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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Published inApplications in plant sciences Vol. 11; no. 4; pp. e11537 - n/a
Main Authors Pezzini, Flávia Fonseca, Ferrari, Giada, Forrest, Laura L., Hart, Michelle L., Nishii, Kanae, Kidner, Catherine A.
Format Journal Article
LanguageEnglish
Published United States John Wiley & Sons, Inc 01.07.2023
John Wiley and Sons Inc
Wiley
Subjects
barcoding
bioinformatics
Chromosomes
coalescent analysis
Deoxyribonucleic acid
Design
DNA
Evolution
Flowers & plants
genome
Genomes
Genomics
herbaria
Next-generation sequencing
non‐model plants
Nucleotide sequence
Plant mitochondria
Plant sciences
Review
Ribosomal DNA
short‐read sequencing
species diversity
Whole genome sequencing
United States > US
barcoding
short‐read sequencing
herbaria
non‐model plants
coalescent analysis
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Abstract 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.
AbstractList 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.
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.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.
Abstract 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.
Author Pezzini, Flávia Fonseca
Kidner, Catherine A.
Nishii, Kanae
Forrest, Laura L.
Ferrari, Giada
Hart, Michelle L.
AuthorAffiliation 2 School of Biological Sciences University of Edinburgh Edinburgh United Kingdom
1 Royal Botanic Garden Edinburgh Edinburgh United Kingdom
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– name: 1 Royal Botanic Garden Edinburgh Edinburgh United Kingdom
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  givenname: Flávia Fonseca
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  email: fpezzini@rbge.org.uk
  organization: Royal Botanic Garden Edinburgh
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  givenname: Giada
  orcidid: 0000-0002-0850-1518
  surname: Ferrari
  fullname: Ferrari, Giada
  organization: Royal Botanic Garden Edinburgh
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  givenname: Laura L.
  surname: Forrest
  fullname: Forrest, Laura L.
  organization: Royal Botanic Garden Edinburgh
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Copyright 2023 The Authors. published by Wiley Periodicals LLC on behalf of Botanical Society of America.
2023 The Authors. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.
2023. This work is published under http://creativecommons.org/licenses/by-nc/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
Copyright_xml – notice: 2023 The Authors. published by Wiley Periodicals LLC on behalf of Botanical Society of America.
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Issue 4
Keywords barcoding
short‐read sequencing
herbaria
non‐model plants
coalescent analysis
Language English
License Attribution-NonCommercial
2023 The Authors. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.
This is an open access article under the terms of the http://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.
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Notes This article is part of the special issue “Bioinformatics for Plant Biology.”
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Snippet Recent technological advances in long‐read high‐throughput sequencing and assembly methods have facilitated the generation of annotated chromosome‐scale...
Recent technological advances in long-read high-throughput sequencing and assembly methods have facilitated the generation of annotated chromosome-scale...
Abstract Recent technological advances in long‐read high‐throughput sequencing and assembly methods have facilitated the generation of annotated...
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StartPage e11537
SubjectTerms barcoding
bioinformatics
Chromosomes
coalescent analysis
Deoxyribonucleic acid
Design
DNA
Evolution
Flowers & plants
genome
Genomes
Genomics
herbaria
Next-generation sequencing
non‐model plants
Nucleotide sequence
Plant mitochondria
Plant sciences
Review
Ribosomal DNA
short‐read sequencing
species diversity
Whole genome sequencing
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Title Target capture and genome skimming for plant diversity studies
URI https://onlinelibrary.wiley.com/doi/abs/10.1002%2Faps3.11537
https://www.ncbi.nlm.nih.gov/pubmed/37601316
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https://pubmed.ncbi.nlm.nih.gov/PMC10439825
https://doaj.org/article/ad2b1bbab6264618bef32bcbeceeac74
Volume 11
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