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Target capture and genome skimming for plant diversity studies

Recent technological advances in long‐read high‐throughput sequencing and assembly methods have facilitated the generation of annotated chromosome‐scale whole‐genome sequence data for evolutionary studies; however, generating such data can still be difficult for many plant species. For example, obta...

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Autores principales: Pezzini, Flávia Fonseca, Ferrari, Giada, Forrest, Laura L., Hart, Michelle L., Nishii, Kanae, Kidner, Catherine A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10439825/
https://www.ncbi.nlm.nih.gov/pubmed/37601316
http://dx.doi.org/10.1002/aps3.11537
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author Pezzini, Flávia Fonseca
Ferrari, Giada
Forrest, Laura L.
Hart, Michelle L.
Nishii, Kanae
Kidner, Catherine A.
author_facet Pezzini, Flávia Fonseca
Ferrari, Giada
Forrest, Laura L.
Hart, Michelle L.
Nishii, Kanae
Kidner, Catherine A.
author_sort Pezzini, Flávia Fonseca
collection PubMed
description Recent technological advances in long‐read high‐throughput sequencing and assembly methods have facilitated the generation of annotated chromosome‐scale whole‐genome sequence data for evolutionary studies; however, generating such data can still be difficult for many plant species. For example, obtaining high‐molecular‐weight DNA is typically impossible for samples in historical herbarium collections, which often have degraded DNA. The need to fast‐freeze newly collected living samples to conserve high‐quality DNA can be complicated when plants are only found in remote areas. Therefore, short‐read reduced‐genome representations, such as target capture and genome skimming, remain important for evolutionary studies. Here, we review the pros and cons of each technique for non‐model plant taxa. We provide guidance related to logistics, budget, the genomic resources previously available for the target clade, and the nature of the study. Furthermore, we assess the available bioinformatic analyses, detailing best practices and pitfalls, and suggest pathways to combine newly generated data with legacy data. Finally, we explore the possible downstream analyses allowed by the type of data generated using each technique. We provide a practical guide to help researchers make the best‐informed choice regarding reduced genome representation for evolutionary studies of non‐model plants in cases where whole‐genome sequencing remains impractical.
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spelling pubmed-104398252023-08-20 Target capture and genome skimming for plant diversity studies Pezzini, Flávia Fonseca Ferrari, Giada Forrest, Laura L. Hart, Michelle L. Nishii, Kanae Kidner, Catherine A. Appl Plant Sci Review Article Recent technological advances in long‐read high‐throughput sequencing and assembly methods have facilitated the generation of annotated chromosome‐scale whole‐genome sequence data for evolutionary studies; however, generating such data can still be difficult for many plant species. For example, obtaining high‐molecular‐weight DNA is typically impossible for samples in historical herbarium collections, which often have degraded DNA. The need to fast‐freeze newly collected living samples to conserve high‐quality DNA can be complicated when plants are only found in remote areas. Therefore, short‐read reduced‐genome representations, such as target capture and genome skimming, remain important for evolutionary studies. Here, we review the pros and cons of each technique for non‐model plant taxa. We provide guidance related to logistics, budget, the genomic resources previously available for the target clade, and the nature of the study. Furthermore, we assess the available bioinformatic analyses, detailing best practices and pitfalls, and suggest pathways to combine newly generated data with legacy data. Finally, we explore the possible downstream analyses allowed by the type of data generated using each technique. We provide a practical guide to help researchers make the best‐informed choice regarding reduced genome representation for evolutionary studies of non‐model plants in cases where whole‐genome sequencing remains impractical. John Wiley and Sons Inc. 2023-08-10 /pmc/articles/PMC10439825/ /pubmed/37601316 http://dx.doi.org/10.1002/aps3.11537 Text en © 2023 The Authors. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America. https://creativecommons.org/licenses/by-nc/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
spellingShingle Review Article
Pezzini, Flávia Fonseca
Ferrari, Giada
Forrest, Laura L.
Hart, Michelle L.
Nishii, Kanae
Kidner, Catherine A.
Target capture and genome skimming for plant diversity studies
title Target capture and genome skimming for plant diversity studies
title_full Target capture and genome skimming for plant diversity studies
title_fullStr Target capture and genome skimming for plant diversity studies
title_full_unstemmed Target capture and genome skimming for plant diversity studies
title_short Target capture and genome skimming for plant diversity studies
title_sort target capture and genome skimming for plant diversity studies
topic Review Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10439825/
https://www.ncbi.nlm.nih.gov/pubmed/37601316
http://dx.doi.org/10.1002/aps3.11537
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