Mitochondrial genomes of Danish vertebrate species generated for the national DNA reference database, DNAmark. Issue 2 (5th October 2020)

• Record Type: Journal Article
• 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
• Is Part Of: Environmental DNA. Volume 3:Issue 2(2021)
• Page Start: 472
• Page End: 480
• Publication Date: 2020-10-05
• Subjects: biodiversity assessment -- COI -- DNA barcoding -- DNA metabarcoding -- DNA reference databases -- environmental DNA -- genome skimming -- mitochondrial DNA -- molecular biodiversity assessment -- next‐generation sequencing -- taxonomic identification; DNA -- Periodicals; Biology -- Periodicals; Microbial ecology -- Periodicals; Biology; DNA; Microbial ecology; Electronic journals; Periodicals; 572.86
• DOI: 10.1002/edn3.138
• Languages: English
• ISSNs: 2637-4943

Abstract

Abstract: 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. Abstract : 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.