Abstract
Large yellow croaker is an economically important fish in China and East Asia. Despite its economic importance, genome-wide adaptions of domesticated large yellow croaker are largely unknown. Here, we performed whole-genome resequencing of 198 individuals of large yellow croaker obtained in the sea or from farmers in Zhoushan or Ningde. Population genomics analyses revealed the genetic population structure of our samples, reflecting the living environment. Each effective population size is estimated to be declining over generations. Moreover, we identified genetically differentiated genomic regions between the sea-captured population in the Zhoushan Sea area and that of the Ningde Sea area or between the sea-captured population and the farmed population in either area. Gene ontology analyses revealed the gene groups under selective sweep for the adaptation to the domesticated environment. All these results suggest that individuals of the large yellow croaker populations show genomic signatures of adaptation to different living environments.
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Introduction
Larimichthys crocea, more commonly known as the large yellow croaker, is a sciaenid fish species. The ecological and genetic studies of large yellow croakers are important because they are economically important in Chinese coastal regions. Wild large yellow croaker was originally distributed from the southern Yellow Sea to the South China Sea1. However, wild stocks of the large yellow croaker have suffered severely from overfishing and are on the brink of extinction. Large yellow croaker was initially domesticated in the early 1980s. The annual yield of large yellow croaker aquaculture in China has been greater than that of any other domesticated marine fish2. After the initial artificial breeding attempts were successful in the 1980s, enhancement and release were also carried out. It has been reported that the first enhancement and release of 16,200 individuals took place in the Ningde Sea as early as 1987. This was followed by a rapid increase with the release of millions of large yellow croaker carried out annually3. It is hard to define whether a large yellow croaker captured in the sea is wild or domesticated based on the above background. Therefore, in this study, we defined the populations of our samples as sea-captured population and the farmed population.
The culture performance of farmed large yellow croaker populations has declined, mainly because of irrational artificial breeding, inbreeding, and blind introduction. They have caused the degradation of genetic resources and hybrid germplasm in the large yellow croaker4. Previous genetic studies of the population structure of large yellow croaker are available for both domesticated and sea-captured populations; however, these studies have been limited by putative neutral markers; e.g., microsatellites5 and single nucleotide polymorphism (SNP) loci6 including narrow regions of the genome7. This is not enough genetic data to describe the structure of the population. In this study, whole-genome resequencing of the 198 croakers were performed to obtain a better information of the critical uncertainties associated with population structure, genetic diversity and the analysis of mixed stocks across the domesticated and sea-captured populations of large yellow croaker.
As mentioned above, for each generation over the last decades, large yellow croaker has been exposed to directional selection for an increasing number of economically important traits, such as growth, anti-freeze capacity, desirable flesh characteristics and disease resistance8,9. Genetic improvement of strains of large yellow croaker for commercial aquaculture is in the process of establishment in China at the current time23. The reference genome sequence of large yellow croaker was downloaded from Ensembl Release 100 (http://www.ensembl.org), and indexed for BWA v0.7.16a-r118124. The filtered reads were aligned to the large yellow croaker reference genome by BWA-MEM with default parameters.
Variant calling, filtering and annotations
Variant calling was performed using samtools mpileup with default parameters25. To obtain high quality SNPs, only biallelic SNPs were analysed further. Variants with a call rate < 100% and minor allele frequency < 5% were filtered out. To perform variant annotations, the large yellow croaker genome annotation was downloaded from Ensembl Release 100. SNPs were annotated with SnpEff v4.226. Finally, we retained 6,302,244 SNPs as the initial dataset for the downstream analysis.
PCA and UMAP analysis
The SNP data in VCF format was converted to PLINK binary format using PLINK v1.90b4.527. PCA was then carried out with PLINK. UMAP was performed on the top five principal components with the R umap library.
Construction of the neighbour-joining tree
To construct a neighbour-joining phylogenetic tree of the samples, we calculated pairwise genome-wide identical-by-state (IBS) distances based on the SNPs using PLINK. Based on the pairwise distance matrix (1-IBS), a neighbour-joining tree was constructed using MEGA728.
Admixture analysis
The admixture analysis was performed with ADMIXTURE v1.3.0 software29. CV errors were estimated for each K-value. The K-value with the lowest CV error was regarded as optimal for estimating the level of admixture in each sample.
Analysis of effective population sizes
The effective population size was calculated for each group using SNeP v1.130. The parameter for maximum number of SNPs per chromosome was set at 10,000.
Fst analysis
Fixation index (Fst) values between populations were calculated for all SNPs using PLINK. Fst values more than 0.25 were regarded as significant. Also, average Fst values were calculated using a 40 kb window with 10 kb step. Average Fst values more than 0.05 were regarded as significant. Significant regions were merged and the genes in these regions were reported.
Gene ontology analysis
Gene ontology (GO) analysis was performed by Metascape31 with the following parameters: Min Overlap = 3, Min Enrichment = 1.5, P cut-off value = 0.05. Input gene lists were analysed as zebrafish. The p-values were adjusted for multiple comparisons.
Ethics approval and consent to participate
The farmed fish were reared in a nucleus farm named ‘Fisheries research institute of Zhoushan’ in Zhoushan City, Zhejiang Province, P.R. China and Fufa Aquaculture Co. Ltd in Ningde City, Fujian Province, P.R. China, respectively; The Zhoushan sea-captured individuals were caught by trawler around the Zhongjieshan islands (August–September 2019; latitude 30.198; longitude: 122.682); the Ningde sea-captured individuals were captured around **yang Island (November–December 2019; latitude: 26.508; longitude: 120.53); This study was approved by the Animal Care and Use Committee of Zhejiang Ocean University. All experimental protocols followed ARRIVE guidelines. All participants consented to publish the paper.
Consent for publication
Consent for publication is not applicable in this study, because there is not any individual person’s data.
Data availability
The raw reads were deposited in the DDBJ Sequence Read Archive (DRA) under accession number DRP007207. The scripts for the analyses in the current study are available at GitHub (https://github.com/ironman-tetsuo/Whole_genome_resequencing_of_Large_yellow_croaker).
Abbreviations
- Fst:
-
Fixation index
- GO:
-
Gene ontology
- IBS:
-
Identical-by-state
- PCA:
-
Principal component analysis
- SNP:
-
Single nucleotide polymorphism
- UMAP:
-
Uniform manifold approximation and projection
References
Wu, C. et al. The draft genome of the large yellow croaker reveals well-developed innate immunity. Nat. Commun. 5, 5227 (2014).
Ao, J. et al. Genome sequencing of the perciform fish Larimichthys crocea provides insights into molecular and genetic mechanisms of stress adaptation. PLoS Genet. 11, e1005118 (2015).
Liu, M. & de Mitcheson, Y. S. Profile of a fishery collapse: Why mariculture failed to save the large yellow croaker. Fish Fish. 9, 219–242 (2008).
Liu, X. et al. Estimated reproductive success of brooders and heritability of growth traits for large yellow croaker (Larimichthys crocea) using microsatellites. Chin. J. Oceanol. Limnol. 29, 990–995 (2011).
Wang, L., Shi, X., Su, Y., Meng, Z. & Lin, H. Loss of genetic diversity in the cultured stocks of the large yellow croaker, Larimichthys crocea, revealed by microsatellites. Int. J. Mol. Sci. 13, 5584–5597 (2012).
Jiang, L. et al. Population structure of large yellow croaker (Larimichthys crocea) revealed by single nucleotide polymorphisms. Biochem. Syst. Ecol. 63, 136–142 (2015).
Liu, Q. et al. Genetic variation and population genetic structure of the large yellow croaker (Larimichthys crocea) based on genome-wide single nucleotide polymorphisms in farmed and wild populations. Fish. Res. 232, 105718 (2020).
Wan, H.-F. et al. Genome-wide investigation of Dmrt gene family in large yellow croaker (Larimichthys crocea). Theriogenology 156, 272–282 (2020).
Zhou, Z. et al. Genome-Wide association study of growth and body-shape-related traits in large yellow croaker (Larimichthys crocea) using ddRAD sequencing. Mar. Biotechnol. (NY) 21, 655–670 (2019).
Dong, L., **ao, S., Wang, Q. & Wang, Z. Comparative analysis of the GBLUP, emBayesB, and GWAS algorithms to predict genetic values in large yellow croaker (Larimichthys crocea). BMC Genomics 17, 460 (2016).
Teletchea, F. & Fontaine, P. Levels of domestication in fish: Implications for the sustainable future of aquaculture. Fish Fish. 15, 181–195 (2014).
Glover, K. A., Solberg, M. F., Besnier, F. & Skaala, Ø. Cryptic introgression: Evidence that selection and plasticity mask the full phenotypic potential of domesticated Atlantic salmon in the wild. Sci. Rep. 8, 13966 (2018).
Pan, Z. et al. Selection signature in domesticated animals. Yi chuan Hered. 38, 1069–1080 (2016).
Lorenzen, K., Beveridge, M. C. M. & Mangel, M. Cultured fish: Integrative biology and management of domestication and interactions with wild fish. Biol. Rev. Camb. Philos. Soc. 87, 639–660 (2012).
Piétu, G. et al. Novel gene transcripts preferentially expressed in human muscles revealed by quantitative hybridization of a high density cDNA array. Genome Res. 6, 492–503 (1996).
Grindheim, A. K., Saraste, J. & Vedeler, A. Protein phosphorylation and its role in the regulation of Annexin A2 function. Biochim. Biophys. Acta Gen. Subj. 1861, 2515–2529 (2017).
Fursova, O. V., Pogorelko, G. V. & Tarasov, V. A. Identification of ICE2, a gene involved in cold acclimation which determines freezing tolerance in Arabidopsis thaliana. Gene 429, 98–103 (2009).
Chen, S., Su, Y. & Hong, W. Aquaculture of the large yellow croaker. in Aquaculture in China 297–308 (Wiley, 2018). https://doi.org/10.1002/9781119120759.ch3_10.
Ai, Q. et al. Effects of dietary vitamin C on survival, growth, and immunity of large yellow croaker, Pseudosciaena crocea. Aquaculture 261, 327–336 (2006).
Zhang, Q., Hong, W., Yang, S. & Liu, M. Review and prospects in the restocking of the large yellow croaker (Larimichthys crocea). Mod. Fish. Inf. 25, 3–5 (2010).
Gu, Z. et al. High level of dietary soybean oil affects the glucose and lipid metabolism in large yellow croaker Larimichthys crocea through the insulin-mediated PI3K/AKT signaling pathway. Comp. Biochem. Physiol. Part B Biochem. Mol. Biol. 231, 34–41 (2019).
Defour, A. et al. Annexin A2 links poor myofiber repair with inflammation and adipogenic replacement of the injured muscle. Hum. Mol. Genet. 26, 1979–1991 (2017).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Li, H. A statistical framework for SNP calling, mutation discovery, association map** and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987–2993 (2011).
Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6, 80–92 (2012).
Purcell, S. et al. PLINK: A tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).
Kumar, S., Stecher, G. & Tamura, K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870–1874 (2016).
Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).
Barbato, M., Orozco-terWengel, P., Tapio, M. & Bruford, M. W. SNeP: A tool to estimate trends in recent effective population size trajectories using genome-wide SNP data. Front. Genet. 6, 109 (2015).
Zhou, Y. et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat. Commun. 10, 1523 (2019).
Acknowledgements
**aolong Yin, **zhi Xu and Ying Pan in the laboratory participated in fish sampling and measuring the traits.
Funding
This study was supported by National Key R&D Program of China (2019YFD0900901), Zhoushan Large Yellow Croaker Innovation and Development Project (ZSLZ2019-004), Zhejiang Key Science and Technology (2020C02004) and Grant-in-Aid for Scientific Research (17H06399 to A.O., 20K21452 to A.O., 19H03420 to Y.O., and 19K22426 to Y.O.) from the Japan Society for the Promotion of Science.
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L.J. conceived this research and designed the experiment. L.J. and L.P. performed experiments. T.K., L.J., R.I., Y.O., A.O., C.C., P.W., I.T., Y.Y., X.Y., B.G., W.L., H.N.L., H.T., and H.P. analyzed data. T.K., L.J., Y.O., and A.O. wrote the manuscript. All authors read and approved the manuscript.
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Kon, T., Pei, L., Ichikawa, R. et al. Whole-genome resequencing of large yellow croaker (Larimichthys crocea) reveals the population structure and signatures of environmental adaptation. Sci Rep 11, 11235 (2021). https://doi.org/10.1038/s41598-021-90645-1
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DOI: https://doi.org/10.1038/s41598-021-90645-1
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