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Use of RN ase H‐dependent PCR for discrimination and detection of closely related species from environmental DNA
Author(s) -
Rodgers Torrey W.,
Olson John R.,
Mock Karen E.
Publication year - 2019
Publication title -
methods in ecology and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.425
H-Index - 105
ISSN - 2041-210X
DOI - 10.1111/2041-210x.13187
Subject(s) - taqman , environmental dna , biology , real time polymerase chain reaction , dna , polymerase chain reaction , microbiology and biotechnology , genetics , gene , ecology , biodiversity
Species‐specific, probe‐based quantitative PCR (qPCR) assays are now commonly used to detect aquatic species from environmental DNA . However, probe‐based qPCR alone does not always provide the specificity needed to distinguish closely related, congeneric species, which may result in amplification of non‐target DNA , causing false positives from eDNA samples. Here, we developed species‐specific qPCR assays using RN ase H‐dependent PCR (rh PCR ) for detecting closely related fish species from environmental DNA . We found that rh PCR allowed us to achieve specificity that was not possible with TaqMan ® qPCR alone, and we used these assays for species detection from eDNA samples. Use of rh PCR will allow species‐specific detection from environmental DNA for a broad range of species including those that occur in sympatry with other closely related, congeneric species, which has not always been possible with probe‐based qPCR alone.