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A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae

Relationships within the major clades of Cactaceae are relatively well known based on DNA sequence data mostly from the chloroplast genome. Nevertheless, some nodes along the backbone of the phylogeny, and especially generic and species-level relationships, remain poorly resolved and are in need of...

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Autores principales: Acha, Serena, Majure, Lucas C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8871817/
https://www.ncbi.nlm.nih.gov/pubmed/35205394
http://dx.doi.org/10.3390/genes13020350
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author Acha, Serena
Majure, Lucas C.
author_facet Acha, Serena
Majure, Lucas C.
author_sort Acha, Serena
collection PubMed
description Relationships within the major clades of Cactaceae are relatively well known based on DNA sequence data mostly from the chloroplast genome. Nevertheless, some nodes along the backbone of the phylogeny, and especially generic and species-level relationships, remain poorly resolved and are in need of more informative genetic markers. In this study, we propose a new approach to solve the relationships within Cactaceae, applying a targeted sequence capture pipeline. We designed a custom probe set for Cactaceae using MarkerMiner and complemented it with the Angiosperms353 probe set. We then tested both probe sets against 36 different transcriptomes using Hybpiper preferentially retaining phylogenetically informative loci and reconstructed the relationships using RAxML-NG and Astral. Finally, we tested each probe set through sequencing 96 accessions, representing 88 species across Cactaceae. Our preliminary analyses recovered a well-supported phylogeny across Cactaceae with a near identical topology among major clade relationships as that recovered with plastome data. As expected, however, we found incongruences in relationships when comparing our nuclear probe set results to plastome datasets, especially at the generic level. Our results reveal great potential for the combination of Cactaceae-specific and Angiosperm353 probe set application to improve phylogenetic resolution for Cactaceae and for other studies.
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spelling pubmed-88718172022-02-25 A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae Acha, Serena Majure, Lucas C. Genes (Basel) Article Relationships within the major clades of Cactaceae are relatively well known based on DNA sequence data mostly from the chloroplast genome. Nevertheless, some nodes along the backbone of the phylogeny, and especially generic and species-level relationships, remain poorly resolved and are in need of more informative genetic markers. In this study, we propose a new approach to solve the relationships within Cactaceae, applying a targeted sequence capture pipeline. We designed a custom probe set for Cactaceae using MarkerMiner and complemented it with the Angiosperms353 probe set. We then tested both probe sets against 36 different transcriptomes using Hybpiper preferentially retaining phylogenetically informative loci and reconstructed the relationships using RAxML-NG and Astral. Finally, we tested each probe set through sequencing 96 accessions, representing 88 species across Cactaceae. Our preliminary analyses recovered a well-supported phylogeny across Cactaceae with a near identical topology among major clade relationships as that recovered with plastome data. As expected, however, we found incongruences in relationships when comparing our nuclear probe set results to plastome datasets, especially at the generic level. Our results reveal great potential for the combination of Cactaceae-specific and Angiosperm353 probe set application to improve phylogenetic resolution for Cactaceae and for other studies. MDPI 2022-02-15 /pmc/articles/PMC8871817/ /pubmed/35205394 http://dx.doi.org/10.3390/genes13020350 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Acha, Serena
Majure, Lucas C.
A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae
title A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae
title_full A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae
title_fullStr A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae
title_full_unstemmed A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae
title_short A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae
title_sort new approach using targeted sequence capture for phylogenomic studies across cactaceae
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8871817/
https://www.ncbi.nlm.nih.gov/pubmed/35205394
http://dx.doi.org/10.3390/genes13020350
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