Population genomics provides insights into the population structure and temperature-driven adaptation of Collichthys lucidus

A Possible More Precise Management Unit Delineation Based on Epigenomic Differentiation of a Long-Distance-Migratory Marine Fish Scomberomorus niphonius

Understanding population structure and adaptive history is critical for designing appropriate management regulations for fisheries and conserving adaptive potential for the future. However, this is not easy for marine fish, especially those with long-distance migration abilities. In this study, we constructed a high-quality reference genome for Japanese Spanish mackerel (Scomberomorus niphonius) and explored its population structure using whole genomic and epigenomic data. Despite the high depth of the sequence data, we failed to identify geographical genetic differentiation of Japanese Spanish mackerel across Chinese coastal waters. However, whole-genome bisulphite sequencing can classify this species into the Bohai-Yellow Sea group and the East China Sea-South China Sea group. Genes involved in embryonic skeletal system development, limb morphogenesis functions, and adult locomotory behaviour were differentially methylated in the southern (Zhanjiang, ZJ) and northern (Western Dalian, WDL) populations and may play important roles as drivers of population structure in Japanese Spanish mackerel. Our study not only provides the first reference genome of the Japanese Spanish mackerel and sheds light on population differentiation at the epigenomic level, but also provides a methylome-based framework for population structure analyses of marine fish with long-distance migration ability. These findings are expected to facilitate the development of scientific programmes for the successful conservation of marine fishery resources.

Determining population structure from k-mer frequencies

Background

Understanding population structure within species provides information on connections among different populations and how they evolve over time. This knowledge is important for studies ranging from evolutionary biology to large-scale variant-trait association studies. Current approaches to determining population structure include model-based approaches, statistical approaches, and distance-based ancestry inference approaches.

Methods

In this work, we identify population structure from DNA sequence data using an alignment-free approach. We use the frequencies of short DNA substrings from across the genome (k-mers) with principal component analysis (PCA). K-mer frequencies can be viewed as a summary statistic of a genome and have the advantage of being easily derived from a genome by counting the number of times a k-mer occurred in a sequence. In contrast, most population structure work employing PCA uses multi-locus genotype data (SNPs, microsatellites, or haplotypes). No genetic assumptions must be met to generate k-mers, whereas current population structure approaches often depend on several genetic assumptions and can require careful selection of ancestry informative markers to identify populations. We compare our k-mer based approach to population structure estimated using SNPs with both empirical and simulated data.

Results

In this work, we show that PCA is able to determine population structure just from the frequency of k-mers found in the genome. The application of PCA and a clustering algorithm to k-mer profiles of genomes provides an easy approach to detecting the number and composition of populations (clusters) present in the dataset. Using simulations, we show that results are at least comparable to population structure estimates using SNPs. When using human genomes from populations identified by the 1000 Genomes Project, the results are better than population structure estimates using SNPs from the same samples, and comparable to those found by a model-based approach using genetic markers from larger numbers of samples.

Conclusions

This study shows that PCA, together with the clustering algorithm, is able to detect population structure from k-mer frequencies and can separate samples of admixed and non-admixed origin. Using k-mer frequencies to determine population structure has the potential to avoid some challenges of existing methods and may even improve on estimates from small samples.

Assessment of future habitat suitability and ecological vulnerability of Collichthys at population and species level

BACKGROUND

Global warming and extreme weather events driven by greenhouse gas emissions are significantly impacting fish survival and reproduction, leading to dramatic consequences for marine biodiversity and ecosystem stability. Comparative analysis of closely related species from a phylogenetic perspective provides valuable insights for biodiversity conservation efforts. The study investigates the effects of climate change on the suitability of habitat and ecological vulnerability of two important sibling fishes, Collichthys lucidus and Collichthys niveatus, in the western Pacific.

RESULTS

This study found that the main driver of ecological niche differences between the two species is the niche contraction of C. niveatus. Predictions from species distribution models indicate that C. lucidus has a wider distribution and greater adaptability under future climate scenarios. Both species will experience significant habitat loss and heightened ecological vulnerability in the southern Yellow Sea. Additionally, the two populations of C. lucidus in the Yangtze River estuary display different levels of ecological vulnerability. These two species also exhibit distinct responses to environmental factors such as temperature and chlorophyll concentration.

CONCLUSION

The study's findings indicate that climate change will accelerate the population differentiation of C. lucidus and the habitat loss of C. niveatus. These results underscore the importance of prioritizing the southern Yellow Sea in future research and emphasize the necessity of developing adaptive conservation strategies for both species.

Comparative transcriptome analysis reveals sex bias in expression patterns of genes related to sex steroids and immunity in the skin of spinyhead croaker Collichthys lucidus

Fish skin is the first barrier against external invasion, and also an important interface for communication between males and females during reproduction. Nonetheless, sexual dimorphism in the physiology of fish skins is still poorly understood. Herein, transcriptomes of skin were comparatively analysed between males and females in spinyhead croaker, Collichthys lucidus. Totally, 170 differentially expressed genes (DEG) were detected, including 79 female-biased genes and 91 male-biased genes. Gene ontology (GO) annotation items of the DEGs were mainly enriched in biological process items (86.2%), including regulation of biological processes, responses to chemical and biological stimuli, transport and secretion, movement, immune response, tissue development, etc. In KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis, the male-biased genes were enriched in pathways including those related to immunity such as the TNF signalling pathway and IL-17 signalling pathway, whereas the female-biased genes were enriched in pathways including those related to female steroids such as ovarian steroidogenesis and oestrogen signalling pathway. In addition, odf3 was found to be a male-specific expression gene, being a candidate marker for phenotypic sex. Thus, the sexual difference in gene expression in fish skin in spawning season was uncovered by transcriptome analysis for the first time, providing new insights into sexual dimorphism in the physiology and functions of fish skin.

Small RNA sequencing reveals sex-related miRNAs in Collichthys lucidus

Collichthys lucidus (C. lucidus) is an economically important fish species, exhibiting sexual dimorphism in its growth rate. However, there is a lack of research on its underlying sex-related mechanisms. Therefore, small RNA sequencing was performed to better comprehend these sex-related molecular mechanisms. In total, 171 differentially expressed miRNAs (DE-miRNAs) were identified between the ovaries and testes. Functional enrichment analysis revealed that the target genes of DE-miRNAs were considerably enriched in the p53 signaling, PI3K–Akt signaling, and TGF-beta signaling pathways. In addition, sex-related miRNAs were identified, and the expression of miR-430c-3p and miR-430f-3p was specifically observed in the gonads compared with other organs and their expression was markedly upregulated in the testes relative to the ovaries. Bmp15 was a target of miR-430c-3p and was greatly expressed in the ovaries compared with the testes. Importantly, miR-430c-3p and bmp15 co-expressed in the ovaries and testes. This research provides the first detailed miRNA profiles for C. lucidus concerning sex, likely laying the basis for further studies on sex differentiation in C. lucidus.