Truly the best of both worlds: Merging lineage‐specific and universal probe kits to maximize phylogenomic inference
Abstract Premise Hybridization capture kits are now commonly used for reduced representation approaches in genomic sequencing, with both universal and clade‐specific kits available. Here, we present a probe kit targeting 799 low‐copy genes for the plant family Annonaceae. Methods This new version of...
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Wiley
2024-11-01
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| Series: | Applications in Plant Sciences |
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| Online Access: | https://doi.org/10.1002/aps3.11615 |
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| author | Luiz Henrique M. Fonseca Pieter Asselman Katherine R. Goodrich Francis J. Nge Vincent Soulé Kathryn Mercier Thomas L. P. Couvreur Lars W. Chatrou |
| author_facet | Luiz Henrique M. Fonseca Pieter Asselman Katherine R. Goodrich Francis J. Nge Vincent Soulé Kathryn Mercier Thomas L. P. Couvreur Lars W. Chatrou |
| author_sort | Luiz Henrique M. Fonseca |
| collection | DOAJ |
| description | Abstract Premise Hybridization capture kits are now commonly used for reduced representation approaches in genomic sequencing, with both universal and clade‐specific kits available. Here, we present a probe kit targeting 799 low‐copy genes for the plant family Annonaceae. Methods This new version of the kit combines the original 469 genes from the previous Annonaceae kit with 334 genes from the universal Angiosperms353 kit. We also compare the results obtained using the original Angiosperms353 kit with our custom approach using a subset of specimens. Parsimony‐informative sites and the results of maximum likelihood phylogenetic inference were assessed for combined matrices using the genera Asimina and Deeringothamnus. Results The Annonaceae799 genes derived from the Angiosperms353 kit have extremely high recovery rates. Off‐target reads were also detected. When evaluating size, the proportion of on‐ and off‐target regions, and the number of parsimony‐informative sites, the genes incorporated from the Angiosperms353 panel generally outperformed the genes from the original Annonaceae probe kit. Discussion We demonstrated that the new sequences from the Angiosperms353 probe set are variable and relevant for future studies on species‐level phylogenomics and within‐species studies in the Annonaceae. The integration of kits also establishes a connection between projects and makes new genes available for phylogenetic and population studies. |
| format | Article |
| id | doaj-art-1067b023f4ba4f8e968e07d6b5b5b4e3 |
| institution | Kabale University |
| issn | 2168-0450 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Wiley |
| record_format | Article |
| series | Applications in Plant Sciences |
| spelling | doaj-art-1067b023f4ba4f8e968e07d6b5b5b4e32024-12-02T15:08:29ZengWileyApplications in Plant Sciences2168-04502024-11-01126n/an/a10.1002/aps3.11615Truly the best of both worlds: Merging lineage‐specific and universal probe kits to maximize phylogenomic inferenceLuiz Henrique M. Fonseca0Pieter Asselman1Katherine R. Goodrich2Francis J. Nge3Vincent Soulé4Kathryn Mercier5Thomas L. P. Couvreur6Lars W. Chatrou7Systematic and Evolutionary Botany Laboratory, Department of Biology Ghent University Ghent BelgiumSystematic and Evolutionary Botany Laboratory, Department of Biology Ghent University Ghent BelgiumDepartment of Biology Widener University Chester Pennsylvania USAInstitute of Research for Development (IRD), UMR DIADE Université de Montpellier Montpellier FranceInstitute of Research for Development (IRD), UMR DIADE Université de Montpellier Montpellier FranceDepartment of Biology City College of New York New York New York USAInstitute of Research for Development (IRD), UMR DIADE Université de Montpellier Montpellier FranceSystematic and Evolutionary Botany Laboratory, Department of Biology Ghent University Ghent BelgiumAbstract Premise Hybridization capture kits are now commonly used for reduced representation approaches in genomic sequencing, with both universal and clade‐specific kits available. Here, we present a probe kit targeting 799 low‐copy genes for the plant family Annonaceae. Methods This new version of the kit combines the original 469 genes from the previous Annonaceae kit with 334 genes from the universal Angiosperms353 kit. We also compare the results obtained using the original Angiosperms353 kit with our custom approach using a subset of specimens. Parsimony‐informative sites and the results of maximum likelihood phylogenetic inference were assessed for combined matrices using the genera Asimina and Deeringothamnus. Results The Annonaceae799 genes derived from the Angiosperms353 kit have extremely high recovery rates. Off‐target reads were also detected. When evaluating size, the proportion of on‐ and off‐target regions, and the number of parsimony‐informative sites, the genes incorporated from the Angiosperms353 panel generally outperformed the genes from the original Annonaceae probe kit. Discussion We demonstrated that the new sequences from the Angiosperms353 probe set are variable and relevant for future studies on species‐level phylogenomics and within‐species studies in the Annonaceae. The integration of kits also establishes a connection between projects and makes new genes available for phylogenetic and population studies.https://doi.org/10.1002/aps3.11615Angiosperms353AnnonaceaeAsiminabait setDeeringothamnusphylogenetics |
| spellingShingle | Luiz Henrique M. Fonseca Pieter Asselman Katherine R. Goodrich Francis J. Nge Vincent Soulé Kathryn Mercier Thomas L. P. Couvreur Lars W. Chatrou Truly the best of both worlds: Merging lineage‐specific and universal probe kits to maximize phylogenomic inference Applications in Plant Sciences Angiosperms353 Annonaceae Asimina bait set Deeringothamnus phylogenetics |
| title | Truly the best of both worlds: Merging lineage‐specific and universal probe kits to maximize phylogenomic inference |
| title_full | Truly the best of both worlds: Merging lineage‐specific and universal probe kits to maximize phylogenomic inference |
| title_fullStr | Truly the best of both worlds: Merging lineage‐specific and universal probe kits to maximize phylogenomic inference |
| title_full_unstemmed | Truly the best of both worlds: Merging lineage‐specific and universal probe kits to maximize phylogenomic inference |
| title_short | Truly the best of both worlds: Merging lineage‐specific and universal probe kits to maximize phylogenomic inference |
| title_sort | truly the best of both worlds merging lineage specific and universal probe kits to maximize phylogenomic inference |
| topic | Angiosperms353 Annonaceae Asimina bait set Deeringothamnus phylogenetics |
| url | https://doi.org/10.1002/aps3.11615 |
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