References
Bao W, Kojima KK, Kohany O (2015) Repbase Update, a database of repetitive elements in eukaryotic genomes.Mobile DNA, 6 , 11.
Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research,27 , 573-580.
Chan PP, Lowe TM (2019) tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences. Methods in Molecular Biology, 1962 , 1-14.
Craig MT, Hastings PA (2007) A molecular phylogeny of the groupers of the subfamily Epinephelinae (Serranidae) with a revised classification of the Epinephelini.Ichthyol Research, 54 , 1-17.
De Bie T, Cristianini N, Demuth JP, Hahn MW (2006) CAFE: a computational tool for the study of gene family evolution. Bioinformatics, 22 , 1269-1271.
Doerks T, Copley RR, Schultz J, Ponting CP, Bork P (2002) Systematic identification of novel protein domain families associated with nuclear functions. Genome research, 12 , 47-56.
Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, Shamim MS, Machol I, Lander ES, Aiden AP (2017) De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science (New York, N.Y.),356 , 92.
Durand N, Robinson J, Shamim M, Machol I, Mesirov J, Lander E, Aiden EL (2016) Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom.Cell systems, 3 , 99-101.
Elsik CG, Mackey AJ, Reese JT, Milshina NV, Roos DS, Weinstock GM (2007) Creating a honey bee consensus gene set. Genome biology, 8 , R13.
Fabinyi M (2012) Historical, cultural and social perspectives on luxury seafood consumption in China.Environ Conserv, 39 , 83-92.
Ferreira BP (1995) Reproduction of the common coral trout Plectropomus leopardus (Serranidae: Epinephelinae) from the central and northern Great Barrier Reef, Australia. Bull Mar Sci, 56 , 653-669.
Frisch A, Anderson T (2005) Physiological stress responses of two species of coral trout ( Plectropomus leopardus and Plectropomus maculatus ). Comp Biochem Phys A Mol Integrat Phys, 140 , 317-327.
Froese R, Pauly D (2019) FishBase. World Wide Web electronic publication.
Ge H, Lin K, Shen M, Wu S, Wang Y, Zhang Z, Wang Z, Zhang Y, Huang Z, Zhou C, Lin Q, Wu J, Liu L, Hu J, Huang Z, Zheng L (2019) De novo assembly of a chromosome-level reference genome of red-spotted grouper (Epinephelus akaara) using nanopore sequencing and Hi-C. Molecular ecology resources, 0 , 1-9.
Gong G, Dan C, Xiao S, Guo W, Huang P, Xiong Y, Wu J, He Y, Zhang J, Li X, Chen N, Gui J-F, Mei J (2018) Chromosomal-level assembly of yellow catfish genome using third-generation DNA sequencing and Hi-C analysis. GigaScience,7 .
Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology, 59 , 307-321.
Harris RS (2007) Improved pairwise alignment of genomic DNA. The Pennsylvania State University.
Harrison HB, Feldheim KA, Jones GP, Ma K, Mansour H, Perumal S, Williamson DH, Berumen ML (2014) Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae). Ecol Evol, 4 , 2046-2057.
Herwerden LV, Choat JH, Dudgeon CL, Carlos G, Newman SJ, Frisch A, Oppen MV (2006) Contrasting patterns of genetic structure in two species of the coral trout Plectropomus (Serranidae) from east and west Australia: Introgressive hybridisation or ancestral polymorphisms. Mol Phylogenet Evol, 41 , 420-435.
Jones P, Binns D, Chang H-Y, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong S-Y, Lopez R, Hunter S (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics, 30 , 1236-1240.
Kalvari I, Argasinska J, Quinones-Olvera N, Nawrocki EP, Rivas E, Eddy SR, Bateman A, Finn RD, Petrov AI (2018) Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. Nucleic Acids Res, 46 , D335-d342.
Kozomara A, Griffiths-Jones S (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res, 42 , D68-d73.
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA (2009) Circos: an information aesthetic for comparative genomics. Genome research,19 , 1639-1645.
Leis JM, Carsonewart BM (1999) In situ swimming and settlement behaviour of larvae of an Indo-Pacific coral-reef fish, the coral trout Plectropomus leopardus (Pisces: Serranidae). Mar Biol, 134 , 51-64.
Li H, Coghlan A, Ruan J, Coin LJ, Hériché J-K, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L, Wong GK-S, Zheng W, Dehal P, Wang J, Durbin R (2006) TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic acids research, 34 , D572-D580.
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform.Bioinformatics, 25 , 1754-1760.
Light PR, Jones GP (1997) Habitat preference in newly settled coral trout (Plectropomus leopardus, Serranidae). Coral Reefs, 16 , 117-126.
Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler.GigaScience, 1 , 18.
Marcais G, Kingsford C (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics, 27 , 764-770.
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.Genome research, 20 , 1297-1303.
Mekuchi M, Sakata K, Yamaguchi T, Koiso M, Kikuchi J (2017) Trans-omics approaches used to characterise fish nutritional biorhythms in leopard coral grouper ( Plectropomus leopardus ). Sci Rep, 7 , 9372.
Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A, Brown SD, Chang HY, El-Gebali S, Fraser MI, Gough J, Haft DR, Huang H, Letunic I, Lopez R, Luciani A, Madeira F, Marchler-Bauer A, Mi H, Natale DA, Necci M, Nuka G, Orengo C, Pandurangan AP, Paysan-Lafosse T, Pesseat S, Potter SC, Qureshi MA, Rawlings ND, Redaschi N, Richardson LJ, Rivoire C, Salazar GA, Sangrador-Vegas A, Sigrist CJA, Sillitoe I, Sutton GG, Thanki N, Thomas PD, Tosatto SCE, Yong SY, Finn RD (2019) InterPro in 2019: improving coverage, classification and access to protein sequence annotations.Nucleic Acids Res, 47 , D351-d360.
Nawrocki EP, Eddy SR (2013) Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics,29 , 2933-2935.
Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL (2016) Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc,11 , 1650.
Price AL, Jones NC, Pevzner PA (2005) De novo identification of repeat families in large genomes.Bioinformatics, 21 , i351-358.
Saad YM (2019) Analysis of 16S mitochondrial ribosomal DNA sequence variations and phylogenetic relations among some Serranidae fishes. S Afr J Anim Sci,49 , 80-89.
Servant N, Varoquaux N, Lajoie BR, Viara E, Chen CJ, Vert JP, Heard E, Dekker J, Barillot E (2015) HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.Genome biology, 16 , 259.
Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B (2006) AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res, 34 , W435-439.
Taraio-Graovac M, Chen N (2009) Using RepeatMasker to identify repetitive elements in genomic sequences.Current protocols in bioinformatics , 4.10.11-14.10.14.
Vurture GW, Sedlazeck FJ, Nattestad M, Underwood CJ, Fang H, Gurtowski J, Schatz MC (2017) GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics,33 , 2202-2204.
Wang L, Yu C, Guo L, Lin H, Meng Z (2015) In silico comparative transcriptome analysis of two color morphs of the common coral trout (Plectropomus leopardus). PloS one,10 , e0145868.
Waterhouse RM, Seppey M, Simao FA, Manni M, Ioannidis P, Klioutchnikov G, Kriventseva EV, Zdobnov EM (2017) BUSCO applications from quality assessments to gene prediction and phylogenomics. Molecular biology and evolution, 35 , 543-548.
Weisenfeld NI, Kumar V, Shah P, Church DM, Jaffe DB (2017) Direct determination of diploid genome sequences. Genome research, 27 , 757-767.
Xu M, Guo L, Gu S, Wang O, Zhang R, Fan G, Xu X, Deng L, Liu X (2019) TGS-GapCloser: fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads .
Xu Z, Wang H (2007) LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons.Nucleic Acids Res, 35 , W265-268.
Yang Z (2007) PAML 4: Phylogenetic Analysis by Maximum Likelihood. Molecular biology and evolution,24 , 1586-1591.
Zeller DC (1998) Spawning aggregations:patterns of movement of the coral trout Plectropomus leopardus (Serranidae) as determined by ultrasonic telemetry. Mar Ecol Prog, 162 , 253-263.
Zhang J, Liu H, Yu S (2010) Development and characterization of polymorphic microsatellite loci for a threatened reef fish Plectropomus leopardus. Conserv Genet Resour, 2 , 101-103.
Zhou Q, Gao H, Zhang Y, Fan G, Xu H, Zhai J, Xu W, Chen Z, Zhang H, Liu S, Niu Y, Li W, Li W, Lin H, Chen S (2019) A chromosome-level genome assembly of the giant grouper (Epinephelus lanceolatus) provides insights into its innate immunity and rapid growth. Molecular ecology resources, 0 , 1-11.
Zhou Q, Su X, Jing G, Chen S, Ning K (2018) RNA-QC-Chain: comprehensive and fast quality control for RNA-Seq data. BMC Genomics, 19 , 144.
Zhou Q, Su X, Wang A, Xu J, Ning K (2013) QC-Chain: fast and holistic quality control method for next-generation sequencing data. PloS one, 8 , e60234.