Genome Sequencing of the Perciform Fish Larimichthys crocea Provides Insights into Molecular and Genetic Mechanisms of Stress Adaptation

摘要

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 . Author Summary L . crocea is a temperate-water migratory fish that belongs to the order Perciformes and the family Sciaenidae. In China, the annual yield from L . crocea aquaculture exceeds that of any other net-cage-farmed marine fish species. L . crocea also exhibits peculiar behavioral and physiological characteristics and is especially sensitive to various environmental stresses. 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 . Further genomic analyses showed the significant expansion of several gene families, such as vision-related crystallins, olfactory receptors, and auditory sense-related genes, and provided a genetic basis for the peculiar physiological characteristics of L . crocea . 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, suggesting its multiple protective mechanisms involved in antioxidant functions, oxygen transport, immune defence, and osmotic and ionic regulation. These findings provide novel insights into the mechanisms of fish stress adaptation.