Mitochondrial genomes of Danish vertebrate species generated for the national DNA reference database, DNAmark

Biodiversity monitoring projects using environmental DNA techniques are becoming increasingly widespread. However, these techniques depend heavily on the quality and richness of the available DNA reference database against which the DNA sequences are queried. To create a comprehensive DNA sequence d...

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Bibliographic Details
Published in:	Environmental DNA (Hoboken, N.J.) Vol. 3; no. 2; pp. 472 - 480
Main Authors:	Margaryan, Ashot, Noer, Christina Lehmkuhl, Richter, Stine Raith, Restrup, Marlene Elise, Bülow‐Hansen, Julie Lee, Leerhøi, Frederik, Langkjær, Emilia Marie Rolander, Gopalakrishnan, Shyam, Carøe, Christian, Gilbert, M. Thomas P., Bohmann, Kristine
Format:	Journal Article
Language:	English
Published:	Hoboken John Wiley & Sons, Inc 01-03-2021 Wiley
Subjects:	Animals Assessments Binding sites Biodiversity biodiversity assessment Biopsy COI Deoxyribonucleic acid DNA DNA barcoding DNA metabarcoding DNA reference databases environmental DNA Environmental monitoring Flowers & plants Fungi Gene sequencing genome skimming Genomes Mammals Mitochondrial DNA molecular biodiversity assessment Museums next‐generation sequencing Nucleotide sequence Plant species Ribosomal DNA Species Storage conditions taxonomic identification Taxonomy Vertebrates Denmark
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Summary:	Biodiversity monitoring projects using environmental DNA techniques are becoming increasingly widespread. However, these techniques depend heavily on the quality and richness of the available DNA reference database against which the DNA sequences are queried. To create a comprehensive DNA sequence database for future DNA‐based biodiversity assessments in Denmark, a national DNA reference database, DNAmark, was established, which contains organellar and/or nuclear reference data from vouchered museum species of plants, animals, and fungi from Denmark. Here, we present full or partial mitochondrial genomes of 182 Danish vertebrate species representing ca. 22% of vertebrate species observed in Denmark. Further, we demonstrate that storage conditions of the specimens accounted for ca. 50% of the total variation in mitochondrial DNA (mtDNA) preservation while the age of museum specimens had little effect: ca. 4%. In addition, we roughly estimate the cost of sequencing to be 25 EUR per specimen for obtaining sufficient amounts of DNA reads (ca. 200‐fold coverage) for reliable mitogenome assemblies while also obtaining low coverage genomic data. The large number of mitogenomes of Danish vertebrate species represents the initial groundwork for DNA‐based biodiversity assessments of vertebrates in Denmark and paves the way for practitioners to freely choose mitochondrial DNA markers. Here, we present mitochondrial reference sequences for 182 Danish vertebrate species representing ca. 22% of vertebrates observed in Denmark. This is part of a larger DNA reference database, which aims to pave the way for future DNA‐based biodiversity assessments in Denmark.
ISSN:	2637-4943 2637-4943
DOI:	10.1002/edn3.138