title: The draft genome of the large yellow croaker reveals well-developed innate immunity.
abstract: The large yellow croaker, Larimichthys crocea, is one of the most economically important marine fish species endemic to China. Its wild stocks have severely suffered from overfishing, and the aquacultured species are vulnerable to various marine pathogens. Here we report the creation of a draft genome of a wild large yellow croaker using a whole-genome sequencing strategy. We estimate the genome size to be 728 Mb with 19,362 protein-coding genes. Phylogenetic analysis shows that the stickleback is most closely related to the large yellow croaker. Rapidly evolving genes under positive selection are significantly enriched in pathways related to innate immunity. We also confirm the existence of several genes and identify the expansion of gene families that are important for innate immunity. Our results may reflect a well-developed innate immune system in the large yellow croaker, which could aid in the development of wild resource preservation and mariculture strategies.
authors.affiliation: National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China.
authors.forename: Changwen
authors.initials: C
authors.lastname: Wu
authors.affiliation: Bio-X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China.
authors.forename: Di
authors.initials: D
authors.lastname: Zhang
authors.affiliation: Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Mengyuan
authors.initials: M
authors.lastname: Kan
authors.affiliation: National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China.
authors.forename: Zhengmin
authors.initials: Z
authors.lastname: Lv
authors.affiliation: National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China.
authors.forename: Aiyi
authors.initials: A
authors.lastname: Zhu
authors.affiliation: College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China.
authors.forename: Yongquan
authors.initials: Y
authors.lastname: Su
authors.affiliation: Bio-X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China.
authors.forename: Daizhan
authors.initials: D
authors.lastname: Zhou
authors.affiliation: National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China.
authors.forename: Jianshe
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Bio-X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China.
authors.forename: Zhou
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China.
authors.forename: Meiying
authors.initials: M
authors.lastname: Xu
authors.affiliation: National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China.
authors.forename: Lihua
authors.initials: L
authors.lastname: Jiang
authors.affiliation: National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China.
authors.forename: Baoying
authors.initials: B
authors.lastname: Guo
authors.affiliation: Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Ting
authors.initials: T
authors.lastname: Wang
authors.affiliation: National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China.
authors.forename: Changfeng
authors.initials: C
authors.lastname: Chi
authors.affiliation: College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Mao
authors.affiliation: National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China.
authors.forename: Jiajian
authors.initials: J
authors.lastname: Zhou
authors.affiliation: National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China.
authors.forename: Xinxiu
authors.initials: X
authors.lastname: Yu
authors.affiliation: National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China.
authors.forename: Hailing
authors.initials: H
authors.lastname: Wang
authors.affiliation: Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
authors.forename: Xiaoling
authors.initials: X
authors.lastname: Weng
authors.affiliation: ShanghaiBio Corporation, 675 US Highway One, North Brunswick, New Jersey 08902, USA.
authors.forename: Jason Gang
authors.initials: JG
authors.lastname: Jin
authors.affiliation: Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
authors.forename: Junyi
authors.initials: J
authors.lastname: Ye
authors.affiliation: Bio-X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China.
authors.forename: Lin
authors.initials: L
authors.lastname: He
authors.affiliation: Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
authors.forename: Yun
authors.initials: Y
authors.lastname: Liu
mesh_terms: D000818:Animals; D001483:Base Sequence; D019143:Evolution, Molecular; D016678:Genome; D007113:Immunity, Innate / Q000235:genetics*; D008969:Molecular Sequence Data; D010473:Perciformes / Q000235:genetics* / Q000276:immunology; D010802:Phylogeny