title: Genome sequencing of the perciform fish Larimichthys crocea provides insights into molecular and genetic mechanisms of stress adaptation.
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 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.
authors.affiliation: Key Laboratory of Marine Biogenetics and Resources, Third Institute of Oceanography, State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, P. R. China.
authors.forename: Jingqun
authors.initials: J
authors.lastname: Ao
authors.affiliation: Key Laboratory of Marine Biogenetics and Resources, Third Institute of Oceanography, State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, P. R. China.
authors.forename: Yinnan
authors.initials: Y
authors.lastname: Mu
authors.affiliation: College of Life Sciences, ZheJiang University, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou, ZheJiang, P. R. China.
authors.forename: Li-Xin
authors.initials: LX
authors.lastname: Xiang
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen, Guangdong, P. R. China.
authors.forename: DingDing
authors.initials: D
authors.lastname: Fan
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen, Guangdong, P. R. China.
authors.forename: MingJi
authors.initials: M
authors.lastname: Feng
authors.affiliation: Ocean University of China, Qingdao, Shandong, P. R. China.
authors.forename: Shicui
authors.initials: S
authors.lastname: Zhang
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen, Guangdong, P. R. China.
authors.forename: Qiong
authors.initials: Q
authors.lastname: Shi
authors.affiliation: College of Life Sciences, ZheJiang University, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou, ZheJiang, P. R. China.
authors.forename: Lv-Yun
authors.initials: LY
authors.lastname: Zhu
authors.affiliation: Key Laboratory of Marine Biogenetics and Resources, Third Institute of Oceanography, State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, P. R. China.
authors.forename: Ting
authors.initials: T
authors.lastname: Li
authors.affiliation: Key Laboratory of Marine Biogenetics and Resources, Third Institute of Oceanography, State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, P. R. China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Ding
authors.affiliation: College of Life Sciences, ZheJiang University, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou, ZheJiang, P. R. China.
authors.forename: Li
authors.initials: L
authors.lastname: Nie
authors.affiliation: Key Laboratory of Marine Biogenetics and Resources, Third Institute of Oceanography, State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, P. R. China.
authors.forename: Qiuhua
authors.initials: Q
authors.lastname: Li
authors.affiliation: College of Life Sciences, ZheJiang University, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou, ZheJiang, P. R. China.
authors.forename: Wei-Ren
authors.initials: WR
authors.lastname: Dong
authors.affiliation: College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, P. R. China.
authors.forename: Liang
authors.initials: L
authors.lastname: Jiang
authors.affiliation: Ocean University of China, Qingdao, Shandong, P. R. China.
authors.forename: Bing
authors.initials: B
authors.lastname: Sun
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen, Guangdong, P. R. China.
authors.forename: XinHui
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Marine Biogenetics and Resources, Third Institute of Oceanography, State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, P. R. China.
authors.forename: Mingyu
authors.initials: M
authors.lastname: Li
authors.affiliation: College of Life Sciences, ZheJiang University, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou, ZheJiang, P. R. China.
authors.forename: Hai-Qi
authors.initials: HQ
authors.lastname: Zhang
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen, Guangdong, P. R. China.
authors.forename: ShangBo
authors.initials: S
authors.lastname: Xie
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen, Guangdong, P. R. China.
authors.forename: YaBing
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen, Guangdong, P. R. China.
authors.forename: XuanTing
authors.initials: X
authors.lastname: Jiang
authors.affiliation: Key Laboratory of Marine Biogenetics and Resources, Third Institute of Oceanography, State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, P. R. China.
authors.forename: Xianhui
authors.initials: X
authors.lastname: Wang
authors.affiliation: Key Laboratory of Marine Biogenetics and Resources, Third Institute of Oceanography, State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, P. R. China.
authors.forename: Pengfei
authors.initials: P
authors.lastname: Mu
authors.affiliation: Key Laboratory of Marine Biogenetics and Resources, Third Institute of Oceanography, State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, P. R. China.
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen, Guangdong, P. R. China.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Yue
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen, Guangdong, P. R. China.
authors.forename: Zhuo
authors.initials: Z
authors.lastname: Wang
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen, Guangdong, P. R. China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: College of Life Sciences, ZheJiang University, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou, ZheJiang, P. R. China.
authors.forename: Jian-Zhong
authors.initials: JZ
authors.lastname: Shao
authors.affiliation: Key Laboratory of Marine Biogenetics and Resources, Third Institute of Oceanography, State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, P. R. China.
authors.forename: Xinhua
authors.initials: X
authors.lastname: Chen
mesh_terms: D000222:Adaptation, Physiological; D000818:Animals; D029941:Fish Proteins / Q000235:genetics* / Q000378:metabolism; D016678:Genome; D009997:Osmotic Pressure; D018384:Oxidative Stress; D010473:Perciformes / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome
chemical_list: D029941:Fish Proteins
references.citation: Brain Behav Immun. 2007 Mar;21(3):259-72
references.pmid: 17194565
references.citation: Mar Biotechnol (NY). 2014 Dec;16(6):729-38
references.pmid: 25070688
references.citation: Mol Biol Evol. 2000 Apr;17(4):540-52
references.pmid: 10742046
references.citation: Gigascience. 2012 Dec 27;1(1):18
references.pmid: 23587118
references.citation: Am J Physiol Gastrointest Liver Physiol. 2013 Sep 1;305(5):G348-56
references.pmid: 23832517
references.citation: Cancer Res. 2006 Apr 1;66(7):3688-98
references.pmid: 16585195
references.citation: PLoS One. 2014;9(5):e97471
references.pmid: 24820969
references.citation: Pediatr Res. 1999 Apr;45(4 Pt 1):500-9
references.pmid: 10203141
references.citation: Bioinformatics. 2009 Aug 1;25(15):1966-7
references.pmid: 19497933
references.citation: J Gen Physiol. 1995 May;105(5):569-87
references.pmid: 7658193
references.citation: J Immunol. 2007 Sep 15;179(6):3859-71
references.pmid: 17785823
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D735-40
references.pmid: 18056084
references.citation: J Fish Biol. 2013 Jan;82(1):34-41
references.pmid: 23331136
references.citation: Curr Neurovasc Res. 2008 Feb;5(1):71-81
references.pmid: 18289024
references.citation: Eur J Pharmacol. 2004 Oct 1;500(1-3):51-62
references.pmid: 15464020
references.citation: Genome Biol Evol. 2009 Apr 30;1:34-44
references.pmid: 20333175
references.citation: Physiol Rev. 2001 Jul;81(3):1097-142
references.pmid: 11427693
references.citation: Methods. 2001 Dec;25(4):402-8
references.pmid: 11846609
references.citation: Nat Methods. 2008 Jul;5(7):621-8
references.pmid: 18516045
references.citation: Bioinformatics. 2009 May 1;25(9):1105-11
references.pmid: 19289445
references.citation: BMC Genomics. 2010;11:289
references.pmid: 20459719
references.citation: Nucleic Acids Res. 2012 Jul;40(Web Server issue):W569-72
references.pmid: 22695796
references.citation: Nature. 2011 Sep 8;477(7363):207-10
references.pmid: 21832995
references.citation: Mediators Inflamm. 2013;2013:279365
references.pmid: 23690660
references.citation: Bioinformatics. 2006 May 15;22(10):1269-71
references.pmid: 16543274
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W465-7
references.pmid: 15980513
references.citation: Enzyme. 1985;34(1):27-32
references.pmid: 2935391
references.citation: Peptides. 2003 Jul;24(7):1053-62
references.pmid: 14499284
references.citation: Nat Genet. 2014 Mar;46(3):253-60
references.pmid: 24487278
references.citation: Science. 2013 Aug 23;341(6148):903-6
references.pmid: 23929945
references.citation: BMC Bioinformatics. 2004 May 14;5:59
references.pmid: 15144565
references.citation: Proc Natl Acad Sci U S A. 2001 Feb 13;98(4):1993-8
references.pmid: 11172064
references.citation: J Biol Chem. 2006 Jul 28;281(30):20666-72
references.pmid: 16717100
references.citation: Steroids. 2012 Sep;77(11):1041-9
references.pmid: 22728894
references.citation: Genome Res. 2004 May;14(5):988-95
references.pmid: 15123596
references.citation: Nature. 2012 Oct 4;490(7418):49-54
references.pmid: 22992520
references.citation: J Appl Physiol (1985). 2002 Mar;92(3):1152-8
references.pmid: 11842053
references.citation: J Neurosci. 2003 Jul 2;23(13):5536-44
references.pmid: 12843254
references.citation: Physiol Genomics. 2012 Dec 18;44(24):1165-78
references.pmid: 23092952
references.citation: BMC Bioinformatics. 2010;11:579
references.pmid: 21110866
references.citation: J Mol Biol. 1997 Apr 25;268(1):78-94
references.pmid: 9149143
references.citation: J Proteomics. 2011 May 16;74(6):817-28
references.pmid: 21362502
references.citation: Am J Physiol Regul Integr Comp Physiol. 2005 Nov;289(5):R1512-9
references.pmid: 15994372
references.citation: Neuro Endocrinol Lett. 2005 Feb;26(1):43-9
references.pmid: 15726019
references.citation: Trends Neurosci. 1997 Feb;20(2):78-84
references.pmid: 9023876
references.citation: Cytokine. 2008 Sep;43(3):350-8
references.pmid: 18703349
references.citation: J Proteome Res. 2010 Mar 5;9(3):1424-36
references.pmid: 20099887
references.citation: Food Chem Toxicol. 2014 Oct;72:111-21
references.pmid: 25046389
references.citation: BMC Biol. 2012;10:44
references.pmid: 22626058
references.citation: Nucleic Acids Res. 2004;32(5):1792-7
references.pmid: 15034147
references.citation: Nat Immunol. 2011 Oct;12(10):959-65
references.pmid: 21892174
references.citation: J Virol. 2011 Aug;85(16):8403-12
references.pmid: 21680521
references.citation: Am J Physiol Regul Integr Comp Physiol. 2005 Apr;288(4):R919-27
references.pmid: 15576658
references.citation: Comput Appl Biosci. 1997 Oct;13(5):555-6
references.pmid: 9367129
references.citation: Immunity. 2014 Mar 20;40(3):329-41
references.pmid: 24560620
references.citation: Invest Ophthalmol Vis Sci. 2009 Oct;50(10):4581-7
references.pmid: 19407012
references.citation: J Neurochem. 2000 Nov;75(5):1826-33
references.pmid: 11032871
references.citation: Cell Mol Life Sci. 2007 Mar;64(5):566-80
references.pmid: 17260086
references.citation: BMC Genomics. 2010;11:506
references.pmid: 20858287
references.citation: Nucleic Acids Res. 2009 Aug;37(14):4587-602
references.pmid: 19491311
references.citation: Nat Genet. 2013 May;45(5):567-72
references.pmid: 23542700
references.citation: Lancet. 1984 Jun 16;1(8390):1328-30
references.pmid: 6145029
references.citation: Nat Rev Genet. 2005 Apr;6(4):324-33
references.pmid: 15803200
references.citation: Bioinformatics. 2005 Jun;21 Suppl 1:i351-8
references.pmid: 15961478
references.citation: Bioinformatics. 2011 Feb 15;27(4):578-9
references.pmid: 21149342
references.citation: J Exp Biol. 2011 Jan 15;214(Pt 2):191-9
references.pmid: 21177940
references.citation: Proteomics. 2014 Sep;14(17-18):1990-8
references.pmid: 24737740
references.citation: J Clin Endocrinol Metab. 1993 Dec;77(6):1690-4
references.pmid: 8263159
references.citation: Genome Res. 1997 Oct;7(10):986-95
references.pmid: 9331369
references.citation: Comp Biochem Physiol B Biochem Mol Biol. 2008 May;150(1):85-92
references.pmid: 18342561
references.citation: Dev Comp Immunol. 2011 Sep;35(9):886-97
references.pmid: 21241729
references.citation: BMC Evol Biol. 2011;11:237
references.pmid: 21834959