Mitochondrial DNA sequencing of a wet-collection syntype demonstrates the importance of type material as genetic resource for lantern shark taxonomy (Chondrichthyes: Etmopteridae).

Nicolas Straube,Michaela Preick,Gavin J P Naylor,Michael Hofreiter

doi:10.1098/rsos.210474

Abstract

After initial detection of target archival DNA of a 116-year-old syntype specimen of the smooth lantern shark, Etmopterus pusillus, in a single-stranded DNA library, we shotgun-sequenced additional 9 million reads from this same DNA library. Sequencing reads were used for extracting mitochondrial sequence information for analyses of mitochondrial DNA characteristics and reconstruction of the mitochondrial genome. The archival DNA is highly fragmented. A total of 4599 mitochondrial reads were available for the genome reconstruction using an iterative mapping approach. The resulting genome sequence has 12 times coverage and a length of 16 741 bp. All 37 vertebrate mitochondrial loci plus the control region were identified and annotated. The mitochondrial NADH2 gene was subsequently used to place the syntype haplotype in a network comprising multiple E. pusillus samples from various distant localities as well as sequences from a morphological similar species, the shortfin smooth lantern shark Etmopterus joungi. Results confirm the almost global distribution of E. pusillus and suggest E. joungi to be a junior synonym of E. pusillus. As mitochondrial DNA often represents the only available reference information in non-model organisms, this study illustrates the importance of mitochondrial DNA from an aged, wet collection type specimen for taxonomy.

Highlights

Type material deposited in museum collections is generally essential for taxonomic purposes
Recent methodological advances show that archival DNA from museum wet collection specimens is widely accessible by the application of ancient DNA methods (e.g. [1,2,3,4])
Assuming a total mitochondrial genome sequence length of 16 729 bases, we estimated that a maximum of 13 940 833 reads would need to be sequenced for a minimum fivefold coverage of the mitochondrial genome given the preliminary data

Summary

Introduction

Type material deposited in museum collections is generally essential for taxonomic purposes. Especially in wet collections, damages DNA to a degree that these samples are rarely available for standard DNA sequencing analysis. Recent methodological advances show that archival DNA from museum wet collection specimens is widely accessible by the application of ancient DNA methods Specimen preservation in 75% ethanol commonly causes DNA sequence damage. Our recent increase in taxonomic knowledge partially fuelled by DNA barcoding [5], for example, often results in pending taxonomic questions, where type material DNA sequence information is crucial to answer these. Mitochondrial DNA is of major interest due to growing reference databases as a source for species delimitation based on DNA sequence differences

Methods

Results

Conclusion