Genome sequencing of the perciform fish Larimichthys crocea provides insights into molecular and genetic mechanisms of stress adaptation

PLoS Genet. 2015 Apr 2;11(4):e1005118. doi: 10.1371/journal.pgen.1005118. eCollection 2015 Apr.


The large yellow croaker Larimichthys crocea (L. crocea) is one of the most economically important marine fish in China and East Asian countries. It also exhibits peculiar behavioral and physiological characteristics, especially sensitive to various environmental stresses, such as hypoxia and air exposure. These traits may render L. crocea a good model for investigating the response mechanisms to environmental stress. To understand the molecular and genetic mechanisms underlying the adaptation and response of L. crocea to environmental stress, we sequenced and assembled the genome of L. crocea using a bacterial artificial chromosome and whole-genome shotgun hierarchical strategy. The final genome assembly was 679 Mb, with a contig N50 of 63.11 kb and a scaffold N50 of 1.03 Mb, containing 25,401 protein-coding genes. Gene families underlying adaptive behaviours, such as vision-related crystallins, olfactory receptors, and auditory sense-related genes, were significantly expanded in the genome of L. crocea relative to those of other vertebrates. Transcriptome analyses of the hypoxia-exposed L. crocea brain revealed new aspects of neuro-endocrine-immune/metabolism regulatory networks that may help the fish to avoid cerebral inflammatory injury and maintain energy balance under hypoxia. Proteomics data demonstrate that skin mucus of the air-exposed L. crocea had a complex composition, with an unexpectedly high number of proteins (3,209), suggesting its multiple protective mechanisms involved in antioxidant functions, oxygen transport, immune defence, and osmotic and ionic regulation. Our results reveal the molecular and genetic basis of fish adaptation and response to hypoxia and air exposure. The data generated by this study will provide valuable resources for the genetic improvement of stress resistance and yield potential in L. crocea.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptation, Physiological*
  • Animals
  • Fish Proteins / genetics*
  • Fish Proteins / metabolism
  • Genome*
  • Osmotic Pressure*
  • Oxidative Stress*
  • Perciformes / genetics*
  • Perciformes / metabolism
  • Transcriptome


  • Fish Proteins

Associated data

  • GEO/GSE57608

Grants and funding

The work is supported by grants from the Nation ‘863’ Project (2012AA092202), National Science Fund for Distinguished Young Scholars (31125027), National Basic Research Program of China (2012CB114402), National Natural Science Foundation of China (31372556), and fund of Xiamen south ocean research center (13GZP002NF08). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.