Genome-wide analyses of mitochondrial DNA barcodes of Labeo chrysophekadion in Lower Mekong River basin

Abstract

Background: The Labeo chrysophekadion is an economically important cyprinid that migrates short distances seasonally between the mainstream and floodplains of the Mekong River. However, wild populations are threatened by fishing pressure and environmental impacts. Genome-wide studies have been widely applied in molecular ecology to inform fisheries management. This study aimed to assemble and annotate the complete mitogenome from whole-genome restriction site-associated DNA sequencing data and use the assembled mitogenome to identify aligned mitogenome segments and investigate the population genetics of L. chrysophekadion in the lower Mekong Basin (LMB).

Methods: A total of 255 individuals were collected in the lower Mekong Basin. There were six sites on the Mekong mainstem (Paksan, Pakse-Lao PDR, Ubon Ratchathani-Thailand, Kratié-Cambodia, Dong Thap, An Giang-Vietnam), one site at the confluence of the Mekong and 3S Rivers (Stung Treng-Cambodia), and two sites on tributaries in the LMB: the Khan River, Luang Prabang, Lao PDR, and the Chi River, Roi Et, Thailand. High-quality sequence reads were identified and used to assemble, annotate, and visualize the mitogenome using the Mitoz toolkit. Following the RADbarcoder pipeline, aligned DNA segments were identified and used to estimate the genetic diversity and haplotype network.

Results: The complete mitogenome of L. chrysophekadion was 16,600 base pairs in length and exhibited a high identity of 99.8% to a previously published genome (accession number AP011199) derived from an individual fish in Kandal, Cambodia. This genome comprised 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region gene. When mapping individual sequence reads to the mitogenome, 757 bp were identified as the aligned mitogenome segment data. A total of 49 haplotypes from 247 individuals were detected, with a haplotype diversity of 0.849 (±0.014) and nucleotide diversity of 0.005 (±0.0008). High connectivity was detected among the sample populations, with three dominant common haplotypes shared among 8-9 populations. Additionally, nine haplotypes were shared by at least two populations, while 35 private haplotypes were distributed among all examined populations. This significant finding provides an overview of population structure, serving as a scientific basis for the conservation and management of aquatic resources.

Conclusion: This study provides information on the mitogenomic characteristics and spatial genetics of L. chrysophekadion in the LMB.