Comparison of D-loop and Cytochrome b Sequences Among Different Coilia Species and Their Potential Use in Analysis for the Identification of Species at Early Life Stages

Abstract:

Based on 1022 bp and 1322 bp sequences, partial nucleotide sequences of Cyt b and D-loop segments of mtDNA were analyzed for Coilia nasus, C. nasus taihuensis, C. grayii, and C. mystus to develop a reference dataset for species identification in the genus Coilia. The genetic distances were 0.00360±0.00083 and 0.00378±0.00082 between C. nasus and C. nasus taihuensis, 0.12146±0.01106 and 0.10753±0.01076 between C. mystus and C. nasus, 0.12207±0.01111 and 0.10674±0.01074 between C. mystus and C. nasus taihuensis, 0.03418±0.00561 and 0.05267±0.00686 between C. nasus and C. grayii, 0.03506±0.00568 and 0.05287±0.00698 between C. nasus taihuensis and C. grayii, as well as 0.11585± 0.01109 and 0.11233±0.01114 between C. grayii and C. mystus, respectively. Based on the sequences of the Cyt b gene and D-loop and the neighbor-joining (NJ) molecular dendrogram using Kimura 2-parameters, individuals of C. nasus and C. nasus taihuensis were combined in a cluster while C mystus and C. grayii formed another two clusters. First, based on sampling sites, the identities of the unknown larvae from the estuary of the Yangtze River and unknown juveniles from the Taihu Lake could be deduced preliminarily as C. nasus and C. nasus taihuensis, respectively. Then, nucleotide sequences of Cyt b and D-loop of larvae and eggs of genus Coilia were analyzed and compared with the reference established above. Genetic distance ranged from 0.0024 to 0.0032 and 0.0025 to 0.0082, respectively, within the larva and egg individuals collected from different places. The NJ molecular dendrogram showed that all the unknown larvae, the eggs of C. nasus, adult C. nasus, and C. nasus taihuensis clustered together. In contrast, individual eggs of C. mystus and adult C. mystus formed a separate cluster. Thus, Cyt b and D-loop sequence analysis could be used to identify unknown Coilia nasus, C. grayii, and C. mystus at early life stages, but could not effectively be used to identify unknown individuals at early life stages between C. nasus and C. nasus taihuensis.