The Treasure Vault Can be Opened : Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material
Alsos, Inger Greve (UiT The Arctic University of Norway. The Arctic University Museum of Norway)
Lavergne, Sebastien (LECA. Université Grenoble Alpes. Université Savoie Mont Blanc)
Merkel, Marie Kristine Føreid (UiT The Arctic University of Norway. The Arctic University Museum of Norway)
Boleda, Martí (LECA. Université Grenoble Alpes. Université Savoie Mont Blanc)
Lammers, Youri (UiT The Arctic University of Norway. The Arctic University Museum of Norway)
Alberti, Adriana (Université Paris-Saclay)
Pouchon, Charles (LECA. Université Grenoble Alpes. Université Savoie Mont Blanc)
Denoeud, France (Université Paris-Saclay)
Pitelkova, Iva (UiT The Arctic University of Norway. The Arctic University Museum of Norway)
Pușcaș, Mihai (Babeș-Bolyai University. Faculty of Biology and Geology (Romania))
Roquet, Cristina (Universitat Autònoma de Barcelona. Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia)
Hurdu, Bogdan-Iuliu (National Institute of Research and Development for Biological Sciences (Romania))
Thuiller, Wilfried (LECA. Université Grenoble Alpes. Université Savoie Mont Blanc)
Zimmermann, Niklaus E. (Swiss Federal Research Institute WSL)
Hollingsworth, Peter M. (Royal Botanic Garden Edinburgh)
Coissac, Eric (LECA. Université Grenoble Alpes. Université Savoie Mont Blanc)

Date:	2020
Abstract:	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.
Grants:	European Commission 281422
Note:	Altres ajuts: The Sixth European Framework Programme (GOCE-CT-2007-036866)
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Alpine ; Chloroplast DNA ; Environmental DNA ; ITS ; MatK ; Nuclear ribosomal DNA ; Plant DNA barcode ; Phylogenomic ; Polar ; Rbcl
Published in:	Plants, Vol. 9, Num. 14 (April 2020) , art. 432, ISSN 2223-7747

DOI: 10.3390/plants9040432
PMID: 32244605

18 p, 3.6 MB

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