Development and validation of a TaqMan-based qPCR assay for reliable detection of invasive sailfin catfishes (Pterygoplichthys spp.) through measurements of environmental DNA

Abstract

Sailfin catfishes (Pterygoplichthys spp.) are a group of fishes introduced to several freshwater habitats across the globe. Sailfin catfishes are a hard-armoured fish with no economic importance as a food species. These catfishes have been reported to be affecting the growth of several economically valuable species that are native to different freshwater ecosystems. In this manuscript, we developed a TaqMan-based assay targeting the mitochondrial cytochrome c oxidase subunit 1 (COX1) gene, to specifically detect the presence of catfishes by environmental DNA (eDNA) measurements. The developed assay was screened against 16 species of fish and mussel that co-occur in the habitats along with sailfin catfishes, and the qPCR reaction did not have any non-target amplifications. The assay was further validated under laboratory conditions by measuring eDNA from tanks having different biomass of catfishes (1 and 0.5 g L−1), and the copy number of the amplified product was directly proportional to the biomass maintained in the tanks. Overall, the study provides a robust molecular tool based on eDNA measurements to facilitate detection of invasive sailfin catfishes and, in turn, contributes towards the management of the invaded habitats.