Skip to main content

Advertisement

Springer Nature Link
Log in

De novo characterization of Larimichthys crocea transcriptome for growth-/immune-related gene identification and massive microsatellite (SSR) marker development

  • Biology
  • Published:
Chinese Journal of Oceanology and Limnology Aims and scope Submit manuscript

Abstract

The large yellow croaker, Larimichthys crocea is an important marine fish in China with a high economic value. In the last decade, the stock conservation and aquaculture industry of this species have been facing severe challenges because of wild population collapse and degeneration of important economic traits. However, genes contributing to growth and immunity in L. crocea have not been thoroughly analyzed, and available molecular markers are still not sufficient for genetic resource management and molecular selection. In this work, we sequenced the transcriptome in L. crocea liver tissue with a Roche 454 sequencing platform and assembled the transcriptome into 93 801 transcripts. Of them, 38 856 transcripts were successfully annotated in nt, nr, Swiss-Prot, InterPro, COG, GO and KEGG databases. Based on the annotation information, 3 165 unigenes related to growth and immunity were identified. Additionally, a total of 6 391 simple sequence repeats (SSRs) were identified from the transcriptome, among which 4 498 SSRs had enough flanking regions to design primers for polymerase chain reactions (PCR). To access the polymorphism of these markers, 30 primer pairs were randomly selected for PCR amplification and validation in 30 individuals, and 12 primer pairs (40.0%) exhibited obvious length polymorphisms. This work applied RNA-Seq to assemble and analyze a live transcriptome in L. crocea. With gene annotation and sequence information, genes related to growth and immunity were identified and massive SSR markers were developed, providing valuable genetic resources for future gene functional analysis and selective breeding of L. crocea.

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

Access this article

Log in via an institution

Subscribe and save

Springer+
from $39.99 /Month
  • Starting from 10 chapters or articles per month
  • Access and download chapters and articles from more than 300k books and 2,500 journals
  • Cancel anytime
View plans

Buy Now

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

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

Explore related subjects

Discover the latest articles, books and news in related subjects, suggested using machine learning.

References

  • Altschul S F, Madden T L, Schäaffer A A, Zhang J H, Zhang Z, Miller W, Lipman D J. 1997. Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res earch, 25 (17): 3389–3402.

    Article  Google Scholar 

  • Appleby N, Edwards D, Batley J. 2009. New technologies for ultra-high throughput genotyping in plants. In: Gustafson J P, Langridge P, Somers D J eds. Plant Genomics. Humana Press, Totowa, NJ. 513: 19–39.

    Article  Google Scholar 

  • Botstein D, White R L, Skolnick M, Davis R W. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. The American Journal of Human Genetics, 32 (3): 314–331.

    Google Scholar 

  • Che R B, Sun Y Y, Sun D Q, Xu T J. 2014. Characterization of the miiuy croaker (Miichthys miiuy) transcriptome and development of immune-relevant genes and molecular markers. PLoS One, 9 (4): e94046.

    Article  Google Scholar 

  • Conesa A, Götz S, García-Gómez J M, Terol J, Talón M, Robles M. 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21 (18): 3674–3676.

    Article  Google Scholar 

  • Goliomytis M, Tsoureki D, Simitzis P E, Charismiadou M A, Hager-Theodorides A L, Deligeorgis S G. 2014. The effects of quercetin dietary supplementation on broiler growth performance, meat quality, and oxidative stability. Poultry Scienc e, 93 (8): 1957–1962.

    Article  Google Scholar 

  • Guo W, Wang Z Y, Wang Y L, Zhang Z P, Gui J F. 2005. Isolation and characterization of six microsatellite markers in the large yellow croaker (Pseudosciaena crocea Richardson). Molecular Ecology Notes, 5 (2): 369–371.

    Article  Google Scholar 

  • Hong W S, Zhang Q Y. 2003. Review of captive bred species and fry production of marine fish in China. Aquaculture, 227 (1-4): 305–318.

    Article  Google Scholar 

  • Kale S M, Pardeshi V C, Kadoo N Y, Ghorpade P B, Jana M M, Gupta V S. 2012. Development of genomic simple sequence repeat markers for linseed using next-generation sequencing technology. Molecular Breeding, 30 (1): 597–606.

    Article  Google Scholar 

  • Kalinowski S T, Taper M L, Marshall T C. 2007. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology, 16 (5): 1099–1106.

    Article  Google Scholar 

  • Kang J H, Park J Y, Jo H S. 2012. Rapid development of microsatellite markers with 454 pyrosequencing in a vulnerable fish, the mottled skate, Raja pulchra. International Journal of Molecular Sciences, 13 (12): 7199–7211.

    Article  Google Scholar 

  • Lalitha S. 2000. Primer premier 5. Biotech Software & Internet Report, 1 (6): 270–272.

    Article  Google Scholar 

  • Lapunzina P, López R O, Rodríguez-Laguna L, García-Miguel P, Martínez A R, Martínez-Glez V M. 2014. Impact of NGS in the medical sciences: genetic syndromes with an increased risk of developing cancer as an example of the use of new technologies. Genetics and Molecular Biology, 37 (1): 241–249.

    Article  Google Scholar 

  • Li M Y, Li Q H, Yang Z J, Hu G H, Li T, Chen X H, Ao J Q. 2014. Identification of cathepsin B from large yellow croaker (Pseudosciaena crocea) and its role in the processing of MHC class II-associated invariant chain. Developmental & Comparative Immunology, 45 (2): 313–320.

    Article  Google Scholar 

  • Li Y Y, Cai M Y, Wang Z Y, Guo W, Liu X D, Wang X Q, Ning Y. 2008. Microsatellite-centromere mapping in large yellow croaker (Pseudosciaena crocea) using gynogenetic diploid families. Marine Biotechnology, 10 (1): 83–90.

    Article  Google Scholar 

  • Liao X L, Cheng L, Xu P, Lu G Q, Wachholtz M, Sun X W, Chen S L. 2013. Transcriptome analysis of crucian carp (Carassius auratus), an important aquaculture and hypoxia-tolerant species. PLoS One, 8 (4): e62308.

    Article  Google Scholar 

  • Lü Z M, Li H M, Liu L Q, Cui W T, Hu X Y, Wang C F. 2013. Rapid development of microsatellite markers from the large yellow croaker (Pseudosciaena crocea) using next generation DNA sequencing technology. Biochemical Systematics and Ecology, 51: 314–319.

    Article  Google Scholar 

  • Luo W, Nie Z L, Zhan F B, Wei J, Wang W M, Gao Z X. 2012. Rapid development of microsatellite markers for the endangered fish Schizothorax biddulphi (Günther) using next generation sequencing and cross-species amplification. International Journal of Molecular Sciences, 13 (12): 14946–14955.

    Article  Google Scholar 

  • Mardis E R. 2008. Next-generation DNA sequencing methods. Annual Review of Genomics and Human Genetics, 9 (1): 387–402.

    Article  Google Scholar 

  • Moriya Y, Itoh M, Okuda S, Yoshizawa A C, Kanehisa M. 2007. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Research, 35 (S2): W182–W185.

    Article  Google Scholar 

  • Mu Y N, Ding F, Cui P, Ao J Q, Hu S N, Chen X H. 2010. Transcriptome and expression profiling analysis revealed changes of multiple signaling pathways involved in immunity in the large yellow croaker during Aeromonas hydrophila infection. BMC Genomics, 11 (1): 506.

    Article  Google Scholar 

  • Thiel T, Michalek W, Varshney R, Graner A. 2003. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theoretical and Applied Genetics, 106 (3): 411–422.

    Article  Google Scholar 

  • Tsai H Y, Hamilton A, Guy D R, Tinch A E, Bishop S C, Houston R D. 2015. The genetic architecture of growth and fillet traits in farmed Atlantic salmon (Salmo salar). BMC Genetics, 16 (1): 51.

    Article  Google Scholar 

  • Wang J J, Yu X M, Zhao K, Zhang Y G, Tong J G, Peng Z G. 2012. Microsatellite development for an endangered bream Megalobrama pellegrini (Teleostei, Cyprinidae) using 454 sequencing. International Journal of Molecular Sciences, 13 (12): 3009–3021.

    Article  Google Scholar 

  • Wang J, Ai Q H, Mai K S, Xu H G, Zuo R T. 2014. Dietary chromium polynicotinate enhanced growth performance, feed utilization, and resistance to Cryptocaryon irritans in juvenile large yellow croaker (Larmichthys crocea). Aquaculture, 432: 321–326.

    Article  Google Scholar 

  • Wang Z, Gerstein M, Snyder M. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics, 10 (1): 57–63.

    Article  Google Scholar 

  • Woffelman C. 1994. DNAMAN for Windows. Leiden University, The Netherland.

  • Xiao S J, Han Z F, Wang P P, Han F, Liu Y, Li J T, Wang Z Y. 2015. Functional marker detection and analysis on a comprehensive transcriptome of large yellow croaker by next generation sequencing. PLoS One, 10 (4): e0124432.

    Article  Google Scholar 

  • Xie F J, Zhang Z P, Lin P, Wang S H, Zou Z H, Wang Y L. 2009. Identification of immune responsible fibrinogen beta chain in the liver of large yellow croaker using a modified annealing control primer system. Fish & Shellfish Immunology, 27 (2): 202–209.

    Article  Google Scholar 

  • Yan L L, Qin Y J, Yan X W, Wang L N, Bi C L, Zhang J Y. 2015. Development of microsatellite markers in Ruditapes philipp i narum using next-generation sequencing. Acta Ecologica Sinica, 35 (5): 1573–1580. (in Chinese with English abstract)

    Google Scholar 

  • Yao C L, Kong P, Wang Z Y, Ji P F, Liu X D, Cai M Y, Han X Z. 2009. Molecular cloning and expression of MyD88 in large yellow croaker, Pseudosciaena crocea. Fish & Shellfish Immunology, 26 (2): 249–255.

    Article  Google Scholar 

  • Ye H, Wang X Q, Gao T X, Wang Z Y. 2010. EST-derived microsatellites in Pseudosciaena crocea and their applicability to related species. Acta Oceanologica Sinica, 29 (6): 83–91.

    Article  Google Scholar 

  • Ye J, Fang L, Zheng H K, Zhang Y, Chen J, Zhang Z J, Wang J, Li S T, Li R Q, Bolund L, Wang J. 2006. WEGO: a web tool for plotting GO annotations. Nucleic Acids Research, 34 (S2): W293–W297.

    Article  Google Scholar 

  • Yeh F C, Yang R C, Boyle T B J, Ye Z H, Mao J X. 1997. POPGENE, the User-Friendly Shareware for Population Genetic Analysis. Molecular and Biotechnology Center, University of Alberta, Edmonton, Alberta, Canada.

    Google Scholar 

  • Zdobnov E M, Apweiler R. 2001. InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics, 17 (9): 847–848.

    Article  Google Scholar 

  • Zerbino D R, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 18 (5): 821–829.

    Article  Google Scholar 

  • Zhang J, Ma W G, Song X M, Lin Q H, Gui J F, Mei J. 2014. Characterization and development of EST-SSR markers derived from transcriptome of yellow catfish. Molecules, 19 (10): 16402–16415.

    Article  Google Scholar 

  • Zhou P, Zhang Z P, Wang Y L, Zou Z H, Xie F J. 2010. EST analysis and identification of gonad-related genes from the normalized cDNA library of large yellow croaker, Larimichthys crocea. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 5 (2): 89–97.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Beijing, China

    Zhaofang Han  (韩兆方), Shijun Xiao  (肖世俊), Xiande Liu  (刘贤德), Yang Liu  (刘洋), Jiakai Li  (李佳凯), Yangjie Xie  (谢仰杰) & Zhiyong Wang  (王志勇)

  2. Fisheries College, Jimei University, Xiamen, 361021, China

    Zhaofang Han  (韩兆方), Shijun Xiao  (肖世俊), Xiande Liu  (刘贤德), Yang Liu  (刘洋), Jiakai Li  (李佳凯), Yangjie Xie  (谢仰杰) & Zhiyong Wang  (王志勇)

Authors
  1. Zhaofang Han  (韩兆方)
    View author publications

    Search author on:PubMed Google Scholar

  2. Shijun Xiao  (肖世俊)
    View author publications

    Search author on:PubMed Google Scholar

  3. Xiande Liu  (刘贤德)
    View author publications

    Search author on:PubMed Google Scholar

  4. Yang Liu  (刘洋)
    View author publications

    Search author on:PubMed Google Scholar

  5. Jiakai Li  (李佳凯)
    View author publications

    Search author on:PubMed Google Scholar

  6. Yangjie Xie  (谢仰杰)
    View author publications

    Search author on:PubMed Google Scholar

  7. Zhiyong Wang  (王志勇)
    View author publications

    Search author on:PubMed Google Scholar

Corresponding author

Correspondence to Zhiyong Wang  (王志勇).

Additional information

Supported by the National Natural Science Foundation of China (Nos. U1205122, 31172397), the Key Project of Agricultural Science and Technology of Fujian Province (No. 2011N5010), and the Foundation for Innovation Research Team of Jimei University (No. 2010A02)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Han, Z., Xiao, S., Liu, X. et al. De novo characterization of Larimichthys crocea transcriptome for growth-/immune-related gene identification and massive microsatellite (SSR) marker development. Chin. J. Ocean. Limnol. 35, 225–234 (2017). https://doi.org/10.1007/s00343-016-5288-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00343-016-5288-6

Keywords