Lineage-specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family

Premise Phylogenetic studies in the Compositae are challenging due to the sheer size of the family and the challenges they pose for molecular tools, ranging from the genomic impact of polyploid events to their very conserved plastid genomes. The search for better molecular tools for phylogenetic stu...

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Autores: Siniscalchi, Carolina M., Hidalgo, Oriane, Palazzesi, Luis, Pellicer, Jaume, Pokorny, Lisa, Maurin, Olivier, Leitch, Ilia J., Forest, Félix, Baker, William J., Mandel, Jennifer R.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2021
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/249594
Acceso en línea:http://hdl.handle.net/10261/249594
https://doi.org/10.1002/aps3.11422
Access Level:acceso abierto
Palabra clave:Angiosperms
Asteraceae
Paralogy
Phylogenomics
Target capture
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spelling Lineage-specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower familySiniscalchi, Carolina M.Hidalgo, OrianePalazzesi, LuisPellicer, JaumePokorny, LisaMaurin, OlivierLeitch, Ilia J.Forest, FélixBaker, William J.Mandel, Jennifer R.AngiospermsAsteraceaeParalogyPhylogenomicsTarget capturePremise Phylogenetic studies in the Compositae are challenging due to the sheer size of the family and the challenges they pose for molecular tools, ranging from the genomic impact of polyploid events to their very conserved plastid genomes. The search for better molecular tools for phylogenetic studies led to the development of the family-specific Compositae1061 probe set, as well as the universal Angiosperms353 probe set designed for all flowering plants. In this study, we evaluate the extent to which data generated using the family-specific kit and those obtained with the universal kit can be merged for downstream analyses. Methods We used comparative methods to verify the presence of shared loci between probe sets. Using two sets of eight samples sequenced with Compositae1061 and Angiosperms353, we ran phylogenetic analyses with and without loci flagged as paralogs, a gene tree discordance analysis, and a complementary phylogenetic analysis mixing samples from both sample sets. Results Our results show that the Compositae1061 kit provides an average of 721 loci, with 9¿46% of them presenting paralogs, while the Angiosperms353 set yields an average of 287 loci, which are less affected by paralogy. Analyses mixing samples from both sets showed that the presence of 30 shared loci in the probe sets allows the combination of data generated in different ways. Discussion Combining data generated using different probe sets opens up the possibility of collaborative efforts and shared data within the synantherological community.Funding came from various sources, including the National Science Foundation Division of Environmental Biology (DEB-1745197), and grants from the Calleva Foundation and the Sackler Trust to the Plant and Fungal Trees of Life (PAFTOL) project at the Royal Botanic Gardens, KewAbstract METHODS Identification of shared loci Taxon selection, plant material, DNA extraction, library preparation, and sequencing Sequence assembly and data analysis RESULTS Identification of shared loci Recovered loci and paralogy Phylogenetic relationships and gene tree discordance DISCUSSION Acknowledgments AUTHOR CONTRIBUTIONSJohn Wiley & SonsNational Science Foundation (US)Calleva FoundationRoyal Botanical Gardens, KewConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2021202120212021info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/249594https://doi.org/10.1002/aps3.11422reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Ingléshttps://doi.org/10.1002/aps3.11422Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2495942026-05-22T06:33:51Z
dc.title.none.fl_str_mv Lineage-specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family
title Lineage-specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family
spellingShingle Lineage-specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family
Siniscalchi, Carolina M.
Angiosperms
Asteraceae
Paralogy
Phylogenomics
Target capture
title_short Lineage-specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family
title_full Lineage-specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family
title_fullStr Lineage-specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family
title_full_unstemmed Lineage-specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family
title_sort Lineage-specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family
dc.creator.none.fl_str_mv Siniscalchi, Carolina M.
Hidalgo, Oriane
Palazzesi, Luis
Pellicer, Jaume
Pokorny, Lisa
Maurin, Olivier
Leitch, Ilia J.
Forest, Félix
Baker, William J.
Mandel, Jennifer R.
author Siniscalchi, Carolina M.
author_facet Siniscalchi, Carolina M.
Hidalgo, Oriane
Palazzesi, Luis
Pellicer, Jaume
Pokorny, Lisa
Maurin, Olivier
Leitch, Ilia J.
Forest, Félix
Baker, William J.
Mandel, Jennifer R.
author_role author
author2 Hidalgo, Oriane
Palazzesi, Luis
Pellicer, Jaume
Pokorny, Lisa
Maurin, Olivier
Leitch, Ilia J.
Forest, Félix
Baker, William J.
Mandel, Jennifer R.
author2_role author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv National Science Foundation (US)
Calleva Foundation
Royal Botanical Gardens, Kew
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Angiosperms
Asteraceae
Paralogy
Phylogenomics
Target capture
topic Angiosperms
Asteraceae
Paralogy
Phylogenomics
Target capture
description Premise Phylogenetic studies in the Compositae are challenging due to the sheer size of the family and the challenges they pose for molecular tools, ranging from the genomic impact of polyploid events to their very conserved plastid genomes. The search for better molecular tools for phylogenetic studies led to the development of the family-specific Compositae1061 probe set, as well as the universal Angiosperms353 probe set designed for all flowering plants. In this study, we evaluate the extent to which data generated using the family-specific kit and those obtained with the universal kit can be merged for downstream analyses. Methods We used comparative methods to verify the presence of shared loci between probe sets. Using two sets of eight samples sequenced with Compositae1061 and Angiosperms353, we ran phylogenetic analyses with and without loci flagged as paralogs, a gene tree discordance analysis, and a complementary phylogenetic analysis mixing samples from both sample sets. Results Our results show that the Compositae1061 kit provides an average of 721 loci, with 9¿46% of them presenting paralogs, while the Angiosperms353 set yields an average of 287 loci, which are less affected by paralogy. Analyses mixing samples from both sets showed that the presence of 30 shared loci in the probe sets allows the combination of data generated in different ways. Discussion Combining data generated using different probe sets opens up the possibility of collaborative efforts and shared data within the synantherological community.
publishDate 2021
dc.date.none.fl_str_mv 2021
2021
2021
2021
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/249594
https://doi.org/10.1002/aps3.11422
url http://hdl.handle.net/10261/249594
https://doi.org/10.1002/aps3.11422
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv https://doi.org/10.1002/aps3.11422
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv John Wiley & Sons
publisher.none.fl_str_mv John Wiley & Sons
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,812429

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