Freshwater vertebrate metabarcoding on Illumina platforms using double-indexed primers of the mitochondrial 16S rRNA gene

Miguel Vences, Mariana L. Lyra, R. G.Bina Perl, Molly C. Bletz, David Stanković, Carla Martins Lopes, Michael Jarek, Sabin Bhuju, Robert Geffers, Célio F.B. Haddad, Sebastian Steinfartz

Research output: Contribution to journalArticlepeer-review

53 Scopus citations

Abstract

Metabarcoding is a promising tool for biodiversity inventories and other applications in conservation genetics. We developed a new pair of primers for efficient and affordable high-throughput analysis of a 250 base pair stretch of DNA from the mitochondrial 16S rRNA gene of vertebrates, especially amphibians and fishes. By adapting a double-indexed protocol for Illumina platforms, our approach allows pooling of hundreds of samples in a single sequencing run. We obtained high detection rates of 82–93 % for fish in two German streams, 70 % for mock mixes of DNA from amphibians and fishes, and could distinguish multiple gene copies in amphibians, probably caused by nuclear-mitochondrial transposed DNA or heteroplasmy.

Original languageEnglish (US)
Pages (from-to)323-327
Number of pages5
JournalConservation Genetics Resources
Volume8
Issue number3
DOIs
StatePublished - Sep 1 2016

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

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