DNAbarcode reference data for the Korean herpetofauna and their applications

Abstract

Recently, amphibians and reptiles have drawn attention because of declines in species and populations caused mainly by habitat loss, overexploitation and climate change. This study constructed a DNA barcode database for the Korean herpetofauna, including all the recorded amphibians and 68% of the recorded reptiles, to provide a useful, standardized tool for species identification in monitoring and management. A total of 103 individuals from 18 amphibian and 17 reptile species were used to generate barcode sequences using partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene and to compare it with other suggested barcode loci. Comparing 16S rRNA, cytochrome b (Cytb) and COI for amphibians and 12S rRNA, Cytb and COI for reptiles, our results revealed that COI is better than the other markers in terms of a high level of sequence variation without length variation and moderate amplification success. Although the COI marker had no clear barcoding gap because of the high level of intraspecific variation, all of the analysed individuals from the same species clustered together in a neighbour-joining tree. High intraspecific variation suggests the possibility of cryptic species. Finally, using this database, confiscated snakes were identified as Elaphe schrenckii, designated as endangered in Korea and a food contaminant was identified as the lizard Takydromus amurensis.

Phylogenetic analysis of colubrid snakes based on 12S rDNA reveals distinct lineages of Dendrelaphis pictus (Gmelin, 1789) populations in Sumatra and Java

“…Within Dendrelaphis, p-distance values ranged from 5.9% to 11.8% (mean±sd; 6.36 ± 3.79) ( Table 2). The intraspecies threshold for 12S/16S was previously set at 3% (Jeong et al 2013). Based on our result, we propose that 12S threshold for intra-species is 3.7%, inter-species is 11.8% and inter-generic is 16%.…”

“…Genomic DNA was isolated from muscle tissue using a QIAGEN DNA isolation kit following the manufacturer's instruction. A fragment of the 12S gene was amplified by polymerase chain reaction (PCR) using the primers 12S268 (5'-GTGCCAGCGACCGCGGTTACACG-3') and 12S916 (5'-GTACGCTTACCATGTTACGACTTGCCCTG-3') (Jeong et al 2013). The PCR amplification was performed in 40 μL reaction volumes with 5 min denaturation at 94º C, followed by 35 cycles of 94º C for 30 s, 56,5º C for 1 min, and 72º C for 1 min, and then by post elongation at 72º C for 10 min.…”

Biometric and genetic differences in kelabau (Osteochilus spp.) as revealed using cytochrome c oxidase subunit 1

“…The common mitochondrial (mt) DNA region used as a barcode in protists and animals comprises 600 bp. In addition, CO1 is one of the genetic markers used to identify insects, birds, primates and fish to species [11][12][13] . MtDNA CO1 is selected as a target in DNA barcoding because it is a highly conserved site.…”

Comprehensive DNA barcoding of the herpetofauna of Germany

“…In reptiles and even more in amphibians, DNA barcoding using COI remained difficult (Vences et al 2005a, b) until specific primers and amplification protocols were developed (Che et al 2012;Nagy et al 2012;Xia et al 2012). Therefore, most larger DNA barcoding studies of these groups were undertaken only very recently, such as the worldwide initiative of the Cold Code (Murphy et al 2013) and other initiatives with regional ranges Hawlitschek et al 2013;Jeong et al 2013;Perl et al 2014).…”