1.Gaasterland T, Oprea M. Whole-genome analysis: annotations and updates. Curr Opin Struct Biol. 2001; 11:377–381.
2.Stein L. Genome annotation: from sequence to biology. Nat Rev Genet. 2001; 2:493–503.
3.Rouze P, Pavy N, Rombauts S. Genome annotation: which tools do we have for it? Curr Opin Plant Biol. 1999; 2:90–95.
4.Human Gene Name Committeehttps://www.genenames.org/about/guidelines/]. Last accessed: 11. Feb. 2019.
5.Zebrafish Information Networkhttp://zfin.org/]. Last accessed: 25. March 2019
6.Fitch WM. Distinguishing homologous from analogous proteins. Syst Zool. 1970; 19:99–113.
7.Fitch WM. Homology. A personal view on some of the problems. Trends Genet. 2000; 16:227–231.
8.Hartl DL, Cochrane BJ: Genetics. Analysis of Genes and Genomes, 9th Ed. Burlington, MA: Jones and Bartlett Learning; 2018.
9.Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK et al. The amphioxus genome and the evolution of the chordate karyotype. Nature. 2008; 453:1064–1071.
10.Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD, Manousaki T, Meyer A, Bloom OE et al. Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat Genet. 2013; 45:415–421, 421e411–412.
11.Ohno S: Evolution by Gene Duplication. Berlin: Springer Verlag; 1970.
12.Taylor JS, Braasch I, Frickey T, Meyer A, Van de Peer Y. Genome duplication, a trait shared by 22000 species of ray-finned fish. Genome Res. 2003; 13:382–390.
13.Meyer A, Van de Peer Y. From 2R to 3R: evidence for a fish-specific genome duplication (FSGD). Bioessays. 2005; 27:937–945.
14.Vandepoele K, De Vos W, Taylor JS, Meyer A, Van de Peer Y. 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 U S A. 2004; 101:1638–1643.
15.Wolfe K. Robustness—it’s not where you think it is. Nat Genet. 2000; 25:3–4.
16.Postlethwait JH. The zebrafish genome in context: ohnologs gone missing. J Exp Zool B Mol Dev Evol. 2007; 308:563–577.
17.Martinez Barrio A, Lamichhaney S, Fan G, Rafati N, Pettersson M, Zhang H, Dainat J, Ekman D, Hoppner M, Jern P et al. The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing. eLife. 2016; 5:e12081.
18.Cai H, Li Q, Fang X, Li J, Curtis NE, Altenburger A, Shibata T, Feng M, Maeda T, Schwartz JA et al. A draft genome assembly of the solar-powered sea slug Elysia chlorotica. Sci Data. 2019; 6:190022.
19.Vezzi F, Narzisi G, Mishra B. Reevaluating assembly evaluations with feature response curves: GAGE and assemblathons. PLoS One. 2012; 7:e52210.
20.Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013; 29:1072–1075.
21.Amores A, Force A, Yan YL, Joly L, Amemiya C, Fritz A, Ho RK, Langeland J, Prince V, Wang YL et al. Zebrafish hox clusters and vertebrate genome evolution. Science. 1998; 282:1711–1714.
22.Eastman SD, Chen TH, Falk MM, Mendelson TC, Iovine MK. Phylogenetic analysis of three complete gap junction gene families reveals lineage-specific duplications and highly supported gene classes. Genomics. 2006; 87:265–274.
23.Cruciani V, Mikalsen SO. The vertebrate connexin family. Cell Mol Life Sci. 2006; 63:1125–1140.
24.Cruciani V, Mikalsen SO. Evolutionary selection pressure and family relationships among connexin genes. Biol Chem. 2007; 388:253–264.
25.Glasauer SMK, Neuhauss SCF. Whole-genome duplication in teleost fishes and its evolutionary consequences. Mol Genet Genomics. 2014; 289:1045–1060.
26.Sasakura Y, Shoguchi E, Takatori N, Wada S, Meinertzhagen IA, Satou Y, Satoh N. A genomewide survey of developmentally relevant genes in Ciona intestinalis. X. Genes for cell junctions and extracellular matrix. Dev Genes Evol. 2003; 213:303–313.
27.Bennett MV, Zheng X, Sogin ML. The connexins and their family tree. Soc Gen Physiol Ser. 1994; 49:223–233.
28.Cruciani V, Mikalsen SO. The connexin gene family in mammals. Biol Chem. 2005; 386:325–332.
29.Harris AL. Emerging issues of connexin channels: biophysics fills the gap. Q Rev Biophys. 2001; 34:325–472.
30.Procida K, Jorgensen L, Schmitt N, Delmar M, Taffet SM, Holstein-Rathlou NH, Nielsen MS, Braunstein TH. Phosphorylation of connexin43 on serine 306 regulates electrical coupling. Heart Rhythm. 2009; 6:1632–1638.
31.Kidder GM, Winterhager E. Physiological roles of connexins in labour and lactation. Reproduction. 2015; 150:R129–136.
32.Mesnil M. Connexins and cancer. Biol Cell. 2002; 94:493–500.
33.Genet N, Bhatt N, Bourdieu A, Hirschi KK. Multifaceted roles of connexin 43 in stem cell niches. Curr Stem Cell Rep. 2018; 4:1–12.
34.Sorgen PL, Trease AJ, Spagnol G, Delmar M, Nielsen MS. Protein-protein interactions with connexin 43: regulation and function. Int J Mol Sci. 2018; 19:1428.
35.Sundset R, Ytrehus K, Mikalsen SO. Connexin, connection, conductance: Towards understanding induction of arrhythmias? Heart Rhythm. 2009; 6:1639–1640.
36.Bennett MV, Contreras JE, Bukauskas FF, Saez JC. New roles for astrocytes: gap junction hemichannels have something to communicate. Trends Neurosci. 2003; 26:610–617.
37.Wang N, De Bock M, Decrock E, Bol M, Gadicherla A, Vinken M, Rogiers V, Bukauskas FF, Bultynck G, Leybaert L. Paracrine signaling through plasma membrane hemichannels. Biochim Biophys Acta. 2013; 1828:35–50.
38.Orellana JA, Saez JC, Bennett MV, Berman JW, Morgello S, Eugenin EA. HIV increases the release of dickkopf–1 protein from human astrocytes by a Cx43 hemichannel-dependent mechanism. J Neurochem. 2014; 128:752–763.
39.Star B, Nederbragt AJ, Jentoft S, Grimholt U, Malmstrom M, Gregers TF, Rounge TB, Paulsen J, Solbakken MH, Sharma A et al. The genome sequence of Atlantic cod reveals a unique immune system. Nature. 2011; 477:207–210.
40.Henkel CV, Dirks RP, de Wijze DL, Minegishi Y, Aoyama J, Jansen HJ, Turner B, Knudsen B, Bundgaard M, Hvam KL et al. First draft genome sequence of the Japanese eel, Anguilla japonica. Gene. 2012; 511:195–201.
41.Jansen HJ, Liem M, Jong-Raadsen SA, Dufour S, Weltzien FA, Swinkels W, Koelewijn A, Palstra AP, Pelster B, Spaink HP et al. Rapid de novo assembly of the European eel genome from nanopore sequencing reads. Sci Rep. 2017; 7:7213.
42.Igarashi Y, Zhang H, Tan E, Sekino M, Yoshitake K, Kinoshita S, Mitsuyama S, Yoshinaga T, Chow S, Kurogi H et al. Whole-genome sequencing of 84 Japanese eels reveals evidence against panmixia and support for sympatric speciation. Genes (Basel). 2018; 9:474.
43.Near TJ, Eytan RI, Dornburg A, Kuhn KL, Moore JA, Davis MP, Wainwright PC, Friedman M, Smith WL. Resolution of ray-finned fish phylogeny and timing of diversification. Proc Natl Acad Sci U S A. 2012; 109:13698–13703.
44.Betancur RR, Broughton RE, Wiley EO, Carpenter K, Lopez JA, Li C, Holcroft NI, Arcila D, Sanciangco M, Cureton Ii JC et al. The tree of life and a new classification of bony fishes. PLoS Curr. 2013; 5:10.1371/currents.tol.1353ba26640df26640ccaee26675bb26165c26648c26288.
45.Baldauf SL. Phylogeny for the faint of heart: a tutorial. Trends Genet. 2003; 19:345–351.
46.Bergsten J. A review of long-branch attraction. Cladistics. 2005; 21:163–193.
47.Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, Collins JE, Humphray S, McLaren K, Matthews L et al. The zebrafish reference genome sequence and its relationship to the human genome. Nature. 2013; 496:498–503.
48.Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science. 2002; 297:1301–1310.
49.Ensembl: Fugu (Takifugu rubripes) genome databasehttp://www.ensembl.org/Takifugu_rubripes/Info/Annotation]. Last accessed: 15. March 2019.
50.Gadus morhua (Atlantic cod) chromosome level assembly, GFC_902167405https://www.ncbi.nlm.nih.gov/assembly/GCF_902167405.1/]. Last accessed: 20. Sept. 2019.
51.O’Brien J, al-Ubaidi MR, Ripps H. Connexin 35: a gap-junctional protein expressed preferentially in the skate retina. Mol Biol Cell. 1996; 7:233–243.
52.Clupea harengus (Atlantic herring) chromosome level assembly GCA_900700415https://www.ncbi.nlm.nih.gov/assembly/GCA_900700415.1]. Last accessed: 20 sept 2019.
53.Clupea harengus (Atlantic herring) genome assembly GCA_000966335.1https://www.ncbi.nlm.nih.gov/assembly/GCF_000966335.1]. Last accessed: 20. Sept 2019.
54.Pettersson ME, Rochus CM, Han F, Chen J, Hill J, Wallerman O, Fan G, Hong X, Xu Q, Zhang H et al. A chromosome-level assembly of the Atlantic herring - detection of a supergene and other signals of selection. https://wwwbiorxivorg/content/101101/668384v1. 2019.
55.Clupea harengus (Atlantic herring) genome assembly GCA_900323705https://www.ncbi.nlm.nih.gov/assembly/GCA_900323705.1]. Last accessed: 20 Sept. 2019.
56.Parra G, Bradnam K, Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics. 2007; 23:1061–1067.
57.Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015; 31:3210–3212.
58.Waterhouse RM, Seppey M, Simao FA, Manni M, Ioannidis P, Klioutchnikov G, Kriventseva EV, Zdobnov EM. BUSCO applications from quality assessments to gene prediction and phylogenomics. Mol Biol Evol. 2017; 35:543–548.
59.Ensembl: Three-spined stickleback (Gasterosteus aculeatus) genome databasehttps://www.ensembl.org/Gasterosteus_aculeatus/Info/Index]. Last accessed: 1st Sept 2019.
60.Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol. 2007; 8:R143.
61.Ensembl: Tetraodon (Tetradon nigroviridis) genome databasehttps://www.ensembl.org/Tetraodon_nigroviridis/Info/Index]. Last accessed: 1st Sept 2019.
62.Ensembl: Atlantic cod (Gadus morhua) genome databasehttps://www.ensembl.org/Gadus_morhua/Info/Index]. Last accessed: 1st Sept. 2019.
63.Nomura K, Fujiwara A, Iwasaki Y, Nishiki I, Matsuura A, Ozaki A, Sudo R, Tanaka H. Genetic parameters and quantitative trait loci analysis associated with body size and timing at metamorphosis into glass eels in captive-bred Japanese eels (Anguilla japonica).. PLoS One. 2018; 13:e0201784.
64.Anguilla japonica (Japanese eel) genome assembly GCA_0035977225https://www.ncbi.nlm.nih.gov/assembly/GCA_003597225.1]. Last accessed: 24th Oct, 2019.
65.Nakamura Y, Yasuike M, Mekuchi M, Iwasaki Y, Ojima N, Fujiwara A, Chow S, Saitoh K. Rhodopsin gene copies in Japanese eel originated in a teleost-specific genome duplication. Zoological Lett. 2017; 3:18.
66.Pavey SA, Laporte M, Normandeau E, Gaudin J, Letourneau L, Boisvert S, Corbeil J, Audet C, Bernatchez L. Draft genome of the American eel (Anguilla rostrata).. Mol Ecol Resour. 2017; 17:806–811.
67.Bracamonte SE. Anguilla anguilla spleen and head kidney transcriptomehttps://www.ncbi.nlm.nih.gov/bioproject/PRJNA419718]. Last accessed: 25. May 2019.
68.Pasquier J, Cabau C, Nguyen T, Jouanno E, Severac D, Braasch I, Journot L, Pontarotti P, Klopp C, Postlethwait JH et al. Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. BMC Genomics. 2016; 17:368.
69.Perrier F, Bertucci A, Pierron F, Feurtet-Mazel A, Simon O, Klopp C, Candaudap F, Pokrovsky O, Etcheverria B, Mornet S et al. Transcriptomic profiling responses in liver and brain tissues of European eel Anguilla anguilla after a gold nanoparticle trophic exposure.https://www.ncbi.nlm.nih.gov/bioproject/PRJNA432560]. Last accessed: 25. May 2019.
70.Tse WK, Sun J, Zhang H, Law AY, Yeung BH, Chow SC, Qiu JW, Wong CK. Transcriptomic and iTRAQ proteomic approaches reveal novel short-term hyperosmotic stress responsive proteins in the gill of the Japanese eel (Anguilla japonica).. J Proteomics. 2013; 89:81–94.
71.Kumar S, Stecher G, Tamura K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016; 33:1870–1874.
72.Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018; 35:1547–1549.