@article {Ao008136, author = {Jingqun Ao and Yinnan Mu and Li-Xin Xiang and DingDing Fan and MingJi Feng and Shicui Zhang and Qiong Shi and Lv-Yun Zhu and Ting Li and Yang Ding and Li Nie and Qiuhua Li and Wei-ren Dong and Liang Jiang and Bing Sun and XinHui Zhang and Mingyu Li and Hai-Qi Zhang and ShangBo Xie and YaBing Zhu and XuanTing Jiang and Xianhui Wang and Pengfei Mu and Wei Chen and Zhen Yue and Zhuo Wang and Jun Wang and Jian-Zhong Shao and Xinhua Chen}, title = {Genome sequencing of the perciform fish Larimichthys crocea provides insights into stress adaptation}, elocation-id = {008136}, year = {2014}, doi = {10.1101/008136}, publisher = {Cold Spring Harbor Laboratory}, abstract = {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 provide novel insights into the mechanisms of fish adaptation and response to hypoxia and air exposure.}, URL = {https://www.biorxiv.org/content/early/2014/08/18/008136}, eprint = {https://www.biorxiv.org/content/early/2014/08/18/008136.full.pdf}, journal = {bioRxiv} }