The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material.
ITS
alpine
chloroplast DNA
environmental DNA
matK
nuclear ribosomal DNA
phylogenomic
plant DNA barcode
polar
rbcL
Journal
Plants (Basel, Switzerland)
ISSN: 2223-7747
Titre abrégé: Plants (Basel)
Pays: Switzerland
ID NLM: 101596181
Informations de publication
Date de publication:
01 Apr 2020
01 Apr 2020
Historique:
received:
27
02
2020
revised:
24
03
2020
accepted:
25
03
2020
entrez:
5
4
2020
pubmed:
5
4
2020
medline:
5
4
2020
Statut:
epublish
Résumé
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%
Identifiants
pubmed: 32244605
pii: plants9040432
doi: 10.3390/plants9040432
pmc: PMC7238428
pii:
doi:
Types de publication
Journal Article
Langues
eng
Subventions
Organisme : Norges Forskningsråd
ID : 226134/F50
Organisme : Norwegian Biodiversity Information Centre
ID : 14-14, 70184209
Organisme : Universitetet i Tromsø
ID : PhD internal funded
Organisme : Seventh Framework Programme
ID : FP7/2007-2013 281422
Organisme : Sixth Framework Programme
ID : GOCE-CT-2007-036866
Organisme : Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
ID : Grant 31003A_149508/1
Organisme : Institut Français de Bioinformatique
ID : NextBarcode project
Organisme : Agence Nationale de la Recherche
ID : ANR-07-BDIV-014
Organisme : Agence Nationale de la Recherche
ID : ANR-13-ISV7-0004
Organisme : Agence Nationale de la Recherche
ID : PN-II-ID-JRP-RO-FR-2012
Organisme : Agence Nationale de la Recherche
ID : BRANCUSI No. 32660WB
Organisme : Agence Nationale de la Recherche
ID : PN-II-CT-ROFR-2014-2-0011
Organisme : Romanian Ministry of Education
ID : PN-II-RU-PD-2012-3-0636
Organisme : France Génomique
ID : ANR-10-INBS-09-08
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