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The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material

Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium sp...

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Autores principales: Alsos, Inger Greve, Lavergne, Sebastien, Merkel, Marie Kristine Føreid, Boleda, Marti, Lammers, Youri, Alberti, Adriana, Pouchon, Charles, Denoeud, France, Pitelkova, Iva, Pușcaș, Mihai, Roquet, Cristina, Hurdu, Bogdan-Iuliu, Thuiller, Wilfried, Zimmermann, Niklaus E., Hollingsworth, Peter M., Coissac, Eric
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7238428/
https://www.ncbi.nlm.nih.gov/pubmed/32244605
http://dx.doi.org/10.3390/plants9040432
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author Alsos, Inger Greve
Lavergne, Sebastien
Merkel, Marie Kristine Føreid
Boleda, Marti
Lammers, Youri
Alberti, Adriana
Pouchon, Charles
Denoeud, France
Pitelkova, Iva
Pușcaș, Mihai
Roquet, Cristina
Hurdu, Bogdan-Iuliu
Thuiller, Wilfried
Zimmermann, Niklaus E.
Hollingsworth, Peter M.
Coissac, Eric
author_facet Alsos, Inger Greve
Lavergne, Sebastien
Merkel, Marie Kristine Føreid
Boleda, Marti
Lammers, Youri
Alberti, Adriana
Pouchon, Charles
Denoeud, France
Pitelkova, Iva
Pușcaș, Mihai
Roquet, Cristina
Hurdu, Bogdan-Iuliu
Thuiller, Wilfried
Zimmermann, Niklaus E.
Hollingsworth, Peter M.
Coissac, Eric
author_sort Alsos, Inger Greve
collection PubMed
description Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was > 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications.
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spelling pubmed-72384282020-06-02 The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material Alsos, Inger Greve Lavergne, Sebastien Merkel, Marie Kristine Føreid Boleda, Marti Lammers, Youri Alberti, Adriana Pouchon, Charles Denoeud, France Pitelkova, Iva Pușcaș, Mihai Roquet, Cristina Hurdu, Bogdan-Iuliu Thuiller, Wilfried Zimmermann, Niklaus E. Hollingsworth, Peter M. Coissac, Eric Plants (Basel) Article Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was > 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications. MDPI 2020-04-01 /pmc/articles/PMC7238428/ /pubmed/32244605 http://dx.doi.org/10.3390/plants9040432 Text en © 2020 by the authors. 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 (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Alsos, Inger Greve
Lavergne, Sebastien
Merkel, Marie Kristine Føreid
Boleda, Marti
Lammers, Youri
Alberti, Adriana
Pouchon, Charles
Denoeud, France
Pitelkova, Iva
Pușcaș, Mihai
Roquet, Cristina
Hurdu, Bogdan-Iuliu
Thuiller, Wilfried
Zimmermann, Niklaus E.
Hollingsworth, Peter M.
Coissac, Eric
The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material
title The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material
title_full The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material
title_fullStr The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material
title_full_unstemmed The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material
title_short The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material
title_sort treasure vault can be opened: large-scale genome skimming works well using herbarium and silica gel dried material
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7238428/
https://www.ncbi.nlm.nih.gov/pubmed/32244605
http://dx.doi.org/10.3390/plants9040432
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