Restricted Gene Flow for Gadus macrocephalus from Yellow Sea Based on Microsatellite Markers: Geographic Block of Tsushima Current

Whole-genome survey and phylogenetic analysis of Gadus macrocephalus

Gadus macrocephalus (Pacific cod) is an economically important species on the northern coast of the Pacific. Although numerous studies on G. macrocephalus exist, there are few reports on its genomic data. Here, we used whole-genome sequencing data to elucidate the genomic characteristics and phylogenetic relationship of G. macrocephalus. From the 19-mer frequency distribution, the genome size was estimated to be 658.22 Mb. The heterozygosity, repetitive sequence content and GC content were approximately 0.62%, 27.50% and 44.73%, respectively. The draft genome sequences were initially assembled, yielding a total of 500,760 scaffolds (N50 = 3565 bp). A total of 789,860 microsatellite motifs were identified from the genomic data, and dinucleotide repeat was the most dominant simple sequence repeat motif. As a byproduct of whole-genome sequencing, the mitochondrial genome was assembled to investigate the evolutionary relationships between G. macrocephalus and its relatives. On the basis of 13 protein-coding gene sequences of the mitochondrial genome of Gadidae species, the maximum likelihood phylogenetic tree showed that complicated relationships and divergence times among Gadidae species. Demographic history analysis revealed changes in the G. macrocephalus population during the Pleistocene by using the pairwise sequentially Markovian coalescent model. These findings supplement the genomic data of G. macrocephalus, and make a valuable contribution to the whole-genome studies on G. macrocephalus.

Genetic signatures of polymorphic microsatellite loci in the Ambiguous silver pomfret, Pampusargenteus (Teleostei, Stromateidae)

Pampusargenteus is a broadly exploited pelagic fish species, commonly misidentified as Pampusechinogaster. Genetic variation and population structure in Pampusargenteus was studied based on seven microsatellite loci. The observed high average allele number, heterozygosity values, and polymorphism information content of P.argenteus suggested high genetic diversity. No population genetic differentiation was detected based on the results of pairwise F_st, three-dimensional factorial correspondence analysis (3D-FCA) and STRUCTURE analysis, which implied continuous gene flow. Wilcoxon signed rank tests did not indicate significant heterozygosity excess, and recent genetic bottleneck events were not detected. Coupled with previous mitochondrial DNA results, the findings presented here indicate that high gene flow characterizes the current phylogeographic pattern of the species.

Genetic signatures of polymorphic microsatellite loci in the Ambiguous silver pomfret, Pampus argenteus (Teleostei, Stromateidae)

Pampusargenteus is a broadly exploited pelagic fish species, commonly misidentified as Pampusechinogaster. Genetic variation and population structure in Pampusargenteus was studied based on seven microsatellite loci. The observed high average allele number, heterozygosity values, and polymorphism information content of P.argenteus suggested high genetic diversity. No population genetic differentiation was detected based on the results of pairwise Fst, three-dimensional factorial correspondence analysis (3D-FCA) and STRUCTURE analysis, which implied continuous gene flow. Wilcoxon signed rank tests did not indicate significant heterozygosity excess, and recent genetic bottleneck events were not detected. Coupled with previous mitochondrial DNA results, the findings presented here indicate that high gene flow characterizes the current phylogeographic pattern of the species.