Skip to main content
SpringerLink
Log in

Chromosome-level Genome Assembly of Acanthopagrus latus Provides Insights into Salinity Stress Adaptation of Sparidae

  • Short Communication
  • Published:
Marine Biotechnology Aims and scope Submit manuscript

Abstract

The yellowfin seabream, Acanthopagrus latus, is widely distributed throughout the Indo-West Pacific. This species, as a euryhaline Sparidae fish, inhabits in coastal environments with large and frequent salinity fluctuation. So the A. latus can be considered as an ideal species for elucidating the evolutionary mechanism of salinity stress adaption on teleost fish species. Here, a chromosome-scale assembly of A. latus was obtained with PacBio and Hi-C hybrid sequencing strategy. The final assembly genome of A. latus is 685.14 Mbp. The values of contig N50 and scaffold N50 are 14.88 Mbp and 30.72 Mbp, respectively. 29,227 genes were successfully predicted for A. latus in total. Then, the comparative genomics and phylogenetic analysis were employed for investigating the different osmoregulation strategies of salinity stress adaption on multiple whole genome scale of Sparidae species. The highly accurate chromosomal information provides the important genome resources for understanding the osmoregulation evolutionary pattern of the euryhaline Sparidae species.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Data Availability

All sequencing data, including Illumina short reads, PacBio long reads, Hi-C reads were submitted to the NCBI Sequence Read Archive (SRA) database under Bioproject accession PRJEB40702. The assembled genome was deposited at DDBJ/ENA/GenBank under the accession GCA_904848185.1.

References

  • Burton JN, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J (2013) Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat Biotechnol 31:1119–1125

    Article  CAS  Google Scholar 

  • De Bie T, Cristianini N, Demuth JP, Hahn MWJB (2006) CAFE: a computational tool for the study of gene family evolution. Bioinformatics 22:1269–1271

    Article  Google Scholar 

  • Dos-Santos RC, Monteiro L, Paes-Leme B, Lustrino D, Antunes-Rodrigues J, Mecawi AS, Reis LC (2017) Central angiotensin-(1–7) increases osmotic thirst. Exp Physiol 102:1397–1404

    Article  Google Scholar 

  • Jiahan L, Lisha L (1989) Studies on karyotype of Sparus latus Houttuyn. J Oceanogr Taiwan Strait 8:162–166

    Google Scholar 

  • Krzywinski MI, Schein JE, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19:1639–1645

    Article  CAS  Google Scholar 

  • Kultz D (2015) Physiological mechanisms used by fish to cope with salinity stress. J Exp Biol 218:1907–1914

    Article  Google Scholar 

  • Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL (2004). Versatile and open software for comparing large genomes. Genome Biol 5(2):1–9

  • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760

    Article  CAS  Google Scholar 

  • Lin G, Zheng M, Gao D, Li S, Fang W, Huang J, Xie J, Liu J, Liu Y, Li Z, Lu J (2020a) Hypoosmotic stress induced tissue-specific immune responses of yellowfin seabream (Acanthopagrus latus) revealed by transcriptomic analysis. Fish Shellfish Immunol 99:473–482

    Article  CAS  Google Scholar 

  • Lin G, Zheng M, Li S, Xie J, Fang W, Gao D, Huang J, Lu J (2020b). Response of gut microbiota and immune function to hypoosmotic stress in the yellowfin seabream (Acanthopagrus latus). Sci Total Environ 745:140976

  • Liu H, Chen C, Lv M, Liu N, Hu Y, Zhang H, Enbody ED, Gao Z, Andersson L, Wang WJMB, Evolution, (2021) A chromosome-level assembly of blunt snout bream (Megalobrama amblycephala) genome reveals an expansion of olfactory receptor genes in freshwater fish. Mol Biol Evol 38:4238–4251

    Article  Google Scholar 

  • Loretz CA, Pollina C, Hyodo S, Takei YJG, Endocrinology C (2009) Extracellular calcium-sensing receptor distribution in osmoregulatory and endocrine tissues of the tilapia. Gen Comp Endocrinol 161:216–228

    Article  CAS  Google Scholar 

  • Lv L-Y, Liang X-F, He SJG (2019) Genome-wide identification and characterization of olfactory receptor genes in Chinese perch, Siniperca Chuatsi. Genes 10:178

    Article  CAS  Google Scholar 

  • Marçais G, Kingsford C (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27:764–770

    Article  Google Scholar 

  • Nelson JS, Grande TC, Wilson MV (2016) Fishes of the World: John Wiley & Sons

  • Petitjean Q, Jean S, Gandar A, Cote J, Laffaille P, Jacquin L (2019) Stress responses in fish: from molecular to evolutionary processes. Sci Total Environ 684:371–380

    Article  CAS  Google Scholar 

  • Schultz ET, Mccormick SDJFP (2012) Euryhalinity in an evolutionary context. Fish Physiol 32:477–533

    Article  Google Scholar 

  • Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210–3212

    Article  Google Scholar 

  • Verri T, Terova G, Romano A, Barca A, Pisani P, Storelli C, Saroglia M (2012) The solute carrier (SLC) family series in teleost fish. Funct Genom Aquaculture 219–320

  • Wang H, Chen L, Dong C, Chen B, Li B, Li X, Xu PJG (2021) Genome-wide identification and characterization of olfactory receptor genes in common carp (Cyprinus carpio). Gene 777:145468

  • Yu G, Wang LG, Han Y, He QY (2012). clusterProfiler: an R package for comparing biological themes among gene clusters. Omics J Integr Biol 16(5):284–287

Download references

Funding

This work was supported by the National Natural Science Foundation of China [No. 91858208], [No. 31902427], R&D Project for Jinwan Yellowfin Seabream Breeding System Construction [No. K20-42000–018], Science and Technology Project of Zhanjiang [No. 2019A03011], and Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) [No. 311020005].

Author information

Authors and Affiliations

  1. School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China

    Jianguo Lu, Dong Gao, Wenyu Fang, Genmei Lin & Jingui Xie

  2. Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519080, China

    Jianguo Lu

  3. Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, 510275, China

    Jianguo Lu

  4. Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, China

    Jianguo Lu

  5. Wellcome Sanger Institute, Cambridge, UK

    Ying Sims, Joanna Collins, James Torrance & Kerstin Howe

  6. School of Computer Science, Nankai University, Tianjin, China

    Jian Liu

Authors
  1. Jianguo Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Dong Gao
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ying Sims
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Wenyu Fang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Joanna Collins
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. James Torrance
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Genmei Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Jingui Xie
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Jian Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Kerstin Howe
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

J. L. and D. G. designed the experiments. W. F., J. X., and G. L. collected the samples. D. G., W. F., Y. S., J. C., J. T., G. L., J. X., and K. H. performed the experiments and analyzed the data. D. G. and J. L. wrote the manuscript, D. G. and J. L. revised the manuscript. All authors read and approved the final version of the manuscript.

Corresponding author

Correspondence to Jianguo Lu.

Ethics declarations

Ethics Approval and Consent to Participate

All experimental procedures in our study with A. latus were approved by the Animal Care and Use Committee of the School of Marine Sciences, Sun Yat-Sen University.

Competing Interests

The authors declare no competing interests.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Lu, J., Gao, D., Sims, Y. et al. Chromosome-level Genome Assembly of Acanthopagrus latus Provides Insights into Salinity Stress Adaptation of Sparidae. Mar Biotechnol 24, 655–660 (2022). https://doi.org/10.1007/s10126-022-10119-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10126-022-10119-x

Keywords

Search

Navigation