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Diat.barcode, an open-access curated barcode library for diatoms

Rimet, Frédéric and Vasselon, Valentin and Gusev, Evgenuy and Kahlert, Maria and Kelly, Martyn G. and Kulikovskiy, Maxim and Maltsev, Yevhen and Mann, David G. and Pfannkuchen, Martin and Trobajo, Rosa and Zimmermann, Jonas and Bouchez, Agnes (2019). Diat.barcode, an open-access curated barcode library for diatoms. Scientific Reports. 9 , 1-12
[Journal article]

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Abstract

Diatoms (Bacillariophyta) are ubiquitous microalgae which produce a siliceous exoskeleton and which make a major contribution to the productivity of oceans and freshwaters. They display a huge diversity, which makes them excellent ecological indicators of aquatic ecosystems. Usually, diatoms are identifed using characteristics of their exoskeleton morphology. DNA-barcoding is an alternative to this and the use of High-Throughput-Sequencing enables the rapid analysis of many environmental samples at a lower cost than analyses under microscope. However, to identify environmental sequences correctly, an expertly curated reference library is needed. Several curated libraries for protists exists; none, however are dedicated to diatoms. Diat.barcode is an open-access library dedicated to diatoms which has been maintained since 2012. Data come from two sources (1) the NCBI nucleotide database and (2) unpublished sequencing data of culture collections. Since 2017, several experts have collaborated to curate this library for rbcL, a chloroplast marker suitable for species-level identifcation of diatoms. For the latest version of the database (version 7), 605 of the 3482 taxonomical names originally assigned by the authors of the rbcL sequences were modifed after curation.
The database is accessible at https:// www6.inra.fr/carrtel-collection_eng/Barcoding-database.

Authors/Creators:Rimet, Frédéric and Vasselon, Valentin and Gusev, Evgenuy and Kahlert, Maria and Kelly, Martyn G. and Kulikovskiy, Maxim and Maltsev, Yevhen and Mann, David G. and Pfannkuchen, Martin and Trobajo, Rosa and Zimmermann, Jonas and Bouchez, Agnes
Title:Diat.barcode, an open-access curated barcode library for diatoms
Year of publishing :2019
Volume:9
Page range:1-12
Number of Pages:12
Publisher:Springer Nature
Associated Programs and Other Stakeholders:SLU - Environmental assessment > Programme Lakes and watercourses
ISSN:2045-2322
Language:English
Publication Type:Journal article
Refereed:Yes
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 105 Earth and Related Environmental Sciences > Environmental Sciences (social aspects to be 507)
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Botany
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Biological Systematics
Keywords:diatoms, microalgae, molecular phylogeny, DNA-barcoding, species identification
URN:NBN:urn:nbn:se:slu:epsilon-p-103427
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-103427
Additional ID:
Type of IDID
DOI10.1038/s41598-019-51500-6
ID Code:16599
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Dept. of Aquatic Sciences and Assessment
Deposited By: SLUpub Connector
Deposited On:05 Mar 2020 08:00
Metadata Last Modified:23 Jul 2020 08:56

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