Ravi V, Venkatesh B. The divergent genomes of Teleosts. Annu Rev Anim Biosci. 2018;6:47–68. https://doi.org/10.1146/annurev-animal-030117-014821.
Article
CAS
PubMed
Google Scholar
Nelson JS. Fishes of the World. 4th ed. Hoboken: Wiley; 2006. ISBN 978-0-471-25031-9.
Google Scholar
Hastings P, Walker H, Galland G. Fishes: a guide to their diversity. Oakland: University of California Press; 2015.
Book
Google Scholar
Ballagh AC, Welch DJ, Newman SJ, Allsop Q, Stapley JM. Stock structure of the blue threadfin (Eleutheronema tetradactylum) across northern Australia derived from life-history characteristics. Fish Res. 2012;121–122:63–72.
Article
Google Scholar
Motomura H. Threadfins of the world (family Polynemidae): an annotated and illustrated catalogue of polynemid species known to date. Food Agriculture Organisation Species Catalogue for Fishery Purposes. 2004;117(3):151.http://www.fao.org/3/y5398e/y5398e00.htm.
Motomura H, Matsuura K, Bishop J, Kaymaram F. Eleutheronema tetradactylum. The IUCN Red List of Threatened Species. 2015:e.T46087646A57168342. https://www.iucnredlist.org/species/46087646/57168342.
Shihab I, Gopalakrishnan A, Vineesh N, Muktha M, Akhilesh KV, Vijayagopal P. Histological profiling of gonads depicting protandrous hermaphroditism in Eleutheronema tetradactylum. J Fish Biol. 2017;90:2402–11.
Article
CAS
PubMed
Google Scholar
Seppey M, Manni M, Zdobnov EM. BUSCO: Assessing Genome Assembly and Annotation Completeness. Methods Mol Biol. 2019;1962:227–45.
Article
CAS
PubMed
Google Scholar
Joly-Lopez Z, Bureau TE. Exaptation of transposable element coding sequences. Curr Opin Genet Dev. 2018;49:34–42.
Article
CAS
PubMed
Google Scholar
Rebollo R, Romanish MT, Mager DL. Transposable elements: an abundant and natural source of regulatory sequences for host genes. Annu Rev Genet. 2012;46:21–42.
Article
CAS
PubMed
Google Scholar
Han Z, Li W, Zhu W, Sun S, Ye K, Xie Y, Wang Z. Near-complete genome assembly and annotation of the yellow drum (Nibea albiflora) provide insights into population and evolutionary characteristics of this species. Ecol Evol. 2019;9(1):568–75. https://doi.org/10.1002/ece3.4778.
Article
PubMed
Google Scholar
Ferrier DEK, Holland PWH. Ancient origin of the Hox gene cluster. Nat Rev Genet. 2001;2(1):33–8.
Article
CAS
PubMed
Google Scholar
Mallo M, Alonso CR. The regulation of Hox gene expression during animal development. Development. 2013;140:3951–63. https://doi.org/10.1242/dev.068346.
Article
CAS
PubMed
Google Scholar
Mulley JF, C-h C, Holland PWH. Breakup of a homeobox cluster after genome duplication in teleosts. Proc Natl Acad Sci. 2006;103(27):10369–72.
Article
CAS
PubMed
PubMed Central
Google Scholar
Siegel N, Hoegg S, Salzburger W, Braasch I, Meyer A. Comparative genomics of ParaHox clusters of teleost fishes: gene cluster breakup and the retention of gene sets following whole genome duplications. BMC Genomics. 2007;8(1):312.
Article
PubMed
PubMed Central
CAS
Google Scholar
Shimeld SM, Holland PWH. Vertebrate innovations. Proc Natl Acad Sci. 2000;97:4449–52. https://doi.org/10.1073/pnas.97.9.4449.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bowles J, Schepers G, Koopman P. Phylogeny of the SOX family of developmental transcription factors based on sequence and structural indicators. Dev Biol. 2000;227(2):239–55.
Article
CAS
PubMed
Google Scholar
Wegner M. From head to toes: the multiple facets of sox proteins. Nucleic Acids Res. 1999;27(6):1409–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kozomara A, Griffiths-Jones S. MiRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014;42(D1):68–73.
Article
CAS
Google Scholar
Fromm B, Domanska D, Høye E, Ovchinnikov V, Kang W, Aparicio-Puerta E, Johansen M, Flatmark K, Mathelier A, Hovig E, et al. MirGeneDB 2.0: the metazoan microRNA complement. Nucleic Acids Res. 2019;48(D1):132–41.
Article
CAS
Google Scholar
Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, et al. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat Genet. 2016;48(4):427–37.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ohno S. Evolution by gene duplication. Berlin: Springer-Verlag; 1970. p. 160.
Book
Google Scholar
Dehal P, Boore JL. Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol. 2005;3(10):e314.
Article
PubMed
PubMed Central
CAS
Google Scholar
Taylor JS, Braasch I, Frickey T, Meyer A, van de Peer Y. Genome duplication, a trait shared by 22,000 species of ray-finned fish. Genome Res. 2003;13:382–90. https://doi.org/10.1101/gr.640303.
Article
CAS
PubMed
PubMed Central
Google Scholar
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. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature. 2004;431(7011):946–57.
Article
PubMed
Google Scholar
Amores A, Force A, Yan Y-L, Joly L, Amemiya C, Fritz A, Ho RK, Langeland J, Prince V, Wang Y-L, et al. Zebrafish Hox clusters and vertebrate genome evolution. Science. 1998;282(5394):1711.
Article
CAS
PubMed
Google Scholar
Amores A, Catchen J, Ferrara A, Fontenot Q, Postlethwait JH. Genome evolution and meiotic maps by massively parallel DNA sequencing: spotted gar, an outgroup for the teleost genome duplication. Genetics. 2011;188:799–808.
Article
CAS
PubMed
PubMed Central
Google Scholar
Christoffels A, Koh EG, Chia JM, Brenner S, Aparicio S, Venkatesh B. Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. Mol Biol Evol. 2004;21:1146–51.
Article
CAS
PubMed
Google Scholar
Kasahara M, Naruse K, Sasaki S, Nakatani Y, Qu W, Ahsan B, Yamada T, Nagayasu Y, Doi K, Kasai Y, et al. The medaka draft genome and insights into vertebrate genome evolution. Nature. 2007;447(7145):714–9.
Article
CAS
PubMed
Google Scholar
Lien S, Koop BF, Sandve SR, Miller JR, Kent MP, Nome T, Hvidsten TR, Leong JS, Minkley DR, Zimin A, et al. The Atlantic salmon genome provides insights into rediploidization. Nature. 2016;533(7602):200–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen Z, Omori Y, Koren S, Shirokiya T, Kuroda T, Miyamoto A, Wada H, Fujiyama A, Toyoda A, Zhang S, et al. De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication. Sci Adv. 2019;5(6):eaav0547.
Article
PubMed
PubMed Central
CAS
Google Scholar
Nguinkal JA, Brunner RM, Verleih M, Rebl A, de Los R-PL, Schäfer N, Hadlich F, Stüeken M, Wittenburg D, Goldammer T. The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe. Genes (Basel). 2019;10(9). https://doi.org/10.3390/genes10090708.
Xu S, Xiao S, Zhu S, Zeng X, Luo J, Liu J, Gao T, Chen N. A draft genome assembly of the Chinese sillago (Sillago sinica), the first reference genome for Sillaginidae fishes. Gigascience. 2018;7(9):giy108. https://academic.oup.com/gigascience/article/7/9/giy108/5094561.
Chénais B, Caruso A, Hiard S, Casse N. The impact of transposable elements on eukaryotic genomes: from genome size increase to genetic adaptation to stressful environments. Gene. 2012;509:7–15.
Article
PubMed
CAS
Google Scholar
Yuan Z, Liu S, Zhou T, Tian C, Bao L, Dunham R, Liu Z. Comparative genome analysis of 52 fish species suggests differential associations of repetitive elements with their living aquatic environments. BMC Genomics. 2018;19(1):141.
Article
PubMed
PubMed Central
CAS
Google Scholar
Amores A, Suzuki T, Yan Y-L, Pomeroy J, Singer A, Amemiya C, Postlethwait JH. Developmental roles of pufferfish Hox clusters and genome evolution in ray-fin fish. Genome Res. 2004;14(1):1–10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Malmstrøm M, Britz R, Matschiner M, Tørresen OK, Hadiaty RK, Yaakob N, Tan HH, Jakobsen KS, Salzburger W, Rüber L. The Most developmentally truncated fishes show extensive Hox gene loss and miniaturized genomes. Genome Biol Evol. 2018;10(4):1088–103.
Article
PubMed
PubMed Central
CAS
Google Scholar
Xu P, Zhang X, Wang X, Li J, Liu G, Kuang Y, Xu J, Zheng X, Ren L, Wang G, et al. Genome sequence and genetic diversity of the common carp, , Cyprinus carpio. Nat Genet. 2014;46(11):1212–9.
Article
CAS
PubMed
Google Scholar
Vurture GW, Sedlazeck FJ, Nattestad M, Underwood CJ, Fang H, Gurtowski J, Schatz MC. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics. 2017;33:2202–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nong W, Law STS, Wong AYP, Baril T, Swale T, Chu LM, Hayward A, Lau DTW, Hui JHL. Chromosomal-level reference genome of the incense tree Aquilaria sinensis. Mol Ecol Resour. 2020;20(4):971–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Qu Z, Nong W, So WL, Barton-Owen T, Li Y, Leung TCN, Li C, Baril T, Wong AYP, Swale T, et al. Millipede genomes reveal unique adaptations during myriapod evolution. PLoS Biol. 2020;18(9):e3000636.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005;110:462–7.
Article
CAS
PubMed
Google Scholar
Smit AFA, Hubley RR, Green PR. RepeatMasker Open-4.0. http://repeatmasker.org. 2013.
Wong WY, Simakov O. Repeat craft: a meta-pipeline for repetitive element de-fragmentation and annotation. Bioinformatics. 2018;35:1051–2.
Article
PubMed Central
CAS
Google Scholar
Xu Z, Wang H. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 2007;35:W265–8.
Article
PubMed
PubMed Central
Google Scholar
Ou S, Jiang N. LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons. Mob DNA. 2019;10.
Racine JS. Rstudio: a platform-independent IDE for R and Sweave. J Appl Econ. 2013;27:167–72.
Article
Google Scholar
TeamRC. R: A language and environment for statistical computing. 2013.
Google Scholar
Wickham H. ggplot2: Elegant graphics for data analysis. New York: Springer-Verlag; 2016. p. 260.
Book
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Palmer J, Stajich J. Funannotate: eukaryotic genome annotation pipeline; 2018.
Google Scholar
Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, et al. De novo transcript sequence reconstruction from RNA-seq using the trinity platform for reference generation and analysis. Nat Protoc. 2013;8(8):1494–512.
Article
CAS
PubMed
Google Scholar
Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Robin CR, Wortman JR. Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol. 2008;9.
Nong W, Cao J, Li Y, Qu Z, Sun J, Swale T, Yip HY, Qian PY, Qiu J-W, Kwan HS, et al. Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing. Nat Commun. 2020;11(1):3051.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sato K, Hamada M, Asai K, Mituyama T. CENTROIDFOLD: a web server for RNA secondary structure prediction. Nucleic Acids Res. 2009;37:W277–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003;13:2178–89.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhong YF, Holland PWH. HomeoDB2: functional expansion of a comparative homeobox gene database for evolutionary developmental biology. Evol Dev. 2011;13:567–8.
Article
PubMed
PubMed Central
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Article
CAS
PubMed
Google Scholar
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80. https://doi.org/10.1093/molbev/mst010.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35:1547–9. https://doi.org/10.1093/molbev/msy096.
Article
CAS
PubMed
PubMed Central
Google Scholar
Letunic I, Bork P. Interactive tree of life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019;47(W1):W256–9.
Article
CAS
PubMed
PubMed Central
Google Scholar