Mare-MAGE curated reference database of fish mitochondrial genes
Abstract 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....
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-03-01
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| Series: | BMC Genomic Data |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12863-023-01119-4 |
| _version_ | 1797863402570252288 |
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| author | Yassine Kasmi Erik Eschbach Reinhold Hanel |
| author_facet | Yassine Kasmi Erik Eschbach Reinhold Hanel |
| author_sort | Yassine Kasmi |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-04-09T22:35:01Z |
| format | Article |
| id | doaj.art-71306687265d4f98a7799009b4fae92a |
| institution | Directory Open Access Journal |
| issn | 2730-6844 |
| language | English |
| last_indexed | 2024-04-09T22:35:01Z |
| publishDate | 2023-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomic Data |
| spelling | doaj.art-71306687265d4f98a7799009b4fae92a2023-03-22T12:31:25ZengBMCBMC Genomic Data2730-68442023-03-0124111210.1186/s12863-023-01119-4Mare-MAGE curated reference database of fish mitochondrial genesYassine Kasmi0Erik Eschbach1Reinhold Hanel2Thünen Institute of Fisheries EcologyThünen Institute of Fisheries EcologyThünen Institute of Fisheries EcologyAbstract 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.https://doi.org/10.1186/s12863-023-01119-4Mare-MAGEMitochondrial databaseFishMetabarcodingeDNA |
| spellingShingle | Yassine Kasmi Erik Eschbach Reinhold Hanel Mare-MAGE curated reference database of fish mitochondrial genes BMC Genomic Data Mare-MAGE Mitochondrial database Fish Metabarcoding eDNA |
| 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 | Mare-MAGE Mitochondrial database Fish Metabarcoding eDNA |
| url | https://doi.org/10.1186/s12863-023-01119-4 |
| work_keys_str_mv | AT yassinekasmi maremagecuratedreferencedatabaseoffishmitochondrialgenes AT erikeschbach maremagecuratedreferencedatabaseoffishmitochondrialgenes AT reinholdhanel maremagecuratedreferencedatabaseoffishmitochondrialgenes |