PT  - JOURNAL ARTICLE
AU  - Jingqun Ao
AU  - Yinnan Mu
AU  - Li-Xin Xiang
AU  - DingDing Fan
AU  - MingJi Feng
AU  - Shicui Zhang
AU  - Qiong Shi
AU  - Lv-Yun Zhu
AU  - Ting Li
AU  - Yang Ding
AU  - Li Nie
AU  - Qiuhua Li
AU  - Wei-ren Dong
AU  - Liang Jiang
AU  - Bing Sun
AU  - XinHui Zhang
AU  - Mingyu Li
AU  - Hai-Qi Zhang
AU  - ShangBo Xie
AU  - YaBing Zhu
AU  - XuanTing Jiang
AU  - Xianhui Wang
AU  - Pengfei Mu
AU  - Wei Chen
AU  - Zhen Yue
AU  - Zhuo Wang
AU  - Jun Wang
AU  - Jian-Zhong Shao
AU  - Xinhua Chen
TI  - Genome sequencing of the perciform fish <em>Larimichthys crocea</em> provides insights into stress adaptation
AID  - 10.1101/008136
DP  - 2014 Jan 01
TA  - bioRxiv
PG  - 008136
4099  - http://biorxiv.org/content/early/2014/08/18/008136.short
4100  - http://biorxiv.org/content/early/2014/08/18/008136.full
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.