A: Genome-wide Hi-C heatmap of
K. punctatus
. B: Genome characteristics of
K. punctatus
: a) genomic information; b) GC content distribution; c) second-generation read depth distribution; d) third-generation read depth distribution; e) outer circle shows homozygous SNP distribution, inner circle shows heterozygous SNP distribution; f) outer circle shows homozygous InDel distribution, inner circle shows heterozygous InDel distribution; g) outer ring is single-copy BUSCO, inner ring shows duplicated BUSCOs. C: Estimated divergence time of 11 species.
The mitochondrial genome provides important information for phylogenetic analysis and an understanding of evolutionary origin. In this study, the mitochondrial genomes of Ilisha elongata and Setipinna tenuifilis were sequenced, which are typical circular vertebrate mitochondrial genomes composed of 16,770 and 16,805 bp, respectively. The mitogenomes of I. elongata and S. tenuifilis include 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA), two ribosomal RNA (rRNA) genes and one control region (CR). Both two species' genome compositions were highly A + T biased and exhibited positive AT-skews and negative GC-skews. The genetic distance and Ka/Ks ratio analyses indicated that 13 PCGs were affected by purifying selection and the selection pressures were different from certain deep-sea fishes, which were most likely due to the difference in their living environment. Results of phylogenetic analysis support close relationships among Chirocentridae, Denticipitidae, Clupeidae, Engraulidae and Pristigasteridae based on the nucleotide and amino acid sequences of 13 PCGs. Within Clupeoidei, I. elongata and S. tenuifilis were most closely related to the family Pristigasteridae and Engraulidae, respectively. These results will help to better understand the evolutionary position of Clupeiformes and provide a reference for further phylogenetic research on Clupeiformes species.
Uncovering the fine-scale genetic structure has been long recognized as a key component in policymaking for the management of marine fisheries. Many species of Clupeiformes have suffered declines owing to overexploitation and habitat destruction. In this study, twenty polymorphic microsatellite markers were used to evaluate the genetic diversity and population structure of Konosirus punctatus, a pelagic fish of economic and ecological importance in the Northwestern Pacific Ocean. Although most of the variance occurred within individuals, significant differentiation (FST = 0.00384~0.19346) was shown in wild K. punctatus populations. Population structure analyses revealed five genetically divergent clades in K. punctatus in the Northwestern Pacific. Significant isolation by distance and one potentially outlier locus were revealed in K. punctatus, suggesting that interactions between historical climate shifts and environmental factors may contribute to the present-day genetic architecture. In summary, these results provided new perspectives on the population genetic structure of K. punctatus, facilitating the development of effective management strategies for this species.
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