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

Author(s):Show less -

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

• Document type: Journal article
• Source: CONSERVATION GENETICS RESOURCES; v. 8, n. 3, p. 323-327, SEP 2016.
• Web of Science Citations: 9

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. (AU)

• FAPESP's process: 13/50741-7 - Diversity and conservation of Brazilian amphibians
• Grantee: Célio Fernando Baptista Haddad
• Support Opportunities: BIOTA-FAPESP Program - Thematic Grants