Cargando…

Mare-MAGE curated reference database of fish mitochondrial genes

Biodiversity assessment approaches based on molecular biology techniques such as metabarcoding, RAD-seq, or SnaPshot sequencing are increasingly applied in assessing marine and aquatic ecosystems. Here we present a new reference database for fish meta-barcoding based on mitochondrial genes. The Mare...

Descripción completa

Detalles Bibliográficos
Autores principales: Kasmi, Yassine, Eschbach, Erik, Hanel, Reinhold
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10024356/
https://www.ncbi.nlm.nih.gov/pubmed/36932341
http://dx.doi.org/10.1186/s12863-023-01119-4
_version_ 1784909084711976960
author Kasmi, Yassine
Eschbach, Erik
Hanel, Reinhold
author_facet Kasmi, Yassine
Eschbach, Erik
Hanel, Reinhold
author_sort Kasmi, Yassine
collection PubMed
description Biodiversity assessment approaches based on molecular biology techniques such as metabarcoding, RAD-seq, or SnaPshot sequencing are increasingly applied in assessing marine and aquatic ecosystems. Here we present a new reference database for fish meta-barcoding based on mitochondrial genes. The Mare-MAGE database contains quality-checked sequences of the mitochondrial 12S ribosomal RNA and Cytochrome c Oxidase I gene. All sequences were obtained from the National Center for Biotechnology Information- GenBank (NBCI-GenBank), the European Nucleotide Archive (ENA), AquaGene Database and BOLD database, and have undergone intensive processing. They were checked for false annotations and non-target anomalies, according to the Integrated Taxonomic Information System (ITIS) and FishBase. The dataset is compiled in ARB-Home, FASTA and Qiime2 formats, and is publicly available from the Mare-MAGE database website (http://mare-mage.weebly.com/). It includes altogether 231,333 COI and 12S rRNA gene sequences of fish, covering 19,506 species of 4,058 genera and 586 families. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12863-023-01119-4.
format Online
Article
Text
id pubmed-10024356
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-100243562023-03-19 Mare-MAGE curated reference database of fish mitochondrial genes Kasmi, Yassine Eschbach, Erik Hanel, Reinhold BMC Genom Data Database Biodiversity assessment approaches based on molecular biology techniques such as metabarcoding, RAD-seq, or SnaPshot sequencing are increasingly applied in assessing marine and aquatic ecosystems. Here we present a new reference database for fish meta-barcoding based on mitochondrial genes. The Mare-MAGE database contains quality-checked sequences of the mitochondrial 12S ribosomal RNA and Cytochrome c Oxidase I gene. All sequences were obtained from the National Center for Biotechnology Information- GenBank (NBCI-GenBank), the European Nucleotide Archive (ENA), AquaGene Database and BOLD database, and have undergone intensive processing. They were checked for false annotations and non-target anomalies, according to the Integrated Taxonomic Information System (ITIS) and FishBase. The dataset is compiled in ARB-Home, FASTA and Qiime2 formats, and is publicly available from the Mare-MAGE database website (http://mare-mage.weebly.com/). It includes altogether 231,333 COI and 12S rRNA gene sequences of fish, covering 19,506 species of 4,058 genera and 586 families. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12863-023-01119-4. BioMed Central 2023-03-17 /pmc/articles/PMC10024356/ /pubmed/36932341 http://dx.doi.org/10.1186/s12863-023-01119-4 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Database
Kasmi, Yassine
Eschbach, Erik
Hanel, Reinhold
Mare-MAGE curated reference database of fish mitochondrial genes
title Mare-MAGE curated reference database of fish mitochondrial genes
title_full Mare-MAGE curated reference database of fish mitochondrial genes
title_fullStr Mare-MAGE curated reference database of fish mitochondrial genes
title_full_unstemmed Mare-MAGE curated reference database of fish mitochondrial genes
title_short Mare-MAGE curated reference database of fish mitochondrial genes
title_sort mare-mage curated reference database of fish mitochondrial genes
topic Database
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10024356/
https://www.ncbi.nlm.nih.gov/pubmed/36932341
http://dx.doi.org/10.1186/s12863-023-01119-4
work_keys_str_mv AT kasmiyassine maremagecuratedreferencedatabaseoffishmitochondrialgenes
AT eschbacherik maremagecuratedreferencedatabaseoffishmitochondrialgenes
AT hanelreinhold maremagecuratedreferencedatabaseoffishmitochondrialgenes