RT Journal Article SR Electronic T1 Genome sequencing of the perciform fish Larimichthys crocea provides insights into stress adaptation JF bioRxiv FD Cold Spring Harbor Laboratory SP 008136 DO 10.1101/008136 A1 Jingqun Ao A1 Yinnan Mu A1 Li-Xin Xiang A1 DingDing Fan A1 MingJi Feng A1 Shicui Zhang A1 Qiong Shi A1 Lv-Yun Zhu A1 Ting Li A1 Yang Ding A1 Li Nie A1 Qiuhua Li A1 Wei-ren Dong A1 Liang Jiang A1 Bing Sun A1 XinHui Zhang A1 Mingyu Li A1 Hai-Qi Zhang A1 ShangBo Xie A1 YaBing Zhu A1 XuanTing Jiang A1 Xianhui Wang A1 Pengfei Mu A1 Wei Chen A1 Zhen Yue A1 Zhuo Wang A1 Jun Wang A1 Jian-Zhong Shao A1 Xinhua Chen YR 2014 UL http://biorxiv.org/content/early/2014/08/18/008136.abstract AB 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.