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

doi:10.1007/s12686-016-0550-y

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 journal › Article › peer-review

62 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 language	English (US)
Pages (from-to)	323-327
Number of pages	5
Journal	Conservation Genetics Resources
Volume	8
Issue number	3
DOIs	https://doi.org/10.1007/s12686-016-0550-y
State	Published - Sep 1 2016

All Science Journal Classification (ASJC) codes

Ecology, Evolution, Behavior and Systematics
Genetics

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10.1007/s12686-016-0550-y

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Vences, M., Lyra, M. L., Perl, R. G. B., Bletz, M. C., Stanković, D., Lopes, C. M., Jarek, M., Bhuju, S., Geffers, R., Haddad, C. F. B., & Steinfartz, S. (2016). Freshwater vertebrate metabarcoding on Illumina platforms using double-indexed primers of the mitochondrial 16S rRNA gene. Conservation Genetics Resources, 8(3), 323-327. https://doi.org/10.1007/s12686-016-0550-y

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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.",

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AU - Vences, Miguel

AU - Lyra, Mariana L.

AU - Perl, R. G.Bina

AU - Bletz, Molly C.

AU - Stanković, David

AU - Lopes, Carla Martins

AU - Jarek, Michael

AU - Bhuju, Sabin

AU - Geffers, Robert

AU - Haddad, Célio F.B.

AU - Steinfartz, Sebastian

PY - 2016/9/1

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N2 - 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.

AB - 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.

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

Abstract

All Science Journal Classification (ASJC) codes

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