department of Biological Sciences University of Memphis 3700 Walker Ave. Memphis Tennessee 38152 USADepartment of Biological Sciences Auburn University 101 Rouse Life Sciences Auburn Alabama 36849 USADepartment of Biological Sciences University of Memphis 3700 Walker Ave. Memphis Tennessee 38152 USAAbstract Premise A family‐specific probe set for sunflowers, Compositae‐1061, enables family‐wide phylogenomic studies and investigations at lower taxonomic levels, but may lack resolution at genus to species levels, especially in groups complicated by polyploidy and hybridization. Methods We developed a Hyb‐Seq probe set, Compositae‐ParaLoss‐1272, that targets orthologous loci in Asteraceae. We tested its efficiency across the family by simulating target enrichment sequencing in silico. Additionally, we tested its effectiveness at lower taxonomic levels in the historically complex genus Packera. We performed Hyb‐Seq with Compositae‐ParaLoss‐1272 for 19 Packera taxa that were previously studied using Compositae‐1061. The resulting sequences from each probe set, plus a combination of both, were used to generate phylogenies, compare topologies, and assess node support. Results We report that Compositae‐ParaLoss‐1272 captured loci across all tested Asteraceae members, had less gene tree discordance, and retained longer loci than Compositae‐1061. Most notably, Compositae‐ParaLoss‐1272 recovered substantially fewer paralogous sequences than Compositae‐1061, with only ~5% of the recovered loci reporting as paralogous, compared to ~59% with Compositae‐1061. Discussion Given the complexity of plant evolutionary histories, assigning orthology for phylogenomic analyses will continue to be challenging. However, we anticipate Compositae‐ParaLoss‐1272 will provide improved resolution and utility for studies of complex groups and lower taxonomic levels in the sunflower family.https://doi.org/10.1002/aps3.11568Asteraceaedouble‐captureHyb‐SeqMarkerMinerPackerapolyploidy |
| spellingShingle | Erika R. Moore‐Pollard Daniel S. Jones Jennifer R. Mandel Compositae‐ParaLoss‐1272: A complementary sunflower‐specific probe set reduces paralogs in phylogenomic analyses of complex systems Applications in Plant Sciences Asteraceae double‐capture Hyb‐Seq MarkerMiner Packera polyploidy |
| title | Compositae‐ParaLoss‐1272: A complementary sunflower‐specific probe set reduces paralogs in phylogenomic analyses of complex systems |
| title_full | Compositae‐ParaLoss‐1272: A complementary sunflower‐specific probe set reduces paralogs in phylogenomic analyses of complex systems |
| title_fullStr | Compositae‐ParaLoss‐1272: A complementary sunflower‐specific probe set reduces paralogs in phylogenomic analyses of complex systems |
| title_full_unstemmed | Compositae‐ParaLoss‐1272: A complementary sunflower‐specific probe set reduces paralogs in phylogenomic analyses of complex systems |
| title_short | Compositae‐ParaLoss‐1272: A complementary sunflower‐specific probe set reduces paralogs in phylogenomic analyses of complex systems |
| title_sort | compositae paraloss 1272 a complementary sunflower specific probe set reduces paralogs in phylogenomic analyses of complex systems |
| topic | Asteraceae double‐capture Hyb‐Seq MarkerMiner Packera polyploidy |
| url | https://doi.org/10.1002/aps3.11568 |
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