DNA barcoding and phylogenetics of two anadromous herring (Tenualosa spp.) from the Eastern Coast of Sumatra using the mitochondrial coi gene

¹ Department of Biology Education, Labuhanbatu University, Rantauprapat, Indonesia
² Doctoral Programme in Marine Science, Riau University, Pekanbaru, Indonesia
³ Master’s Programme in Marine Science, Riau University, Pekanbaru, Indonesia
⁴ Department of Biology, Faculty of Mathematics and Natural Sciences, Riau University, Pekanbaru, Indonesia

^* Corresponding author: This email address is being protected from spambots. You need JavaScript enabled to view it.

Abstract

This study aimed to use DNA barcoding to identify two herring species caught in the waters off the east coast of Sumatra. DNA extraction was performed using the 10% Chelex protocol, followed by PCR amplification using the FISH F1/R1 primer set. DNA amplification yielded fragments of 687 bp for samples LB01 and NL02, and 655 bp for samples SB01 and SM01. After trimming low-quality ends and multiple sequence alignment, a 569 bp consensus fragment was used for all downstream analyses. Nucleotide base composition and genetic distances (Kimura 2-parameter model) were calculated using MEGA XII, and phylogenetic trees were reconstructed using the Neighbour-Joining (NJ) method with 1,000 bootstrap replicates. The nucleotide base composition of samples LB01 and NL02 was AT (51.14%) GC (48.86%), while samples SM01 and SB01 were AT (53.43%) GC (46.57%). Genetic distance analysis based on the COI gene showed that samples SM01 and SB01 with Tenualosa macrura from Malaysian waters ranged from 0.002 to 0.000 (0.0%–0.2%), while samples LB01 and NL02 had genetic distances with Tenualosa ilisha from Vietnamese and Indian waters ranging from 0.018 to 0.000 (0%–1.8%). Phylogenetic tree reconstruction confirmed that samples SB01 and SM01 were T. macrura, while samples LB01 and NL02 were T. ilisha, as each sample was in the same clade as the existing reference sequence.