Divergence, evolution and adaptation in ray-finned fish genomes
|
摘要
With the rapid development of next-generation sequencing technologies and bioinformatics, over 50 ray-finned fish genomes by far have been sequenced with high quality. The genomic work provides abundant genetic resources for deep understanding of divergence, evolution and adaptation in the fish genomes. They are also instructive for identification of candidate genes for functional verification, molecular breeding, and development of novel marine drugs. As an example of other omics data, the Fish-T1 K project generated a big database of fish transcriptomes to integrate with these published fish genomes for potential applications. In this review, we highlight the above-mentioned recent investigations and core topics on the ray-finned fish genome research, with a main goal to obtain a deeper understanding of fish biology for theoretical and practical applications.
With the rapid development of next-generation sequencing technologies and bioinformatics, over 50 ray-finned fish genomes by far have been sequenced with high quality. The genomic work provides abundant genetic resources for deep understanding of divergence, evolution and adaptation in the fish genomes. They are also instructive for identification of candidate genes for functional verification, molecular breeding, and development of novel marine drugs. As an example of other omics data, the Fish-T1 K project generated a big database of fish transcriptomes to integrate with these published fish genomes for potential applications. In this review, we highlight the above-mentioned recent investigations and core topics on the ray-finned fish genome research, with a main goal to obtain a deeper understanding of fish biology for theoretical and practical applications.
With the rapid development of next-generation sequencing technologies and bioinformatics, over 50 ray-finned fish genomes by far have been sequenced with high quality. The genomic work provides abundant genetic resources for deep understanding of divergence, evolution and adaptation in the fish genomes. They are also instructive for identification of candidate genes for functional verification, molecular breeding, and development of novel marine drugs. As an example of other omics data, the Fish-T1 K project generated a big database of fish transcriptomes to integrate with these published fish genomes for potential applications. In this review, we highlight the above-mentioned recent investigations and core topics on the ray-finned fish genome research, with a main goal to obtain a deeper understanding of fish biology for theoretical and practical applications.
引文
Aanes,H.,Winata,C.L.,Lin,C.H.,Chen,J.P.,Srinivasan,K.G.,Lee,S.G.P.,Lim,A.Y.M.,Hajan,H.S.,Collas,P.,Bourque,G.,et al.(2011).Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition.Genome Res 21,1328-1338.
Ahnelt,H.(2018).Imprecise naming:the anadromous and the sea spawning threespine stickleback should be discriminated by names.Biologia 73,389-392.
Alexandrou,M.A.,Swartz,B.A.,Matzke,N.J.,and Oakley,T.H.(2013).Genome duplication and multiple evolutionary origins of complex migratory behavior in Salmonidae.Mol Phylogenet Evol 69,514-523.
Alfaro,M.E.(2018).Resolving the ray-finned fish tree of life.Proc Natl Acad Sci USA 115,6107-6109.
Amores,A.,Force,A.,Yan,Y.L.,Joly,L.,Amemiya,C.,Fritz,A.,Ho,R.K.,Langeland,J.,Prince,V.,Wang,Y.L.,et al.(1998).Zebrafish hox clusters and vertebrate genome evolution.Science 282,1711-1714.
Ao,J.,Mu,Y.,Xiang,L.X.,Fan,D.D.,Feng,M.J.,Zhang,S.,Shi,Q.,Zhu,L.Y.,Li,T.,Ding,Y.,et al.(2015).Genome sequencing of the perciform fish Larimichthys crocea provides insights into molecular and genetic mechanisms of stress adaptation.PLoS Genet 11,e1005118.
Aparicio,S.,Chapman,J.,Stupka,E.,Putnam,N.,Chia,J.M.,Dehal,P.,Christoffels,A.,Rash,S.,Hoon,S.,Smit,A.,et al.(2002).Wholegenome shotgun assembly and analysis of the genome of Fugu rubripes.Science 297,1301-1310.
Austin,C.M.,Tan,M.H.,Croft,L.J.,Hammer,M.P.,and Gan,H.M.(2015).Whole genome sequencing of the Asian arowana(Scleropages formosus)provides insights into the evolution of ray-finned fishes.Genome Biol Evol 7,2885-2895.
Barrett,R.D.H.,Rogers,S.M.,and Schluter,D.(2008).Natural selection on a major armor gene in threespine stickleback.Science 322,255-257.
Berthelot,C.,Brunet,F.,Chalopin,D.,Juanchich,A.,Bernard,M.,No?l,B.,Bento,P.,Da Silva,C.,Labadie,K.,Alberti,A.,et al.(2014).The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates.Nat Commun 5,3657.
Bian,C.,Hu,Y.,Ravi,V.,Kuznetsova,I.S.,Shen,X.,Mu,X.,Sun,Y.,You,X.,Li,J.,Li,X.,et al.(2016).The Asian arowana(Scleropages formosus)genome provides new insights into the evolution of an early lineage of teleosts.Sci Rep 6,24501.
Bilyk,K.T.,and Cheng,C.H.C.(2013).Model of gene expression in extreme cold-reference transcriptome for the high-Antarctic cryopelagic notothenioid fish Pagothenia borchgrevinki.BMCGenomics 14,634.
Braasch,I.,Brunet,F.,Volff,J.N.,and Schartl,M.(2009).Pigmentation pathway evolution after whole-genome duplication in fish.Genome Biol Evol 1,479-493.
Braasch,I.,Gehrke,A.R.,Smith,J.J.,Kawasaki,K.,Manousaki,T.,Pasquier,J.,Amores,A.,Desvignes,T.,Batzel,P.,Catchen,J.,et al.(2016).Erratum:Corrigendum:The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.Nat Genet 48,700.
Brawand,D.,Wagner,C.E.,Li,Y.I.,Malinsky,M.,Keller,I.,Fan,S.,Simakov,O.,Ng,A.Y.,Lim,Z.W.,Bezault,E.,et al.(2014).The genomic substrate for adaptive radiation in African cichlid fish.Nature513,375-381.
Byrne,A.,Beaudin,A.E.,Olsen,H.E.,Jain,M.,Cole,C.,Palmer,T.,DuBois,R.M.,Forsberg,E.C.,Akeson,M.,and Vollmers,C.(2017).Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells.Nat Commun 8,16027.
Carmona,S.J.,Teichmann,S.A.,Ferreira,L.,Macaulay,I.C.,Stubbington,M.J.T.,Cvejic,A.,and Gfeller,D.(2017).Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types.Genome Res 27,451-461.
Carruthers,M.,Yurchenko,A.A.,Augley,J.J.,Adams,C.E.,Herzyk,P.,and Elmer,K.R.(2018).De novo transcriptome assembly,annotation and comparison of four ecological and evolutionary model salmonid fish species.BMC Genomics 19,32.
Casewell,N.R.,Huttley,G.A.,and Wüster,W.(2012).Dynamic evolution of venom proteins in squamate reptiles.Nat Commun 3,1066.
Chen,S.,Zhang,G.,Shao,C.,Huang,Q.,Liu,G.,Zhang,P.,Song,W.,An,N.,Chalopin,D.,Volff,J.N.,et al.(2014).Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle.Nat Genet 46,253-260.
Chen,X.,Zhong,L.,Bian,C.,Xu,P.,Qiu,Y.,You,X.,Zhang,S.,Huang,Y.,Li,J.,Wang,M.,et al.(2016).High-quality genome assembly of channel catfish,Ictalurus punctatus.Gigascience 5,39.
Chen,Z.,Cheng,C.H.C.,Zhang,J.,Cao,L.,Chen,L.,Zhou,L.,Jin,Y.,Ye,H.,Deng,C.,Dai,Z.,et al.(2008).Transcriptomic and genomic evolution under constant cold in Antarctic notothenioid fish.Proc Natl Acad Sci USA 105,12944-12949.
Chinchar,V.G.,Bryan,L.,Silphadaung,U.,Noga,E.,Wade,D.,and Rollins-Smith,L.(2004).Inactivation of viruses infecting ectothermic animals by amphibian and piscine antimicrobial peptides.Virology 323,268-275.
Chinen,A.,Matsumoto,Y.,and Kawamura,S.(2005).Reconstitution of ancestral green visual pigments of zebrafish and molecular mechanism of their spectral differentiation.Mol Biol Evol 22,1001-1010.
Christoffels,A.,Koh,E.G.L.,Chia,J.M.,Brenner,S.,Aparicio,S.,and Venkatesh,B.(2004).Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes.Mol Biol Evol 21,1146-1151.
Collins,J.E.,White,S.,Searle,S.M.J.,and Stemple,D.L.(2012).Incorporating RNA-seq data into the zebrafish Ensembl genebuild.Genome Res 22,2067-2078.
Colosimo,P.F.,Hosemann,K.E.,Balabhadra,S.,Villarreal,G.,Dickson,M.,Grimwood,J.,Schmutz,J.,Myers,R.M.,Schluter,D.,and Kingsley,D.M.(2005).Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles.Science 307,1928-1933.
Coppe,A.,Agostini,C.,Marino,I.A.M.,Zane,L.,Bargelloni,L.,Bortoluzzi,S.,and Patarnello,T.(2013).Genome evolution in the cold:Antarctic icefish muscle transcriptome reveals selective duplications increasing mitochondrial function.Genome Biol Evol 5,45-60.
Crossa,J.,Pérez-Rodríguez,P.,Cuevas,J.,Montesinos-López,O.,Jarquín,D.,de Los Campos,G.,Burgue?o,J.,González-Camacho,J.M.,PérezElizalde,S.,Beyene,Y.,et al.(2017).Genomic selection in plant breeding:methods,models,and perspectives.Trends Plant Sci 22,961-975.
Day,J.J.(2006).Fishes of the world,4th edition.Fish Fisheries 7,334.
Deamer,D.,Akeson,M.,and Branton,D.(2016).Three decades of nanopore sequencing.Nat Biotechnol 34,518-524.
Dehal,P.,and Boore,J.L.(2005).Two rounds of whole genome duplication in the ancestral vertebrate.PLoS Biol 3,e314.
Detrich,H.W.,Stuart,A.,Schoenborn,M.,Parker,S.K.,Methé,B.A.,and Amemiya,C.T.(2010).Genome enablement of the notothenioidei:genome size estimates from 11 species and BAC libraries from 2representative taxa.J Exp Zool 314B,369-381.
Domingos,J.A.,Zenger,K.R.,and Jerry,D.R.(2015).Whole-genome shotgun sequence assembly enables rapid gene characterization in the tropical fish barramundi,Lates calcarifer.Anim Genet 46,468-469.
Don,E.K.,de Jong-Curtain,T.A.,Doggett,K.,Hall,T.E.,Heng,B.,Badrock,A.P.,Winnick,C.,Nicholson,G.A.,Guillemin,G.J.,Currie,P.D.,et al.(2016).Genetic basis of hindlimb loss in a naturally occurring vertebrate model.Biol Open 5,359-366.
Eid,J.,Fehr,A.,Gray,J.,Luong,K.,Lyle,J.,Otto,G.,Peluso,P.,Rank,D.,Baybayan,P.,Bettman,B.,et al.(2009).Real-time DNA sequencing from single polymerase molecules.Science 323,133-138.
Feldkaemper,M.,and Schaeffel,F.(2013).An updated view on the role of dopamine in myopia.Exp Eye Res 114,106-119.
Fraser,B.A.,Künstner,A.,Reznick,D.N.,Dreyer,C.,and Weigel,D.(2015).Population genomics of natural and experimental populations of guppies(Poecilia reticulata).Mol Ecol 24,389-408.
Froese,R.,and Pauly,D.(2011).FishBase.In World Wide Web electronic publication wwwfishbaseorg ver 08/2012(2011).
Gallant,J.R.,Traeger,L.L.,Volkening,J.D.,Moffett,H.,Chen,P.H.,Novina,C.D.,Phillips,G.N.,Jr.,Anand,R.,Wells,G.B.,Pinch,M.,et al.(2014).Nonhuman genetics.Genomic basis for the convergent evolution of electric organs.Science 344,1522-1525.
Genomic Resources Development Consortium,Alvarez,P.,Arthofer,W.,Coelho,M.M.,Conklin,D.,Estonba,A.,Grosso,A.R.,Helyar,S.J.,Langa,J.,Machado,M.P.,et al.(2015).Genomic Resources Notes Accepted 1 June 2015-31 July 2015.Mol Ecol Resour 15,1510-1512.
Glasauer,S.M.K.,and Neuhauss,S.C.F.(2014).Whole-genome duplication in teleost fishes and its evolutionary consequences.Mol Genet Genomics 289,1045-1060.
Grabherr,M.G.,Haas,B.J.,Yassour,M.,Levin,J.Z.,Thompson,D.A.,Amit,I.,Adiconis,X.,Fan,L.,Raychowdhury,R.,Zeng,Q.,et al.(2011).Full-length transcriptome assembly from RNA-Seq data without a reference genome.Nat Biotechnol 29,644-652.
Guan,L.,Chi,W.,Xiao,W.,Chen,L.,and He,S.(2014).Analysis of hypoxia-inducible factor alpha polyploidization reveals adaptation to Tibetan Plateau in the evolution of schizothoracine fish.BMC Evol Biol14,192.
Gui,J.,Liu,B.,Cao,G.,Lipchik,A.M.,Perez,M.,Dekan,Z.,Mobli,M.,Daly,N.L.,Alewood,P.F.,Parker,L.L.,et al.(2014).A tarantula-venom peptide antagonizes the TRPA1 nociceptor ion channel by binding to the S1-S4 gating domain.Curr Biol 24,473-483.
Harel,I.,Benayoun,B.A.,Machado,B.,Singh,P.P.,Hu,C.K.,Pech,M.F.,Valenzano,D.R.,Zhang,E.,Sharp,S.C.,Artandi,S.E.,et al.(2015).Aplatform for rapid exploration of aging and diseases in a naturally shortlived vertebrate.Cell 160,1013-1026.
Hattori,R.S.,Murai,Y.,Oura,M.,Masuda,S.,Majhi,S.K.,Sakamoto,T.,Fernandino,J.I.,Somoza,G.M.,Yokota,M.,and Strüssmann,C.A.(2012).A Y-linked anti-Mullerian hormone duplication takes over a critical role in sex determination.Proc Natl Acad Sci USA 109,2955-2959.
Hedges,S.B.,and Kumar,S.(2009).Discovering the timetree of life.In The Timetree of Life.S.B.Hedges,and S.Kumar,eds.(New York:Oxford University Press),pp.3-18.
Henkel,C.V.,Dirks,R.P.,de Wijze,D.L.,Minegishi,Y.,Aoyama,J.,Jansen,H.J.,Turner,B.,Knudsen,B.,Bundgaard,M.,Hvam,K.L.,et al.(2012).First draft genome sequence of the Japanese eel,Anguilla japonica.Gene 511,195-201.
Hohenlohe,P.A.,Bassham,S.,Etter,P.D.,Stiffler,N.,Johnson,E.A.,and Cresko,W.A.(2010).Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags.PLoS Genet 6,e1000862.
Howe,K.,Clark,M.D.,Torroja,C.F.,Torrance,J.,Berthelot,C.,Muffato,M.,Collins,J.E.,Humphray,S.,McLaren,K.,Matthews,L.,et al.(2013).The zebrafish reference genome sequence and its relationship to the human genome.Nature 496,498-503.
Hubert,S.,Higgins,B.,Borza,T.,and Bowman,S.(2010).Development of a SNP resource and a genetic linkage map for Atlantic cod(Gadus morhua).BMC Genomics 11,191.
Hughes,L.C.,Ortí,G.,Huang,Y.,Sun,Y.,Baldwin,C.C.,Thompson,A.W.,Arcila,D.,Betancur-R.,R.,Li,C.,Becker,L.,et al.(2018).Comprehensive phylogeny of ray-finned fishes(Actinopterygii)based on transcriptomic and genomic data.Proc Natl Acad Sci USA 115,6249-6254.
Hurley,I.A.,Mueller,R.L.,Dunn,K.A.,Schmidt,E.J.,Friedman,M.,Ho,R.K.,Prince,V.E.,Yang,Z.,Thomas,M.G.,and Coates,M.I.(2007).Anew time-scale for ray-finned fish evolution.Proc R Soc B-Biol Sci274,489-498.
Huth,T.J.,and Place,S.P.(2016).Transcriptome wide analyses reveal a sustained cellular stress response in the gill tissue of Trematomus bernacchii after acclimation to multiple stressors.BMC Genomics 17,127.
Innan,H.,and Kondrashov,F.(2010).The evolution of gene duplications:classifying and distinguishing between models.Nat Rev Genet 11,97-108.
Jaillon,O.,Aury,J.M.,Brunet,F.,Petit,J.L.,Stange-Thomann,N.,Mauceli,E.,Bouneau,L.,Fischer,C.,Ozouf-Costaz,C.,Bernot,A.,et al.(2004).Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype.Nature 431,946-957.
Jones,F.C.,Brown,C.,Pemberton,J.M.,and Braithwaite,V.A.(2006).Reproductive isolation in a threespine stickleback hybrid zone.J Evol Biol 19,1531-1544.
Jones,F.C.,Grabherr,M.G.,Chan,Y.F.,Russell,P.,Mauceli,E.,Johnson,J.,Swofford,R.,Pirun,M.,Zody,M.C.,White,S.,et al.(2012).The genomic basis of adaptive evolution in threespine sticklebacks.Nature484,55-61.
Kasahara,M.,Naruse,K.,Sasaki,S.,Nakatani,Y.,Qu,W.,Ahsan,B.,Yamada,T.,Nagayasu,Y.,Doi,K.,Kasai,Y.,et al.(2007).The medaka draft genome and insights into vertebrate genome evolution.Nature447,714-719.
Kawaguchi,M.,Yasumasu,S.,Shimizu,A.,Kudo,N.,Sano,K.,Iuchi,I.,and Nishida,M.(2013).Adaptive evolution of fish hatching enzyme:one amino acid substitution results in differential salt dependency of the enzyme.J Exp Biol 216,1609-1615.
Kelley,J.L.,Yee,M.C.,Brown,A.P.,Richardson,R.R.,Tatarenkov,A.,Lee,C.C.,Harkins,T.T.,Bustamante,C.D.,and Earley,R.L.(2016).The genome of the self-fertilizing mangrove rivulus fish,Kryptolebias marmoratus:A model for studying phenotypic plasticity and adaptations to extreme environments.Genome Biol Evol 8,2145-2154.
Kettleborough,R.N.W.,Busch-Nentwich,E.M.,Harvey,S.A.,Dooley,C.M.,de Bruijn,E.,van Eeden,F.,Sealy,I.,White,R.J.,Herd,C.,Nijman,I.J.,et al.(2013).A systematic genome-wide analysis of zebrafish protein-coding gene function.Nature 496,494-497.
Kim,J.B.,Porreca,G.J.,Song,L.,Greenway,S.C.,Gorham,J.M.,Church,G.M.,Seidman,C.E.,and Seidman,J.G.(2007).Polony multiplex analysis of gene expression(PMAGE)in mouse hypertrophic cardiomyopathy.Science 316,1481-1484.
Kodzius,R.,Kojima,M.,Nishiyori,H.,Nakamura,M.,Fukuda,S.,Tagami,M.,Sasaki,D.,Imamura,K.,Kai,C.,Harbers,M.,et al.(2006).CAGE:cap analysis of gene expression.Nat Methods 3,211-222.
Laranjeiro,R.,and Whitmore,D.(2014).Transcription factors involved in retinogenesis are co-opted by the circadian clock following photoreceptor differentiation.Development 141,2644-2656.
Li,J.,Bian,C.,Hu,Y.,Mu,X.,Shen,X.,Ravi,V.,Kuznetsova,I.S.,Sun,Y.,You,X.,Qiu,Y.,et al.(2016).A chromosome-level genome assembly of the Asian arowana,Scleropages formosus.Sci Data 3,160105.
Li,J.,You,X.,Bian,C.,Yu,H.,Coon,S.L.,and Shi,Q.(2015a).Molecular evolution of aralkylamine N-acetyltransferase in fish:A genomic survey.Int J Mol Sci 17,51.
Li,M.,Sun,Y.,Zhao,J.,Shi,H.,Zeng,S.,Ye,K.,Jiang,D.,Zhou,L.,Sun,L.,Tao,W.,et al.(2015b).A tandem duplicate of anti-Müllerian hormone with a missense SNP on the Y chromosome is essential for male sex determination in Nile tilapia,Oreochromis niloticus.PLoSGenet 11,e1005678.
Li,M.,and Wang,D.(2017).Gene editing nuclease and its application in tilapia.Sci Bull 62,165-173.
Li,X.Y.,and Gui,J.F.(2018a).Diverse and variable sex determination mechanisms in vertebrates.Sci China Life Sci 61,1503-1514.
Li,X.Y.,and Gui,J.F.(2018b).An epigenetic regulatory switch controlling temperature-dependent sex determination in vertebrates.Sci China Life Sci 61,996-998.
Lieberman-Aiden,E.,van Berkum,N.L.,Williams,L.,Imakaev,M.,Ragoczy,T.,Telling,A.,Amit,I.,Lajoie,B.R.,Sabo,P.J.,Dorschner,M.O.,et al.(2009).Comprehensive mapping of long-range interactions reveals folding principles of the human genome.Science 326,289-293.
Lien,S.,Koop,B.F.,Sandve,S.R.,Miller,J.R.,Kent,M.P.,Nome,T.,Hvidsten,T.R.,Leong,J.S.,Minkley,D.R.,Zimin,A.,et al.(2016).The Atlantic salmon genome provides insights into rediploidization.Nature533,200-205.
Lin,J.J.,Wang,F.Y.,Li,W.H.,and Wang,T.Y.(2017).The rises and falls of opsin genes in 59 ray-finned fish genomes and their implications for environmental adaptation.Sci Rep 7,15568.
Lin,Q.,Fan,S.,Zhang,Y.,Xu,M.,Zhang,H.,Yang,Y.,Lee,A.P.,Woltering,J.M.,Ravi,V.,Gunter,H.M.,et al.(2016).The seahorse genome and the evolution of its specialized morphology.Nature 540,395-399.
Lin,Q.,Qiu,Y.,Gu,R.,Xu,M.,Li,J.,Bian,C.,Zhang,H.,Qin,G.,Zhang,Y.,Luo,W.,et al.(2017).Draft genome of the lined seahorse,Hippocampus erectus.Gigascience 6,1-6.
Liu,K.,Xu,D.,Li,J.,Bian,C.,Duan,J.,Zhou,Y.,Zhang,M.,You,X.,You,Y.,Chen,J.,et al.(2017).Whole genome sequencing of Chinese clearhead icefish,Protosalanx hyalocranius.Gigascience 6,1-6.
Liu,S.,Zhang,Y.,Zhou,Z.,Waldbieser,G.,Sun,F.,Lu,J.,Zhang,J.,Jiang,Y.,Zhang,H.,Wang,X.,et al.(2012).Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote.BMC Genomics 13,595.
Liu,Y.,Xu,P.,Xu,J.,Huang,Y.,Liu,Y.,Fang,H.,Hu,Y.,You,X.,Bian,C.,Sun,M.,et al.(2017).China is initiating the Aquatic 10-100-1,000Genomics Program.Sci China Life Sci 60,329-332.
Liu,Z.,Liu,S.,Yao,J.,Bao,L.,Zhang,J.,Li,Y.,Jiang,C.,Sun,L.,Wang,R.,Zhang,Y.,et al.(2016).The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts.Nat Commun 7,11757.
Lopez,M.E.,Neira,R.,and Yanez,J.M.(2014).Applications in the search for genomic selection signatures in fish.Front Genet 5,458.
Lynch,M.,and Force,A.(2000).The probability of duplicate gene preservation by subfunctionalization.Genetics 154,459-473.
Ma,X.,Dai,W.,Kang,J.,Yang,L.,and He,S.(2015).Comprehensive transcriptome analysis of six catfish species from an altitude gradient reveals adaptive evolution in Tibetan fishes.G3 6,141-148.
Manzon,L.A.(2002).The role of prolactin in fish osmoregulation:a review.Gen Comp Endocrinol 125,291-310.
Marioni,J.C.,Mason,C.E.,Mane,S.M.,Stephens,M.,and Gilad,Y.(2008).RNA-seq:an assessment of technical reproducibility and comparison with gene expression arrays.Genome Res 18,1509-1517.
Martinez Barrio,A.,Lamichhaney,S.,Fan,G.,Rafati,N.,Pettersson,M.,Zhang,H.,Dainat,J.,Ekman,D.,Hoppner,M.,Jern,P.,et al.(2016).The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing.Elife 5.
Masso-Silva,J.A.,and Diamond,G.(2014).Antimicrobial peptides from fish.Pharmaceuticals 7,265-310.
Matsuda,M.,Nagahama,Y.,Shinomiya,A.,Sato,T.,Matsuda,C.,Kobayashi,T.,Morrey,C.E.,Shibata,N.,Asakawa,S.,Shimizu,N.,et al.(2002).DMY is a Y-specific DM-domain gene required for male development in the medaka fish.Nature 417,559-563.
Matsumura,H.,Kruger,D.,Kahl,G.,and Terauchi,R.(2008).SuperSAGE:a modern platform for genome-wide quantitative transcript profiling.Curr Pharm Biotechnol 9,368-374.
McGaugh,S.E.,Gross,J.B.,Aken,B.,Blin,M.,Borowsky,R.,Chalopin,D.,Hinaux,H.,Jeffery,W.R.,Keene,A.,Ma,L.,et al.(2014).The cavefish genome reveals candidate genes for eye loss.Nat Commun 5,5307.
Mei,J.,and Gui,J.F.(2015).Genetic basis and biotechnological manipulation of sexual dimorphism and sex determination in fish.Sci China Life Sci 58,124-136.
Murdy,E.O.(1989).A taxonomic revision and cladistic analysis of the oxudercine gobies(Gobiidae:Oxudercinae)(Australian Museum),pp.1-93.
Nakamura,Y.,Mori,K.,Saitoh,K.,Oshima,K.,Mekuchi,M.,Sugaya,T.,Shigenobu,Y.,Ojima,N.,Muta,S.,Fujiwara,A.,et al.(2013).Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna.Proc Natl Acad Sci USA 110,11061-11066.
Near,T.J.,Eytan,R.I.,Dornburg,A.,Kuhn,K.L.,Moore,J.A.,Davis,M.P.,Wainwright,P.C.,Friedman,M.,and Smith,W.L.(2012).Resolution of ray-finned fish phylogeny and timing of diversification.Proc Natl Acad Sci USA 109,13698-13703.
Noga,E.J.,and Silphaduang,U.(2003).Piscidins:a novel family of peptide antibiotics from fish.Drug News Perspect 16,87-92.
Nudelman,G.,Frasca,A.,Kent,B.,Sadler,K.C.,Sealfon,S.C.,Walsh,M.J.,and Zaslavsky,E.(2018).High resolution annotation of zebrafish transcriptome using long-read sequencing.Genome Res 28,1415-1425.
Otto,S.P.,and Whitton,J.(2000).Polyploid incidence and evolution.Annu Rev Genet 34,401-437.
Palaiokostas,C.,Bekaert,M.,Khan,M.G.Q.,Taggart,J.B.,Gharbi,K.,McAndrew,B.J.,and Penman,D.J.(2015).A novel sex-determining QTL in Nile tilapia(Oreochromis niloticus).BMC Genomics 16,171.
Pan,H.,Yu,H.,Ravi,V.,Li,C.,Lee,A.P.,Lian,M.M.,Tay,B.H.,Brenner,S.,Wang,J.,Yang,H.,et al.(2016).The genome of the largest bony fish,ocean sunfish(Mola mola),provides insights into its fast growth rate.Gigascience 5,36.
Patton,E.E.,Mathers,M.E.,and Schartl,M.(2011).Generating and analyzing fish models of melanoma.Methods Cell Biol 105,339-366.
Pauli,A.,Valen,E.,Lin,M.F.,Garber,M.,Vastenhouw,N.L.,Levin,J.Z.,Fan,L.,Sandelin,A.,Rinn,J.L.,Regev,A.,et al.(2012).Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis.Genome Res 22,577-591.
Picelli,S.,Faridani,O.R.,Bj?rklund,A.K.,Winberg,G.,Sagasser,S.,and Sandberg,R.(2014).Full-length RNA-seq from single cells using Smart-seq2.Nat Protoc 9,171-181.
Pope,E.C.,Hays,G.C.,Thys,T.M.,Doyle,T.K.,Sims,D.W.,Queiroz,N.,Hobson,V.J.,Kubicek,L.,and Houghton,J.D.R.(2010).The biology and ecology of the ocean sunfish Mola mola:a review of current knowledge and future research perspectives.Rev Fish Biol Fisheries 20,471-487.
Postlethwait,J.H.,Woods,I.G.,Ngo-Hazelett,P.,Yan,Y.L.,Kelly,P.D.,Chu,F.,Huang,H.,Hill-Force,A.,and Talbot,W.S.(2000).Zebrafish comparative genomics and the origins of vertebrate chromosomes.Genome Res 10,1890-1902.
Prohaska,S.J.,and Stadler,P.F.(2004).The duplication of the Hox gene clusters in teleost fishes.Theor Biosci 123,89-110.
Rajanbabu,V.,and Chen,J.Y.(2011).Applications of antimicrobial peptides from fish and perspectives for the future.Peptides 32,415-420.
Reitzel,A.M.,Karchner,S.I.,Franks,D.G.,Evans,B.R.,Nacci,D.,Champlin,D.,Vieira,V.M.,and Hahn,M.E.(2014).Genetic variation at aryl hydrocarbon receptor(AHR)loci in populations of Atlantic killifish(Fundulus heteroclitus)inhabiting polluted and reference habitats.BMC Evol Biol 14,6.
Rennison,D.J.,Owens,G.L.,and Taylor,J.S.(2012).Opsin gene duplication and divergence in ray-finned fish.Mol Phylogenet Evol62,986-1008.
Rhoads,A.,and Au,K.F.(2015).PacBio sequencing and its applications.Genom Proteom BioInf 13,278-289.
Rondeau,E.B.,Minkley,D.R.,Leong,J.S.,Messmer,A.M.,Jantzen,J.R.,von Schalburg,K.R.,Lemon,C.,Bird,N.H.,and Koop,B.F.(2014).The genome and linkage map of the northern pike(Esox lucius):conserved synteny revealed between the salmonid sister group and the Neoteleostei.PLoS ONE 9,e102089.
Salem,M.,Vallejo,R.L.,Leeds,T.D.,Palti,Y.,Liu,S.,Sabbagh,A.,Rexroad,C.E.,and Yao,J.(2012).RNA-Seq identifies SNP markers for growth traits in rainbow trout.PLoS ONE 7,e36264.
Schartl,M.,Walter,R.B.,Shen,Y.,Garcia,T.,Catchen,J.,Amores,A.,Braasch,I.,Chalopin,D.,Volff,J.N.,Lesch,K.P.,et al.(2013).The genome of the platyfish,Xiphophorus maculatus,provides insights into evolutionary adaptation and several complex traits.Nat Genet 45,567-572.
Schena,M.,Shalon,D.,Davis,R.W.,and Brown,P.O.(1995).Quantitative monitoring of gene expression patterns with a complementary DNAmicroarray.Science 270,467-470.
Shao,C.,Bao,B.,Xie,Z.,Chen,X.,Li,B.,Jia,X.,Yao,Q.,Ortí,G.,Li,W.,Li,X.,et al.(2017).The genome and transcriptome of Japanese flounder provide insights into flatfish asymmetry.Nat Genet 49,119-124.
Shi,Y.,and Yokoyama,S.(2003).Molecular analysis of the evolutionary significance of ultraviolet vision in vertebrates.Proc Natl Acad Sci USA 100,8308-8313.
Shin,S.C.,Ahn,D.H.,Kim,S.J.,Pyo,C.W.,Lee,H.,Kim,M.K.,Lee,J.,Lee,J.E.,Detrich,H.W.,Postlethwait,J.H.,et al.(2014).The genome sequence of the Antarctic bullhead notothen reveals evolutionary adaptations to a cold environment.Genome Biol 15,468.
Shin,S.C.,Kim,S.J.,Lee,J.K.,Ahn,D.H.,Kim,M.G.,Lee,H.,Lee,J.,Kim,B.K.,and Park,H.(2012).Transcriptomics and comparative analysis of three antarctic notothenioid fishes.PLoS ONE 7,e43762.
Skene,D.J.(1992).N-Acetyltransferase and melatonin in the retina:regulation,function and mode of action.Biochm Soc Trans 20,312-315.
Small,C.M.,Bassham,S.,Catchen,J.,Amores,A.,Fuiten,A.M.,Brown,R.S.,Jones,A.G.,and Cresko,W.A.(2016).The genome of the Gulf pipefish enables understanding of evolutionary innovations.Genome Biol 17,258.
Soltis,P.S.S.D.E.(2012).Polyploidy and genome evolution,Chapter 17(USA:Springer),pp.341-384.
Sonesson,A.K.,and Meuwissen,T.H.E.(2009).Testing strategies for genomic selection in aquaculture breeding programs.Genet Sel Evol41,37.
Star,B.,Nederbragt,A.J.,Jentoft,S.,Grimholt,U.,Malmstr?m,M.,Gregers,T.F.,Rounge,T.B.,Paulsen,J.,Solbakken,M.H.,Sharma,A.,et al.(2011).The genome sequence of Atlantic cod reveals a unique immune system.Nature 477,207-210.
Sudhagar,A.,Kumar,G.,and El-Matbouli,M.(2018).Transcriptome analysis based on RNA-seq in understanding pathogenic mechanisms of diseases and the immune system of fish:A comprehensive review.Int JMol Sci 19,245.
Sun,Y.,Guo,C.Y.,Wang,D.D.,Li,X.F.,Xiao,L.,Zhang,X.,You,X.,Shi,Q.,Hu,G.J.,Fang,C.,et al.(2016a).Transcriptome analysis reveals the molecular mechanisms underlying growth superiority in a novel grouper hybrid(Epinephelus fuscogutatus♀×E.lanceolatus♂).BMCGenet 17,24.
Sun,Y.,Huang,Y.,Hu,G.,Zhang,X.,Ruan,Z.,Zhao,X.,Guo,C.,Tang,Z.,Li,X.,You,X.,et al.(2016b).Comparative transcriptomic study of muscle provides new insights into the growth superiority of a novel grouper hybrid.PLoS ONE 11,e0168802.
Sun,Y.,Huang,Y.,Li,X.,Baldwin,C.C.,Zhou,Z.,Yan,Z.,Crandall,K.A.,Zhang,Y.,Zhao,X.,Wang,M.,et al.(2016c).Fish-T1K(Transcriptomes of 1,000 Fishes)Project:large-scale transcriptome data for fish evolution studies.Gigascience 5,18.
Takehana,Y.,Matsuda,M.,Myosho,T.,Suster,M.L.,Kawakami,K.,ShinI,T.,Kohara,Y.,Kuroki,Y.,Toyoda,A.,Fujiyama,A.,et al.(2014).Co-option of Sox3 as the male-determining factor on the Ychromosome in the fish Oryzias dancena.Nat Commun 5,4157.
Taylor,J.S.,Braasch,I.,Frickey,T.,Meyer,A.,and Van de Peer,Y.(2003).Genome duplication,a trait shared by 22,000 species of ray-finned fish.Genome Res 13,382-390.
Tine,M.,Kuhl,H.,Gagnaire,P.A.,Louro,B.,Desmarais,E.,Martins,R.S.T.,Hecht,J.,Knaust,F.,Belkhir,K.,Klages,S.,et al.(2014).European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation.Nat Commun 5,5770.
Van Norren,D.,and Schellekens,P.(1990).Blue light hazard in rat.Vision Res 30,1517-1520.
Vandepoele,K.,De Vos,W.,Taylor,J.S.,Meyer,A.,and Van de Peer,Y.(2004).Major events in the genome evolution of vertebrates:paranome age and size differ considerably between ray-finned fishes and land vertebrates.Proc Natl Acad Sci USA 101,1638-1643.
Wang,G.,Yang,E.,Smith,K.J.,Zeng,Y.,Ji,G.,Connon,R.,Fangue,N.A.,and Cai,J.J.(2014).Gene expression responses of threespine stickleback to salinity:implications for salt-sensitive hypertension.Front Genet 5,312.
Wang,J.T.,Li,J.T.,Zhang,X.F.,and Sun,X.W.(2012).Transcriptome analysis reveals the time of the fourth round of genome duplication in common carp(Cyprinus carpio).BMC Genomics 13,96.
Wang,W.,Yi,Q.,Ma,L.,Zhou,X.,Zhao,H.,Wang,X.,Qi,J.,Yu,H.,Wang,Z.,and Zhang,Q.(2014).Sequencing and characterization of the transcriptome of half-smooth tongue sole(Cynoglossus semilaevis).BMC Genomics 15,470.
Wang,Y.,Lu,Y.,Zhang,Y.,Ning,Z.,Li,Y.,Zhao,Q.,Lu,H.,Huang,R.,Xia,X.,Feng,Q.,et al.(2015).The draft genome of the grass carp(Ctenopharyngodon idellus)provides insights into its evolution and vegetarian adaptation.Nat Genet 47,625-631.
Wang,Z.,Gerstein,M.,and Snyder,M.(2009).RNA-Seq:a revolutionary tool for transcriptomics.Nat Rev Genet 10,57-63.
Watson,W.,and Walker,H.J.(2004).The world’s smallest vertebrate,Schindleria brevipinguis,a new paedomorphic species in the family Schindleriidae(Perciformes:Gobioidei).Rec Aust Mus 56,139-142.
Windisch,H.S.,Frickenhaus,S.,John,U.,Knust,R.,P?rtner,H.O.,and Lucassen,M.(2014).Stress response or beneficial temperature acclimation:transcriptomic signatures in Antarctic fish(Pachycara brachycephalum).Mol Ecol 23,3469-3482.
Wu,C.,Zhang,D.,Kan,M.,Lv,Z.,Zhu,A.,Su,Y.,Zhou,D.,Zhang,J.,Zhang,Z.,Xu,M.,et al.(2014).The draft genome of the large yellow croaker reveals well-developed innate immunity.Nat Commun 5,5227.
Xia,J.H.,Bai,Z.,Meng,Z.,Zhang,Y.,Wang,L.,Liu,F.,Jing,W.,Yi Wan,Z.,Li,J.,Lin,H.,et al.(2015).Signatures of selection in tilapia revealed by whole genome resequencing.Sci Rep 5,14168.
Xie,B.,Li,X.,Lin,Z.,Ruan,Z.,Wang,M.,Liu,J.,Tong,T.,Li,J.,Huang,Y.,Wen,B.,et al.(2016).Prediction of toxin genes from Chinese yellow catfish based on transcriptomic and proteomic sequencing.Int JMol Sci 17,556.
Xu,J.,Bian,C.,Chen,K.,Liu,G.,Jiang,Y.,Luo,Q.,You,X.,Peng,W.,Li,J.,Huang,Y.,et al.(2017a).Draft genome of the Northern snakehead,Channa argus.Gigascience 6,11.
Xu,J.,Li,J.T.,Jiang,Y.,Peng,W.,Yao,Z.,Chen,B.,Jiang,L.,Feng,J.,Ji,P.,Liu,G.,et al.(2017b).Genomic basis of adaptive evolution:The survival of Amur Ide(Leuciscus waleckii)in an extremely alkaline environment.Mol Biol Evol 34,145-159.
Xu,P.,Zhang,X.,Wang,X.,Li,J.,Liu,G.,Kuang,Y.,Xu,J.,Zheng,X.,Ren,L.,Wang,G.,et al.(2014).Genome sequence and genetic diversity of the common carp,Cyprinus carpio.Nat Genet 46,1212-1219.
Xu,T.,Xu,G.,Che,R.,Wang,R.,Wang,Y.,Li,J.,Wang,S.,Shu,C.,Sun,Y.,Liu,T.,et al.(2016).The genome of the miiuy croaker reveals welldeveloped innate immune and sensory systems.Sci Rep 6,21902.
Yang,J.,Chen,X.,Bai,J.,Fang,D.,Qiu,Y.,Jiang,W.,Yuan,H.,Bian,C.,Lu,J.,He,S.,et al.(2016).The Sinocyclocheilus cavefish genome provides insights into cave adaptation.BMC Biol 14,1.
Yi,Y.,You,X.,Bian,C.,Chen,S.,Lv,Z.,Qiu,L.,and Shi,Q.(2017).High-throughput identification of antimicrobial peptides from amphibious mudskippers.Mar Drugs 15,364.
Yokoyama,S.(2002).Molecular evolution of color vision in vertebrates.Gene 300,69-78.
Yokoyama,S.,and Radlwimmer,F.B.(2001).The molecular genetics and evolution of red and green color vision in vertebrates.Genetics 158,1697-1710.
Yokoyama,S.,Yang,H.,and Starmer,W.T.(2008).Molecular basis of spectral tuning in the red-and green-sensitive(M/LWS)pigments in vertebrates.Genetics 179,2037-2043.
You,X.,Bian,C.,Zan,Q.,Xu,X.,Liu,X.,Chen,J.,Wang,J.,Qiu,Y.,Li,W.,Zhang,X.,et al.(2014).Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes.Nat Commun 5,5594.
You,X.,Sun,M.,Li,J.,Bian,C.,Chen,J.,Yi,Y.,Yu,H.,and Shi,Q.(2018).Mudskippers and their genetic adaptations to an amphibious lifestyle.Animals 8,24.
Yu,H.,You,X.,Li,J.,Zhang,X.,Zhang,S.,Jiang,S.,Lin,X.,Lin,H.R.,Meng,Z.,and Shi,Q.(2018).A genome-wide association study on growth traits in orange-spotted grouper(Epinephelus coioides)with RAD-seq genotyping.Sci China Life Sci 61,934-946.
Yue,G.H.,Liew,W.C.,and Orban,L.(2006).The complete mitochondrial genome of a basal teleost,the Asian arowana(Scleropages formosus,Osteoglossidae).BMC Genomics 7,242.
Yue,G.H.,and Wang,L.(2017).Current status of genome sequencing and its applications in aquaculture.Aquaculture 468,337-347.
Zhang,S.,Li,J.,Qin,Q.,Liu,W.,Bian,C.,Yi,Y.,Wang,M.,Zhong,L.,You,X.,Tang,S.,et al.(2018).Whole-genome sequencing of Chinese yellow catfish provides a valuable genetic resource for high-throughput identification of toxin genes.Toxins 10,488.
Zhang,Z.,Zhang,K.,Chen,S.,Zhang,Z.,Zhang,J.,You,X.,Bian,C.,Xu,J.,Jia,C.,Qiang,J.,et al.(2018).Draft genome of the protandrous Chinese black porgy,Acanthopagrus schlegelii.Gigascience 7.
Ziegman,R.,and Alewood,P.(2015).Bioactive components in fish venoms.Toxins 7,1497-1531.
Ahnelt,H.(2018).Imprecise naming:the anadromous and the sea spawning threespine stickleback should be discriminated by names.Biologia 73,389-392.
Alexandrou,M.A.,Swartz,B.A.,Matzke,N.J.,and Oakley,T.H.(2013).Genome duplication and multiple evolutionary origins of complex migratory behavior in Salmonidae.Mol Phylogenet Evol 69,514-523.
Alfaro,M.E.(2018).Resolving the ray-finned fish tree of life.Proc Natl Acad Sci USA 115,6107-6109.
Amores,A.,Force,A.,Yan,Y.L.,Joly,L.,Amemiya,C.,Fritz,A.,Ho,R.K.,Langeland,J.,Prince,V.,Wang,Y.L.,et al.(1998).Zebrafish hox clusters and vertebrate genome evolution.Science 282,1711-1714.
Ao,J.,Mu,Y.,Xiang,L.X.,Fan,D.D.,Feng,M.J.,Zhang,S.,Shi,Q.,Zhu,L.Y.,Li,T.,Ding,Y.,et al.(2015).Genome sequencing of the perciform fish Larimichthys crocea provides insights into molecular and genetic mechanisms of stress adaptation.PLoS Genet 11,e1005118.
Aparicio,S.,Chapman,J.,Stupka,E.,Putnam,N.,Chia,J.M.,Dehal,P.,Christoffels,A.,Rash,S.,Hoon,S.,Smit,A.,et al.(2002).Wholegenome shotgun assembly and analysis of the genome of Fugu rubripes.Science 297,1301-1310.
Austin,C.M.,Tan,M.H.,Croft,L.J.,Hammer,M.P.,and Gan,H.M.(2015).Whole genome sequencing of the Asian arowana(Scleropages formosus)provides insights into the evolution of ray-finned fishes.Genome Biol Evol 7,2885-2895.
Barrett,R.D.H.,Rogers,S.M.,and Schluter,D.(2008).Natural selection on a major armor gene in threespine stickleback.Science 322,255-257.
Berthelot,C.,Brunet,F.,Chalopin,D.,Juanchich,A.,Bernard,M.,No?l,B.,Bento,P.,Da Silva,C.,Labadie,K.,Alberti,A.,et al.(2014).The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates.Nat Commun 5,3657.
Bian,C.,Hu,Y.,Ravi,V.,Kuznetsova,I.S.,Shen,X.,Mu,X.,Sun,Y.,You,X.,Li,J.,Li,X.,et al.(2016).The Asian arowana(Scleropages formosus)genome provides new insights into the evolution of an early lineage of teleosts.Sci Rep 6,24501.
Bilyk,K.T.,and Cheng,C.H.C.(2013).Model of gene expression in extreme cold-reference transcriptome for the high-Antarctic cryopelagic notothenioid fish Pagothenia borchgrevinki.BMCGenomics 14,634.
Braasch,I.,Brunet,F.,Volff,J.N.,and Schartl,M.(2009).Pigmentation pathway evolution after whole-genome duplication in fish.Genome Biol Evol 1,479-493.
Braasch,I.,Gehrke,A.R.,Smith,J.J.,Kawasaki,K.,Manousaki,T.,Pasquier,J.,Amores,A.,Desvignes,T.,Batzel,P.,Catchen,J.,et al.(2016).Erratum:Corrigendum:The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.Nat Genet 48,700.
Brawand,D.,Wagner,C.E.,Li,Y.I.,Malinsky,M.,Keller,I.,Fan,S.,Simakov,O.,Ng,A.Y.,Lim,Z.W.,Bezault,E.,et al.(2014).The genomic substrate for adaptive radiation in African cichlid fish.Nature513,375-381.
Byrne,A.,Beaudin,A.E.,Olsen,H.E.,Jain,M.,Cole,C.,Palmer,T.,DuBois,R.M.,Forsberg,E.C.,Akeson,M.,and Vollmers,C.(2017).Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells.Nat Commun 8,16027.
Carmona,S.J.,Teichmann,S.A.,Ferreira,L.,Macaulay,I.C.,Stubbington,M.J.T.,Cvejic,A.,and Gfeller,D.(2017).Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types.Genome Res 27,451-461.
Carruthers,M.,Yurchenko,A.A.,Augley,J.J.,Adams,C.E.,Herzyk,P.,and Elmer,K.R.(2018).De novo transcriptome assembly,annotation and comparison of four ecological and evolutionary model salmonid fish species.BMC Genomics 19,32.
Casewell,N.R.,Huttley,G.A.,and Wüster,W.(2012).Dynamic evolution of venom proteins in squamate reptiles.Nat Commun 3,1066.
Chen,S.,Zhang,G.,Shao,C.,Huang,Q.,Liu,G.,Zhang,P.,Song,W.,An,N.,Chalopin,D.,Volff,J.N.,et al.(2014).Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle.Nat Genet 46,253-260.
Chen,X.,Zhong,L.,Bian,C.,Xu,P.,Qiu,Y.,You,X.,Zhang,S.,Huang,Y.,Li,J.,Wang,M.,et al.(2016).High-quality genome assembly of channel catfish,Ictalurus punctatus.Gigascience 5,39.
Chen,Z.,Cheng,C.H.C.,Zhang,J.,Cao,L.,Chen,L.,Zhou,L.,Jin,Y.,Ye,H.,Deng,C.,Dai,Z.,et al.(2008).Transcriptomic and genomic evolution under constant cold in Antarctic notothenioid fish.Proc Natl Acad Sci USA 105,12944-12949.
Chinchar,V.G.,Bryan,L.,Silphadaung,U.,Noga,E.,Wade,D.,and Rollins-Smith,L.(2004).Inactivation of viruses infecting ectothermic animals by amphibian and piscine antimicrobial peptides.Virology 323,268-275.
Chinen,A.,Matsumoto,Y.,and Kawamura,S.(2005).Reconstitution of ancestral green visual pigments of zebrafish and molecular mechanism of their spectral differentiation.Mol Biol Evol 22,1001-1010.
Christoffels,A.,Koh,E.G.L.,Chia,J.M.,Brenner,S.,Aparicio,S.,and Venkatesh,B.(2004).Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes.Mol Biol Evol 21,1146-1151.
Collins,J.E.,White,S.,Searle,S.M.J.,and Stemple,D.L.(2012).Incorporating RNA-seq data into the zebrafish Ensembl genebuild.Genome Res 22,2067-2078.
Colosimo,P.F.,Hosemann,K.E.,Balabhadra,S.,Villarreal,G.,Dickson,M.,Grimwood,J.,Schmutz,J.,Myers,R.M.,Schluter,D.,and Kingsley,D.M.(2005).Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles.Science 307,1928-1933.
Coppe,A.,Agostini,C.,Marino,I.A.M.,Zane,L.,Bargelloni,L.,Bortoluzzi,S.,and Patarnello,T.(2013).Genome evolution in the cold:Antarctic icefish muscle transcriptome reveals selective duplications increasing mitochondrial function.Genome Biol Evol 5,45-60.
Crossa,J.,Pérez-Rodríguez,P.,Cuevas,J.,Montesinos-López,O.,Jarquín,D.,de Los Campos,G.,Burgue?o,J.,González-Camacho,J.M.,PérezElizalde,S.,Beyene,Y.,et al.(2017).Genomic selection in plant breeding:methods,models,and perspectives.Trends Plant Sci 22,961-975.
Day,J.J.(2006).Fishes of the world,4th edition.Fish Fisheries 7,334.
Deamer,D.,Akeson,M.,and Branton,D.(2016).Three decades of nanopore sequencing.Nat Biotechnol 34,518-524.
Dehal,P.,and Boore,J.L.(2005).Two rounds of whole genome duplication in the ancestral vertebrate.PLoS Biol 3,e314.
Detrich,H.W.,Stuart,A.,Schoenborn,M.,Parker,S.K.,Methé,B.A.,and Amemiya,C.T.(2010).Genome enablement of the notothenioidei:genome size estimates from 11 species and BAC libraries from 2representative taxa.J Exp Zool 314B,369-381.
Domingos,J.A.,Zenger,K.R.,and Jerry,D.R.(2015).Whole-genome shotgun sequence assembly enables rapid gene characterization in the tropical fish barramundi,Lates calcarifer.Anim Genet 46,468-469.
Don,E.K.,de Jong-Curtain,T.A.,Doggett,K.,Hall,T.E.,Heng,B.,Badrock,A.P.,Winnick,C.,Nicholson,G.A.,Guillemin,G.J.,Currie,P.D.,et al.(2016).Genetic basis of hindlimb loss in a naturally occurring vertebrate model.Biol Open 5,359-366.
Eid,J.,Fehr,A.,Gray,J.,Luong,K.,Lyle,J.,Otto,G.,Peluso,P.,Rank,D.,Baybayan,P.,Bettman,B.,et al.(2009).Real-time DNA sequencing from single polymerase molecules.Science 323,133-138.
Feldkaemper,M.,and Schaeffel,F.(2013).An updated view on the role of dopamine in myopia.Exp Eye Res 114,106-119.
Fraser,B.A.,Künstner,A.,Reznick,D.N.,Dreyer,C.,and Weigel,D.(2015).Population genomics of natural and experimental populations of guppies(Poecilia reticulata).Mol Ecol 24,389-408.
Froese,R.,and Pauly,D.(2011).FishBase.In World Wide Web electronic publication wwwfishbaseorg ver 08/2012(2011).
Gallant,J.R.,Traeger,L.L.,Volkening,J.D.,Moffett,H.,Chen,P.H.,Novina,C.D.,Phillips,G.N.,Jr.,Anand,R.,Wells,G.B.,Pinch,M.,et al.(2014).Nonhuman genetics.Genomic basis for the convergent evolution of electric organs.Science 344,1522-1525.
Genomic Resources Development Consortium,Alvarez,P.,Arthofer,W.,Coelho,M.M.,Conklin,D.,Estonba,A.,Grosso,A.R.,Helyar,S.J.,Langa,J.,Machado,M.P.,et al.(2015).Genomic Resources Notes Accepted 1 June 2015-31 July 2015.Mol Ecol Resour 15,1510-1512.
Glasauer,S.M.K.,and Neuhauss,S.C.F.(2014).Whole-genome duplication in teleost fishes and its evolutionary consequences.Mol Genet Genomics 289,1045-1060.
Grabherr,M.G.,Haas,B.J.,Yassour,M.,Levin,J.Z.,Thompson,D.A.,Amit,I.,Adiconis,X.,Fan,L.,Raychowdhury,R.,Zeng,Q.,et al.(2011).Full-length transcriptome assembly from RNA-Seq data without a reference genome.Nat Biotechnol 29,644-652.
Guan,L.,Chi,W.,Xiao,W.,Chen,L.,and He,S.(2014).Analysis of hypoxia-inducible factor alpha polyploidization reveals adaptation to Tibetan Plateau in the evolution of schizothoracine fish.BMC Evol Biol14,192.
Gui,J.,Liu,B.,Cao,G.,Lipchik,A.M.,Perez,M.,Dekan,Z.,Mobli,M.,Daly,N.L.,Alewood,P.F.,Parker,L.L.,et al.(2014).A tarantula-venom peptide antagonizes the TRPA1 nociceptor ion channel by binding to the S1-S4 gating domain.Curr Biol 24,473-483.
Harel,I.,Benayoun,B.A.,Machado,B.,Singh,P.P.,Hu,C.K.,Pech,M.F.,Valenzano,D.R.,Zhang,E.,Sharp,S.C.,Artandi,S.E.,et al.(2015).Aplatform for rapid exploration of aging and diseases in a naturally shortlived vertebrate.Cell 160,1013-1026.
Hattori,R.S.,Murai,Y.,Oura,M.,Masuda,S.,Majhi,S.K.,Sakamoto,T.,Fernandino,J.I.,Somoza,G.M.,Yokota,M.,and Strüssmann,C.A.(2012).A Y-linked anti-Mullerian hormone duplication takes over a critical role in sex determination.Proc Natl Acad Sci USA 109,2955-2959.
Hedges,S.B.,and Kumar,S.(2009).Discovering the timetree of life.In The Timetree of Life.S.B.Hedges,and S.Kumar,eds.(New York:Oxford University Press),pp.3-18.
Henkel,C.V.,Dirks,R.P.,de Wijze,D.L.,Minegishi,Y.,Aoyama,J.,Jansen,H.J.,Turner,B.,Knudsen,B.,Bundgaard,M.,Hvam,K.L.,et al.(2012).First draft genome sequence of the Japanese eel,Anguilla japonica.Gene 511,195-201.
Hohenlohe,P.A.,Bassham,S.,Etter,P.D.,Stiffler,N.,Johnson,E.A.,and Cresko,W.A.(2010).Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags.PLoS Genet 6,e1000862.
Howe,K.,Clark,M.D.,Torroja,C.F.,Torrance,J.,Berthelot,C.,Muffato,M.,Collins,J.E.,Humphray,S.,McLaren,K.,Matthews,L.,et al.(2013).The zebrafish reference genome sequence and its relationship to the human genome.Nature 496,498-503.
Hubert,S.,Higgins,B.,Borza,T.,and Bowman,S.(2010).Development of a SNP resource and a genetic linkage map for Atlantic cod(Gadus morhua).BMC Genomics 11,191.
Hughes,L.C.,Ortí,G.,Huang,Y.,Sun,Y.,Baldwin,C.C.,Thompson,A.W.,Arcila,D.,Betancur-R.,R.,Li,C.,Becker,L.,et al.(2018).Comprehensive phylogeny of ray-finned fishes(Actinopterygii)based on transcriptomic and genomic data.Proc Natl Acad Sci USA 115,6249-6254.
Hurley,I.A.,Mueller,R.L.,Dunn,K.A.,Schmidt,E.J.,Friedman,M.,Ho,R.K.,Prince,V.E.,Yang,Z.,Thomas,M.G.,and Coates,M.I.(2007).Anew time-scale for ray-finned fish evolution.Proc R Soc B-Biol Sci274,489-498.
Huth,T.J.,and Place,S.P.(2016).Transcriptome wide analyses reveal a sustained cellular stress response in the gill tissue of Trematomus bernacchii after acclimation to multiple stressors.BMC Genomics 17,127.
Innan,H.,and Kondrashov,F.(2010).The evolution of gene duplications:classifying and distinguishing between models.Nat Rev Genet 11,97-108.
Jaillon,O.,Aury,J.M.,Brunet,F.,Petit,J.L.,Stange-Thomann,N.,Mauceli,E.,Bouneau,L.,Fischer,C.,Ozouf-Costaz,C.,Bernot,A.,et al.(2004).Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype.Nature 431,946-957.
Jones,F.C.,Brown,C.,Pemberton,J.M.,and Braithwaite,V.A.(2006).Reproductive isolation in a threespine stickleback hybrid zone.J Evol Biol 19,1531-1544.
Jones,F.C.,Grabherr,M.G.,Chan,Y.F.,Russell,P.,Mauceli,E.,Johnson,J.,Swofford,R.,Pirun,M.,Zody,M.C.,White,S.,et al.(2012).The genomic basis of adaptive evolution in threespine sticklebacks.Nature484,55-61.
Kasahara,M.,Naruse,K.,Sasaki,S.,Nakatani,Y.,Qu,W.,Ahsan,B.,Yamada,T.,Nagayasu,Y.,Doi,K.,Kasai,Y.,et al.(2007).The medaka draft genome and insights into vertebrate genome evolution.Nature447,714-719.
Kawaguchi,M.,Yasumasu,S.,Shimizu,A.,Kudo,N.,Sano,K.,Iuchi,I.,and Nishida,M.(2013).Adaptive evolution of fish hatching enzyme:one amino acid substitution results in differential salt dependency of the enzyme.J Exp Biol 216,1609-1615.
Kelley,J.L.,Yee,M.C.,Brown,A.P.,Richardson,R.R.,Tatarenkov,A.,Lee,C.C.,Harkins,T.T.,Bustamante,C.D.,and Earley,R.L.(2016).The genome of the self-fertilizing mangrove rivulus fish,Kryptolebias marmoratus:A model for studying phenotypic plasticity and adaptations to extreme environments.Genome Biol Evol 8,2145-2154.
Kettleborough,R.N.W.,Busch-Nentwich,E.M.,Harvey,S.A.,Dooley,C.M.,de Bruijn,E.,van Eeden,F.,Sealy,I.,White,R.J.,Herd,C.,Nijman,I.J.,et al.(2013).A systematic genome-wide analysis of zebrafish protein-coding gene function.Nature 496,494-497.
Kim,J.B.,Porreca,G.J.,Song,L.,Greenway,S.C.,Gorham,J.M.,Church,G.M.,Seidman,C.E.,and Seidman,J.G.(2007).Polony multiplex analysis of gene expression(PMAGE)in mouse hypertrophic cardiomyopathy.Science 316,1481-1484.
Kodzius,R.,Kojima,M.,Nishiyori,H.,Nakamura,M.,Fukuda,S.,Tagami,M.,Sasaki,D.,Imamura,K.,Kai,C.,Harbers,M.,et al.(2006).CAGE:cap analysis of gene expression.Nat Methods 3,211-222.
Laranjeiro,R.,and Whitmore,D.(2014).Transcription factors involved in retinogenesis are co-opted by the circadian clock following photoreceptor differentiation.Development 141,2644-2656.
Li,J.,Bian,C.,Hu,Y.,Mu,X.,Shen,X.,Ravi,V.,Kuznetsova,I.S.,Sun,Y.,You,X.,Qiu,Y.,et al.(2016).A chromosome-level genome assembly of the Asian arowana,Scleropages formosus.Sci Data 3,160105.
Li,J.,You,X.,Bian,C.,Yu,H.,Coon,S.L.,and Shi,Q.(2015a).Molecular evolution of aralkylamine N-acetyltransferase in fish:A genomic survey.Int J Mol Sci 17,51.
Li,M.,Sun,Y.,Zhao,J.,Shi,H.,Zeng,S.,Ye,K.,Jiang,D.,Zhou,L.,Sun,L.,Tao,W.,et al.(2015b).A tandem duplicate of anti-Müllerian hormone with a missense SNP on the Y chromosome is essential for male sex determination in Nile tilapia,Oreochromis niloticus.PLoSGenet 11,e1005678.
Li,M.,and Wang,D.(2017).Gene editing nuclease and its application in tilapia.Sci Bull 62,165-173.
Li,X.Y.,and Gui,J.F.(2018a).Diverse and variable sex determination mechanisms in vertebrates.Sci China Life Sci 61,1503-1514.
Li,X.Y.,and Gui,J.F.(2018b).An epigenetic regulatory switch controlling temperature-dependent sex determination in vertebrates.Sci China Life Sci 61,996-998.
Lieberman-Aiden,E.,van Berkum,N.L.,Williams,L.,Imakaev,M.,Ragoczy,T.,Telling,A.,Amit,I.,Lajoie,B.R.,Sabo,P.J.,Dorschner,M.O.,et al.(2009).Comprehensive mapping of long-range interactions reveals folding principles of the human genome.Science 326,289-293.
Lien,S.,Koop,B.F.,Sandve,S.R.,Miller,J.R.,Kent,M.P.,Nome,T.,Hvidsten,T.R.,Leong,J.S.,Minkley,D.R.,Zimin,A.,et al.(2016).The Atlantic salmon genome provides insights into rediploidization.Nature533,200-205.
Lin,J.J.,Wang,F.Y.,Li,W.H.,and Wang,T.Y.(2017).The rises and falls of opsin genes in 59 ray-finned fish genomes and their implications for environmental adaptation.Sci Rep 7,15568.
Lin,Q.,Fan,S.,Zhang,Y.,Xu,M.,Zhang,H.,Yang,Y.,Lee,A.P.,Woltering,J.M.,Ravi,V.,Gunter,H.M.,et al.(2016).The seahorse genome and the evolution of its specialized morphology.Nature 540,395-399.
Lin,Q.,Qiu,Y.,Gu,R.,Xu,M.,Li,J.,Bian,C.,Zhang,H.,Qin,G.,Zhang,Y.,Luo,W.,et al.(2017).Draft genome of the lined seahorse,Hippocampus erectus.Gigascience 6,1-6.
Liu,K.,Xu,D.,Li,J.,Bian,C.,Duan,J.,Zhou,Y.,Zhang,M.,You,X.,You,Y.,Chen,J.,et al.(2017).Whole genome sequencing of Chinese clearhead icefish,Protosalanx hyalocranius.Gigascience 6,1-6.
Liu,S.,Zhang,Y.,Zhou,Z.,Waldbieser,G.,Sun,F.,Lu,J.,Zhang,J.,Jiang,Y.,Zhang,H.,Wang,X.,et al.(2012).Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote.BMC Genomics 13,595.
Liu,Y.,Xu,P.,Xu,J.,Huang,Y.,Liu,Y.,Fang,H.,Hu,Y.,You,X.,Bian,C.,Sun,M.,et al.(2017).China is initiating the Aquatic 10-100-1,000Genomics Program.Sci China Life Sci 60,329-332.
Liu,Z.,Liu,S.,Yao,J.,Bao,L.,Zhang,J.,Li,Y.,Jiang,C.,Sun,L.,Wang,R.,Zhang,Y.,et al.(2016).The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts.Nat Commun 7,11757.
Lopez,M.E.,Neira,R.,and Yanez,J.M.(2014).Applications in the search for genomic selection signatures in fish.Front Genet 5,458.
Lynch,M.,and Force,A.(2000).The probability of duplicate gene preservation by subfunctionalization.Genetics 154,459-473.
Ma,X.,Dai,W.,Kang,J.,Yang,L.,and He,S.(2015).Comprehensive transcriptome analysis of six catfish species from an altitude gradient reveals adaptive evolution in Tibetan fishes.G3 6,141-148.
Manzon,L.A.(2002).The role of prolactin in fish osmoregulation:a review.Gen Comp Endocrinol 125,291-310.
Marioni,J.C.,Mason,C.E.,Mane,S.M.,Stephens,M.,and Gilad,Y.(2008).RNA-seq:an assessment of technical reproducibility and comparison with gene expression arrays.Genome Res 18,1509-1517.
Martinez Barrio,A.,Lamichhaney,S.,Fan,G.,Rafati,N.,Pettersson,M.,Zhang,H.,Dainat,J.,Ekman,D.,Hoppner,M.,Jern,P.,et al.(2016).The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing.Elife 5.
Masso-Silva,J.A.,and Diamond,G.(2014).Antimicrobial peptides from fish.Pharmaceuticals 7,265-310.
Matsuda,M.,Nagahama,Y.,Shinomiya,A.,Sato,T.,Matsuda,C.,Kobayashi,T.,Morrey,C.E.,Shibata,N.,Asakawa,S.,Shimizu,N.,et al.(2002).DMY is a Y-specific DM-domain gene required for male development in the medaka fish.Nature 417,559-563.
Matsumura,H.,Kruger,D.,Kahl,G.,and Terauchi,R.(2008).SuperSAGE:a modern platform for genome-wide quantitative transcript profiling.Curr Pharm Biotechnol 9,368-374.
McGaugh,S.E.,Gross,J.B.,Aken,B.,Blin,M.,Borowsky,R.,Chalopin,D.,Hinaux,H.,Jeffery,W.R.,Keene,A.,Ma,L.,et al.(2014).The cavefish genome reveals candidate genes for eye loss.Nat Commun 5,5307.
Mei,J.,and Gui,J.F.(2015).Genetic basis and biotechnological manipulation of sexual dimorphism and sex determination in fish.Sci China Life Sci 58,124-136.
Murdy,E.O.(1989).A taxonomic revision and cladistic analysis of the oxudercine gobies(Gobiidae:Oxudercinae)(Australian Museum),pp.1-93.
Nakamura,Y.,Mori,K.,Saitoh,K.,Oshima,K.,Mekuchi,M.,Sugaya,T.,Shigenobu,Y.,Ojima,N.,Muta,S.,Fujiwara,A.,et al.(2013).Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna.Proc Natl Acad Sci USA 110,11061-11066.
Near,T.J.,Eytan,R.I.,Dornburg,A.,Kuhn,K.L.,Moore,J.A.,Davis,M.P.,Wainwright,P.C.,Friedman,M.,and Smith,W.L.(2012).Resolution of ray-finned fish phylogeny and timing of diversification.Proc Natl Acad Sci USA 109,13698-13703.
Noga,E.J.,and Silphaduang,U.(2003).Piscidins:a novel family of peptide antibiotics from fish.Drug News Perspect 16,87-92.
Nudelman,G.,Frasca,A.,Kent,B.,Sadler,K.C.,Sealfon,S.C.,Walsh,M.J.,and Zaslavsky,E.(2018).High resolution annotation of zebrafish transcriptome using long-read sequencing.Genome Res 28,1415-1425.
Otto,S.P.,and Whitton,J.(2000).Polyploid incidence and evolution.Annu Rev Genet 34,401-437.
Palaiokostas,C.,Bekaert,M.,Khan,M.G.Q.,Taggart,J.B.,Gharbi,K.,McAndrew,B.J.,and Penman,D.J.(2015).A novel sex-determining QTL in Nile tilapia(Oreochromis niloticus).BMC Genomics 16,171.
Pan,H.,Yu,H.,Ravi,V.,Li,C.,Lee,A.P.,Lian,M.M.,Tay,B.H.,Brenner,S.,Wang,J.,Yang,H.,et al.(2016).The genome of the largest bony fish,ocean sunfish(Mola mola),provides insights into its fast growth rate.Gigascience 5,36.
Patton,E.E.,Mathers,M.E.,and Schartl,M.(2011).Generating and analyzing fish models of melanoma.Methods Cell Biol 105,339-366.
Pauli,A.,Valen,E.,Lin,M.F.,Garber,M.,Vastenhouw,N.L.,Levin,J.Z.,Fan,L.,Sandelin,A.,Rinn,J.L.,Regev,A.,et al.(2012).Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis.Genome Res 22,577-591.
Picelli,S.,Faridani,O.R.,Bj?rklund,A.K.,Winberg,G.,Sagasser,S.,and Sandberg,R.(2014).Full-length RNA-seq from single cells using Smart-seq2.Nat Protoc 9,171-181.
Pope,E.C.,Hays,G.C.,Thys,T.M.,Doyle,T.K.,Sims,D.W.,Queiroz,N.,Hobson,V.J.,Kubicek,L.,and Houghton,J.D.R.(2010).The biology and ecology of the ocean sunfish Mola mola:a review of current knowledge and future research perspectives.Rev Fish Biol Fisheries 20,471-487.
Postlethwait,J.H.,Woods,I.G.,Ngo-Hazelett,P.,Yan,Y.L.,Kelly,P.D.,Chu,F.,Huang,H.,Hill-Force,A.,and Talbot,W.S.(2000).Zebrafish comparative genomics and the origins of vertebrate chromosomes.Genome Res 10,1890-1902.
Prohaska,S.J.,and Stadler,P.F.(2004).The duplication of the Hox gene clusters in teleost fishes.Theor Biosci 123,89-110.
Rajanbabu,V.,and Chen,J.Y.(2011).Applications of antimicrobial peptides from fish and perspectives for the future.Peptides 32,415-420.
Reitzel,A.M.,Karchner,S.I.,Franks,D.G.,Evans,B.R.,Nacci,D.,Champlin,D.,Vieira,V.M.,and Hahn,M.E.(2014).Genetic variation at aryl hydrocarbon receptor(AHR)loci in populations of Atlantic killifish(Fundulus heteroclitus)inhabiting polluted and reference habitats.BMC Evol Biol 14,6.
Rennison,D.J.,Owens,G.L.,and Taylor,J.S.(2012).Opsin gene duplication and divergence in ray-finned fish.Mol Phylogenet Evol62,986-1008.
Rhoads,A.,and Au,K.F.(2015).PacBio sequencing and its applications.Genom Proteom BioInf 13,278-289.
Rondeau,E.B.,Minkley,D.R.,Leong,J.S.,Messmer,A.M.,Jantzen,J.R.,von Schalburg,K.R.,Lemon,C.,Bird,N.H.,and Koop,B.F.(2014).The genome and linkage map of the northern pike(Esox lucius):conserved synteny revealed between the salmonid sister group and the Neoteleostei.PLoS ONE 9,e102089.
Salem,M.,Vallejo,R.L.,Leeds,T.D.,Palti,Y.,Liu,S.,Sabbagh,A.,Rexroad,C.E.,and Yao,J.(2012).RNA-Seq identifies SNP markers for growth traits in rainbow trout.PLoS ONE 7,e36264.
Schartl,M.,Walter,R.B.,Shen,Y.,Garcia,T.,Catchen,J.,Amores,A.,Braasch,I.,Chalopin,D.,Volff,J.N.,Lesch,K.P.,et al.(2013).The genome of the platyfish,Xiphophorus maculatus,provides insights into evolutionary adaptation and several complex traits.Nat Genet 45,567-572.
Schena,M.,Shalon,D.,Davis,R.W.,and Brown,P.O.(1995).Quantitative monitoring of gene expression patterns with a complementary DNAmicroarray.Science 270,467-470.
Shao,C.,Bao,B.,Xie,Z.,Chen,X.,Li,B.,Jia,X.,Yao,Q.,Ortí,G.,Li,W.,Li,X.,et al.(2017).The genome and transcriptome of Japanese flounder provide insights into flatfish asymmetry.Nat Genet 49,119-124.
Shi,Y.,and Yokoyama,S.(2003).Molecular analysis of the evolutionary significance of ultraviolet vision in vertebrates.Proc Natl Acad Sci USA 100,8308-8313.
Shin,S.C.,Ahn,D.H.,Kim,S.J.,Pyo,C.W.,Lee,H.,Kim,M.K.,Lee,J.,Lee,J.E.,Detrich,H.W.,Postlethwait,J.H.,et al.(2014).The genome sequence of the Antarctic bullhead notothen reveals evolutionary adaptations to a cold environment.Genome Biol 15,468.
Shin,S.C.,Kim,S.J.,Lee,J.K.,Ahn,D.H.,Kim,M.G.,Lee,H.,Lee,J.,Kim,B.K.,and Park,H.(2012).Transcriptomics and comparative analysis of three antarctic notothenioid fishes.PLoS ONE 7,e43762.
Skene,D.J.(1992).N-Acetyltransferase and melatonin in the retina:regulation,function and mode of action.Biochm Soc Trans 20,312-315.
Small,C.M.,Bassham,S.,Catchen,J.,Amores,A.,Fuiten,A.M.,Brown,R.S.,Jones,A.G.,and Cresko,W.A.(2016).The genome of the Gulf pipefish enables understanding of evolutionary innovations.Genome Biol 17,258.
Soltis,P.S.S.D.E.(2012).Polyploidy and genome evolution,Chapter 17(USA:Springer),pp.341-384.
Sonesson,A.K.,and Meuwissen,T.H.E.(2009).Testing strategies for genomic selection in aquaculture breeding programs.Genet Sel Evol41,37.
Star,B.,Nederbragt,A.J.,Jentoft,S.,Grimholt,U.,Malmstr?m,M.,Gregers,T.F.,Rounge,T.B.,Paulsen,J.,Solbakken,M.H.,Sharma,A.,et al.(2011).The genome sequence of Atlantic cod reveals a unique immune system.Nature 477,207-210.
Sudhagar,A.,Kumar,G.,and El-Matbouli,M.(2018).Transcriptome analysis based on RNA-seq in understanding pathogenic mechanisms of diseases and the immune system of fish:A comprehensive review.Int JMol Sci 19,245.
Sun,Y.,Guo,C.Y.,Wang,D.D.,Li,X.F.,Xiao,L.,Zhang,X.,You,X.,Shi,Q.,Hu,G.J.,Fang,C.,et al.(2016a).Transcriptome analysis reveals the molecular mechanisms underlying growth superiority in a novel grouper hybrid(Epinephelus fuscogutatus♀×E.lanceolatus♂).BMCGenet 17,24.
Sun,Y.,Huang,Y.,Hu,G.,Zhang,X.,Ruan,Z.,Zhao,X.,Guo,C.,Tang,Z.,Li,X.,You,X.,et al.(2016b).Comparative transcriptomic study of muscle provides new insights into the growth superiority of a novel grouper hybrid.PLoS ONE 11,e0168802.
Sun,Y.,Huang,Y.,Li,X.,Baldwin,C.C.,Zhou,Z.,Yan,Z.,Crandall,K.A.,Zhang,Y.,Zhao,X.,Wang,M.,et al.(2016c).Fish-T1K(Transcriptomes of 1,000 Fishes)Project:large-scale transcriptome data for fish evolution studies.Gigascience 5,18.
Takehana,Y.,Matsuda,M.,Myosho,T.,Suster,M.L.,Kawakami,K.,ShinI,T.,Kohara,Y.,Kuroki,Y.,Toyoda,A.,Fujiyama,A.,et al.(2014).Co-option of Sox3 as the male-determining factor on the Ychromosome in the fish Oryzias dancena.Nat Commun 5,4157.
Taylor,J.S.,Braasch,I.,Frickey,T.,Meyer,A.,and Van de Peer,Y.(2003).Genome duplication,a trait shared by 22,000 species of ray-finned fish.Genome Res 13,382-390.
Tine,M.,Kuhl,H.,Gagnaire,P.A.,Louro,B.,Desmarais,E.,Martins,R.S.T.,Hecht,J.,Knaust,F.,Belkhir,K.,Klages,S.,et al.(2014).European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation.Nat Commun 5,5770.
Van Norren,D.,and Schellekens,P.(1990).Blue light hazard in rat.Vision Res 30,1517-1520.
Vandepoele,K.,De Vos,W.,Taylor,J.S.,Meyer,A.,and Van de Peer,Y.(2004).Major events in the genome evolution of vertebrates:paranome age and size differ considerably between ray-finned fishes and land vertebrates.Proc Natl Acad Sci USA 101,1638-1643.
Wang,G.,Yang,E.,Smith,K.J.,Zeng,Y.,Ji,G.,Connon,R.,Fangue,N.A.,and Cai,J.J.(2014).Gene expression responses of threespine stickleback to salinity:implications for salt-sensitive hypertension.Front Genet 5,312.
Wang,J.T.,Li,J.T.,Zhang,X.F.,and Sun,X.W.(2012).Transcriptome analysis reveals the time of the fourth round of genome duplication in common carp(Cyprinus carpio).BMC Genomics 13,96.
Wang,W.,Yi,Q.,Ma,L.,Zhou,X.,Zhao,H.,Wang,X.,Qi,J.,Yu,H.,Wang,Z.,and Zhang,Q.(2014).Sequencing and characterization of the transcriptome of half-smooth tongue sole(Cynoglossus semilaevis).BMC Genomics 15,470.
Wang,Y.,Lu,Y.,Zhang,Y.,Ning,Z.,Li,Y.,Zhao,Q.,Lu,H.,Huang,R.,Xia,X.,Feng,Q.,et al.(2015).The draft genome of the grass carp(Ctenopharyngodon idellus)provides insights into its evolution and vegetarian adaptation.Nat Genet 47,625-631.
Wang,Z.,Gerstein,M.,and Snyder,M.(2009).RNA-Seq:a revolutionary tool for transcriptomics.Nat Rev Genet 10,57-63.
Watson,W.,and Walker,H.J.(2004).The world’s smallest vertebrate,Schindleria brevipinguis,a new paedomorphic species in the family Schindleriidae(Perciformes:Gobioidei).Rec Aust Mus 56,139-142.
Windisch,H.S.,Frickenhaus,S.,John,U.,Knust,R.,P?rtner,H.O.,and Lucassen,M.(2014).Stress response or beneficial temperature acclimation:transcriptomic signatures in Antarctic fish(Pachycara brachycephalum).Mol Ecol 23,3469-3482.
Wu,C.,Zhang,D.,Kan,M.,Lv,Z.,Zhu,A.,Su,Y.,Zhou,D.,Zhang,J.,Zhang,Z.,Xu,M.,et al.(2014).The draft genome of the large yellow croaker reveals well-developed innate immunity.Nat Commun 5,5227.
Xia,J.H.,Bai,Z.,Meng,Z.,Zhang,Y.,Wang,L.,Liu,F.,Jing,W.,Yi Wan,Z.,Li,J.,Lin,H.,et al.(2015).Signatures of selection in tilapia revealed by whole genome resequencing.Sci Rep 5,14168.
Xie,B.,Li,X.,Lin,Z.,Ruan,Z.,Wang,M.,Liu,J.,Tong,T.,Li,J.,Huang,Y.,Wen,B.,et al.(2016).Prediction of toxin genes from Chinese yellow catfish based on transcriptomic and proteomic sequencing.Int JMol Sci 17,556.
Xu,J.,Bian,C.,Chen,K.,Liu,G.,Jiang,Y.,Luo,Q.,You,X.,Peng,W.,Li,J.,Huang,Y.,et al.(2017a).Draft genome of the Northern snakehead,Channa argus.Gigascience 6,11.
Xu,J.,Li,J.T.,Jiang,Y.,Peng,W.,Yao,Z.,Chen,B.,Jiang,L.,Feng,J.,Ji,P.,Liu,G.,et al.(2017b).Genomic basis of adaptive evolution:The survival of Amur Ide(Leuciscus waleckii)in an extremely alkaline environment.Mol Biol Evol 34,145-159.
Xu,P.,Zhang,X.,Wang,X.,Li,J.,Liu,G.,Kuang,Y.,Xu,J.,Zheng,X.,Ren,L.,Wang,G.,et al.(2014).Genome sequence and genetic diversity of the common carp,Cyprinus carpio.Nat Genet 46,1212-1219.
Xu,T.,Xu,G.,Che,R.,Wang,R.,Wang,Y.,Li,J.,Wang,S.,Shu,C.,Sun,Y.,Liu,T.,et al.(2016).The genome of the miiuy croaker reveals welldeveloped innate immune and sensory systems.Sci Rep 6,21902.
Yang,J.,Chen,X.,Bai,J.,Fang,D.,Qiu,Y.,Jiang,W.,Yuan,H.,Bian,C.,Lu,J.,He,S.,et al.(2016).The Sinocyclocheilus cavefish genome provides insights into cave adaptation.BMC Biol 14,1.
Yi,Y.,You,X.,Bian,C.,Chen,S.,Lv,Z.,Qiu,L.,and Shi,Q.(2017).High-throughput identification of antimicrobial peptides from amphibious mudskippers.Mar Drugs 15,364.
Yokoyama,S.(2002).Molecular evolution of color vision in vertebrates.Gene 300,69-78.
Yokoyama,S.,and Radlwimmer,F.B.(2001).The molecular genetics and evolution of red and green color vision in vertebrates.Genetics 158,1697-1710.
Yokoyama,S.,Yang,H.,and Starmer,W.T.(2008).Molecular basis of spectral tuning in the red-and green-sensitive(M/LWS)pigments in vertebrates.Genetics 179,2037-2043.
You,X.,Bian,C.,Zan,Q.,Xu,X.,Liu,X.,Chen,J.,Wang,J.,Qiu,Y.,Li,W.,Zhang,X.,et al.(2014).Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes.Nat Commun 5,5594.
You,X.,Sun,M.,Li,J.,Bian,C.,Chen,J.,Yi,Y.,Yu,H.,and Shi,Q.(2018).Mudskippers and their genetic adaptations to an amphibious lifestyle.Animals 8,24.
Yu,H.,You,X.,Li,J.,Zhang,X.,Zhang,S.,Jiang,S.,Lin,X.,Lin,H.R.,Meng,Z.,and Shi,Q.(2018).A genome-wide association study on growth traits in orange-spotted grouper(Epinephelus coioides)with RAD-seq genotyping.Sci China Life Sci 61,934-946.
Yue,G.H.,Liew,W.C.,and Orban,L.(2006).The complete mitochondrial genome of a basal teleost,the Asian arowana(Scleropages formosus,Osteoglossidae).BMC Genomics 7,242.
Yue,G.H.,and Wang,L.(2017).Current status of genome sequencing and its applications in aquaculture.Aquaculture 468,337-347.
Zhang,S.,Li,J.,Qin,Q.,Liu,W.,Bian,C.,Yi,Y.,Wang,M.,Zhong,L.,You,X.,Tang,S.,et al.(2018).Whole-genome sequencing of Chinese yellow catfish provides a valuable genetic resource for high-throughput identification of toxin genes.Toxins 10,488.
Zhang,Z.,Zhang,K.,Chen,S.,Zhang,Z.,Zhang,J.,You,X.,Bian,C.,Xu,J.,Jia,C.,Qiang,J.,et al.(2018).Draft genome of the protandrous Chinese black porgy,Acanthopagrus schlegelii.Gigascience 7.
Ziegman,R.,and Alewood,P.(2015).Bioactive components in fish venoms.Toxins 7,1497-1531.