Volume 41 Issue 3
May  2020
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Article Contents
Yang Yang, Li-Na Wu, Jing-Fang Chen, Xi Wu, Jun-Hong Xia, Zi-Ning Meng, Xiao-Chun Liu, Hao-Ran Lin. Whole-genome sequencing of leopard coral grouper (Plectropomus leopardus) and exploration of regulation mechanism of skin color and adaptive evolution. Zoological Research, 2020, 41(3): 328-340. doi: 10.24272/j.issn.2095-8137.2020.038
Citation: Yang Yang, Li-Na Wu, Jing-Fang Chen, Xi Wu, Jun-Hong Xia, Zi-Ning Meng, Xiao-Chun Liu, Hao-Ran Lin. Whole-genome sequencing of leopard coral grouper (Plectropomus leopardus) and exploration of regulation mechanism of skin color and adaptive evolution. Zoological Research, 2020, 41(3): 328-340. doi: 10.24272/j.issn.2095-8137.2020.038

Whole-genome sequencing of leopard coral grouper (Plectropomus leopardus) and exploration of regulation mechanism of skin color and adaptive evolution

doi: 10.24272/j.issn.2095-8137.2020.038
Funds:  This study was supported by the Agriculture Research System of China (ARS-47); Science and Technology Planning Project of Guangzhou (201804020013); National Natural Science Foundation of China (31872572; u1401213; 31802266); Yang Fan Innovative & Entrepreneurial Research Team Project (No.201312H10); and Program of the China-ASEAN Maritime Cooperation Fund of the Chinese Government (42000-41170002)
More Information
  • Leopard coral groupers belong to the Plectropomus genus of the Epinephelidae family and are important fish for coral reef ecosystems and the marine aquaculture industry. To promote future research of this species, a high-quality chromosome-level genome was assembled using PacBio sequencing and Hi-C technology. A 787.06 Mb genome was assembled, with 99.7% (784.57 Mb) of bases anchored to 24 chromosomes. The leopard coral grouper genome size was smaller than that of other groupers, which may be related to its ancient status among grouper species. A total of 22 317 protein-coding genes were predicted. This high-quality genome of the leopard coral grouper is the first genomic resource for Plectropomus and should provide a pivotal genetic foundation for further research. Phylogenetic analysis of the leopard coral grouper and 12 other fish species showed that this fish is closely related to the brown-marbled grouper. Expanded genes in the leopard coral grouper genome were mainly associated with immune response and movement ability, which may be related to the adaptive evolution of this species to its habitat. In addition, we also identified differentially expressed genes (DEGs) associated with carotenoid metabolism between red and brown-colored leopard coral groupers. These genes may play roles in skin color decision by regulating carotenoid content in these groupers.

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  • [1]
    Adams S. 2003. Morphological ontogeny of the gonad of three plectropomid species through sex differentiation and transition. Journal of Fish Biology, 63(1): 22−36. doi: 10.1046/j.1095-8649.2003.00098.x
    Anders S, Pyl PT, Huber W. 2015. HTSeq–a Python framework to work with high-throughput sequencing data. Bioinformatics, 31(2): 166−169. doi: 10.1093/bioinformatics/btu638
    Austin CM, Tan MH, Harrisson KA, Lee YP, Croft LJ, Sunnucks P, Pavlova A, Gan HM. 2017. De novo genome assembly and annotation of Australia's largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read. GigaScience, 6(8): gix063.
    Banerjee M, Arutyunov D, Brandwein D, Janetzki-Flatt C, Kolski H, Hume S, Leonard NJ, Watt J, Lacson A, Baradi M, Leslie EM, Cordat E, Caluseriu O. 2019. The novel p.Ser263Phe mutation in the human high-affinity choline transporter 1 (CHT1/SLC5A7) causes a lethal form of fetal akinesia syndrome. Human Mutation, 40(10): 1676−1683. doi: 10.1002/humu.23828
    Benson G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research, 27(2): 573−580. doi: 10.1093/nar/27.2.573
    Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15): 2114−2120. doi: 10.1093/bioinformatics/btu170
    Bunt CM, Kingsford MJ. 2014. Movement, habitat utilization and behaviour of coral trout Plectropomus leopardus during and after the reproductive period on the southern Great Barrier Reef. Marine Ecology Progress Series, 496: 33−45. doi: 10.3354/meps10645
    Burgess AI, Callan CK, Touse R, Delos Santos M. 2020. Increasing survival and growth in larval leopard coral grouper (Plectropomus leopardus) using intensively cultured Parvocalanus crassirostris nauplii. Journal of the World Aquaculture Society, 51(1): 171−182. doi: 10.1111/jwas.12635
    Cai XP, Qu M, Ding SX, Wang HJ, Wang HJ, Hu LY, Su YQ. 2013. Differentiation of coral trout (Plectropomus leopardus) based on an analysis of morphology and complete mitochondrial DNA: are cryptic species present?. Acta Oceanologica Sinica, 32(6): 40−46. doi: 10.1007/s13131-013-0304-6
    Chen JX, Xiao L, Peng C, Ye ZF, Wang DD, Yang YQ, Zhang HF, Zhao M, Li SS, Lin HR, Zhang Y. 2019. Socially controlled male-to-female sex reversal in the protogynous orange-spotted grouper, Epinephelus coioides. Journal of Fish Biology, 94(3): 414−421. doi: 10.1111/jfb.13911
    Chen SY, Peng XL, Lin SQ, Xu QB. 2018. Identification of Plectropomus leopardus, Promicrops lanceolatus and Cromileptes altivelis using species-specific TaqMan real-time PCR. Food Control, 84: 408−412. doi: 10.1016/j.foodcont.2017.08.019
    Chen WQ, Liu ZM, Wu L, Wang YH, Ma JZ, Wu HX. 2016. The influences of light color on growth, haematological and biochemical indices of juvenile Plectropomus leopardus. Chinese Journal of Ecology, 35(7): 1889−1895. (in Chinese)
    Chintala S, Li W, Lamoreux ML, Ito S, Wakamatsu K, Sviderskaya EV, Bennett DC, Park YM, Gahl WA, Huizing M, Spritz RA, Ben ST, Novak EK, Tan J, Swank RT. 2005. Slc7a11 gene controls production of pheomelanin pigment and proliferation of cultured cells. Proceedings of the National Academy of Sciences of the United States of America, 102(31): 10964−10969. doi: 10.1073/pnas.0502856102
    Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21(18): 3674−3676. doi: 10.1093/bioinformatics/bti610
    Craig MT, Hastings PA. 2007. A molecular phylogeny of the groupers of the subfamily Epinephelinae (Serranidae) with a revised classification of the Epinephelini. Ichthyological Research, 54(1): 1−17. doi: 10.1007/s10228-006-0367-x
    De Bie T, Cristianini N, Demuth JP, Hahn MW. 2006. CAFE: a computational tool for the study of gene family evolution. Bioinformatics, 22(10): 1269−1271. doi: 10.1093/bioinformatics/btl097
    Du K, Wuertz S, Adolfi M, Kneitz S, Stöck M, Oliveira M, Nóbrega R, Ormanns J, Kloas W, Feron R, Klopp C, Parrinello H, Journot L, He SP, Postlethwait J, Meyer A, Guiguen Y, Schartl M. 2019. The genome of the arapaima (Arapaima gigas) provides insights into gigantism, fast growth and chromosomal sex determination system. Scientific Reports, 9(1): 5293. doi: 10.1038/s41598-019-41457-x
    Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, Shamim MS, Machol I, Lander ES, Aiden AP, Aiden EL. 2017. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 356(6333): 92−95. doi: 10.1126/science.aal3327
    Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32(5): 1792−1797. doi: 10.1093/nar/gkh340
    Edgar RC, Myers EW. 2005. PILER: identification and classification of genomic repeats. Bioinformatics, 21(S1): i152−i158.
    Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S, Dalal R, deWinter A, Dixon J, Foquet M, Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G, Kong XX, Kuse R, Lacroix Y, Lin S, Lundquist P, Ma CC, Marks P, Maxham M, Murphy D, Park I, Pham T, Phillips M, Roy J, Sebra R, Shen GE, Sorenson J, Tomaney A, Travers K, Trulson M, Vieceli J, Wegener J, Wu D, Yang A, Zaccarin D, Zhao P, Zhong F, Korlach J, Turner S. 2009. Real-time DNA sequencing from single polymerase molecules. Science, 323(5910): 133−138. doi: 10.1126/science.1162986
    Elieh Ali Komi D, Sharma L, Dela Cruz CS. 2018. Chitin and its effects on inflammatory and immune responses. Clinical Reviews in Allergy & Immunology, 54(2): 213−223.
    Eriksson J, Larson G, Gunnarsson U, Bed'hom B, Tixier-Boichard M, Strömstedt L, Wright D, Jungerius A, Vereijken A, Randi E, Jensen P, Andersson L. 2008. Identification of the Yellow skin gene reveals a hybrid origin of the domestic chicken. PLoS Genetics, 4(2): e1000010. doi: 10.1371/journal.pgen.1000010
    Ge H, Lin KB, Shen M, Wu SQ, Wang YL, Zhang ZP, Wang ZY, Zhang Y, Huang Z, Zhou C, Lin Q, Wu JS, Liu L, Huang ZC, Zheng LY. 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, 19(6): 1461−1469. doi: 10.1111/1755-0998.13064
    Guindon S, Dufayard JF, 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(3): 307−321. doi: 10.1093/sysbio/syq010
    Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR. 2008. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biology, 9(1): R7. doi: 10.1186/gb-2008-9-1-r7
    Harrison EH. 2019. Mechanisms of transport and delivery of vitamin a and carotenoids to the retinal pigment epithelium. Molecular Nutrition and Food Research, 63(15): 1801046. doi: 10.1002/mnfr.201801046
    Ho ALFC, O'shea SK, Pomeroy HF. 2013. Dietary esterified astaxanthin effects on color, carotenoid concentrations, and compositions of clown anemonefish, Amphiprion ocellaris, skin. Aquaculture International, 21(2): 361−374. doi: 10.1007/s10499-012-9558-9
    Ising C, Venegas C, Zhang SS, Scheiblich H, Schmidt SV, Vieira-Saecker A, Schwartz S, Albasset S, McManus RM, Tejera D, Griep A, Santarelli F, Brosseron F, Opitz S, Stunden J, Merten M, Kayed R, Golenbock DT, Blum D, Latz E, Buée L, Heneka MT. 2019. NLRP3 inflammasome activation drives tau pathology. Nature, 575(7784): 669−673. doi: 10.1038/s41586-019-1769-z
    Jones P, Binns D, Chang HY, Fraser M, Li WZ, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S. 2014. InterProScan 5: genome-scale protein function classification. Bioinformatics, 30(9): 1236−1240. doi: 10.1093/bioinformatics/btu031
    Keilwagen J, Wenk M, Erickson JL, Schattat MH, Grau J, Hartung F. 2016. Using intron position conservation for homology-based gene prediction. Nucleic Acids Research, 44(9): e89. doi: 10.1093/nar/gkw092
    Kelm S, Gerlach J, Brossmer R, Danzer CP, Nitschke L. 2002. The ligand-binding domain of CD22 is needed for inhibition of the B cell receptor signal, as demonstrated by a novel human CD22-specific inhibitor compound. Journal of Experimental Medicine, 195(9): 1207−1213. doi: 10.1084/jem.20011783
    Khasanah M, Kadir NN, Jompa J. 2019. Reproductive biology of three important threatened/near-threatened groupers (Plectropomus leopardus, Epinephelus polyphekadion and Plectropomus areolatus) in eastern Indonesia and implications for management. Animals, 9(9): 643. doi: 10.3390/ani9090643
    Kim D, Langmead B, Salzberg SL. 2015. HISAT: a fast spliced aligner with low memory requirements. Nature Methods, 12(4): 357−360. doi: 10.1038/nmeth.3317
    Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. 2017. Canu: scalable and accurate long-read assembly via adaptive κ-mer weighting and repeat separation. Genome Research, 27(5): 722−736. doi: 10.1101/gr.215087.116
    Kumar S, Stecher G, Suleski M, Hedges SB. 2017. TimeTree: a resource for timelines, timetrees, and divergence times. Molecular Biology and Evolution, 34(7): 1812−1819. doi: 10.1093/molbev/msx116
    Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. 2004. Versatile and open software for comparing large genomes. Genome Biology, 5(2): R12. doi: 10.1186/gb-2004-5-2-r12
    Lei X, Shi FJ, Basu D, Huq A, Routhier S, Day R, Jin WJ. 2011. Proteolytic processing of angiopoietin-like protein 4 by proprotein convertases modulates its inhibitory effects on lipoprotein lipase activity. Journal of Biological Chemistry, 286(18): 15747−15756. doi: 10.1074/jbc.M110.217638
    Leskovec J, Sosič R. 2016. SNAP: A general purpose network analysis and graph mining library. ACM Transactions on Intelligent Systems and Technology, 8(1): 1.
    Li H, Durbin R. 2010. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 26(5): 589−595. doi: 10.1093/bioinformatics/btp698
    Li RQ, Fan W, Tian G, Zhu HM, He L, Cai J, Huang QF, Cai QL, Li B, Bai YQ, Zhang ZH, Zhang YP, Wang W, Li J, Wei FW, Li H, Jian M, Li JW, Zhang ZL, Nielsen R, Li DW, Gu WJ, Yang ZT, Xuan ZL, Ryder OA, Leung FCC, Zhou Y, Cao JJ, Sun X, Fu YG, Fang XD, Guo XS, Wang B, Hou R, Shen FJ, Mu B, Ni PX, Lin RM, Qian WB, Wang GD, Yu C, Nie WH, Wang JH, Wu ZG, Liang HQ, Min JM, Wu Q, Cheng SF, Ruan J, Wang MW, Shi ZB, Wen M, Liu BH, Ren XL, Zheng HS, Dong D, Cook K, Shan G, Zhang H, Kosiol C, Xie XY, Lu ZH, Zheng HC, Li YR, Steiner CC, Lam TTY, Lin SY, Zhang QH, Li GQ, Tian J, Gong TM, Liu HD, Zhang DJ, Fang L, Ye C, Zhang JB, Hu WB, Xu AL, Ren YY, Zhang GJ, Bruford MW, Li QB, Ma LJ, Guo YR, An N, Hu YJ, Zheng Y, Shi YY, Li ZQ, Liu Q, Chen YL, Zhao J, Qu N, Zhao SC, Tian F, Wang XL, Wang HY, Xu LZ, Liu X, Vinar T, Wang YJ, Lam TW, Yiu SM, Liu SP, Zhang HM, Li DS, Huang Y, Wang X, Yang GH, Jiang Z, Wang JY, Qin N, Li L, Li JX, Bolund L, Kristiansen K, Wong GKS, Olson M, Zhang XQ, Li SG, Yang HM, Wang J, Wang J. 2010. The sequence and de novo assembly of the giant panda genome. Nature, 463(7279): 311−317. doi: 10.1038/nature08696
    Lieberman-Aiden E, Van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science, 326(5950): 289−293. doi: 10.1126/science.1181369
    Lillis AP, Muratoglu SC, Au DT, Migliorini M, Lee MJ, Fried SK, Mikhailenko I, Strickland DK. 2015. LDL receptor-related protein-1 (LRP1) regulates cholesterol accumulation in macrophages. PLoS One, 10(6): e0128903. doi: 10.1371/journal.pone.0128903
    Liu BH, Shi YJ, Yuan JY, Hu XS, Zhang H, Li N, Li ZY, Chen YX, Mu DS, Fan W. 2013. Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. arXiv: 1308.2012.
    Liu H, Chen CH, Gao ZX, Min JM, Gu YM, Jian JB, Jiang XW, Cai HM, Ebersberger I, Xu M, Zhang XH, Chen JW, Luo W, Chen BX, Chen JH, Liu H, Li J, Lai RF, Bai MZ, Wei J, Yi SK, Wang HL, Cao XJ, Zhou XY, Zhao YH, Wei KJ, Yang RB, Liu BN, Zhao SC, Fang XD, Schartl M, Qian XQ, Wang WM. 2017. The draft genome of blunt snout bream (Megalobrama amblycephala) reveals the development of intermuscular bone and adaptation to herbivorous diet. GigaScience, 6(7): gix039.
    Lomsadze A, Burns PD, Borodovsky M. 2014. Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm. Nucleic Acids Research, 42(15): e119. doi: 10.1093/nar/gku557
    Lowe TM, Eddy SR. 1996. TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research, 25(5): 955−964.
    Lutz EP, Merkel M, Kako Y, Melford K, Radner H, Breslow JL, Bensadoun A, Goldberg IJ. 2001. Heparin-binding defective lipoprotein lipase is unstable and causes abnormalities in lipid delivery to tissues. Journal of Clinical Investigation, 107(9): 1183−1192. doi: 10.1172/JCI11774
    Ma KY, Craig MT, Choat JH, Van Herwerden L. 2016. The historical biogeography of groupers: clade diversification patterns and processes. Molecular Phylogenetics and Evolution, 100: 21−30. doi: 10.1016/j.ympev.2016.02.012
    Majoros WH, Pertea M, Salzberg SL. 2004. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics, 20(16): 2878−2879. doi: 10.1093/bioinformatics/bth315
    Maoka T, Sato W, Nagai H, Takahashi T. 2017. Carotenoids of red, brown, and black specimens of plectropomus leopardus, the coral trout (Suziara in Japanese). Journal of Oleo Science, 66(6): 579−584. doi: 10.5650/jos.ess16179
    McHeyzer-Williams M, Okitsu S, Wang N, McHeyzer-Williams L. 2012. Molecular programming of B cell memory. Nature Reviews Immunology, 12(1): 24−34. doi: 10.1038/nri3128
    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). Scientific Reports, 7(1): 9372. doi: 10.1038/s41598-017-09531-4
    Melianawati R, Astuti NWW, Suwirya K. 2013. The use of copepods to improve juveniles production of coral trout Plectropomus leopardus (Lacepède, 1802). Middle East Journal of Scientific Research, 16(2): 237−244.
    Metcalfe SS, Kroon FJ, Beale DJ, Miller G. 2018. Development of a validation protocol of enzyme immunoassay kits used for the analysis of steroid hormones in fish plasma. Journal of Experimental Marine Biology and Ecology, 499: 26−34. doi: 10.1016/j.jembe.2017.12.001
    Nguinkal JA, Brunner RM, Verleih M, Rebl A, Ríos-Pérez L, Schäfer N, Hadlich F, Stüeken M, Wittenburg D, Goldammer T. 2019. The first highly contiguous genome assembly of pikeperch (Sander lucioperca), an emerging aquaculture species in Europe. Genes, 10(9): 708. doi: 10.3390/genes10090708
    Ozerov MY, Ahmad F, Gross R, Pukk L, Kahar S, Kisand V, Vasemägi A. 2018. Highly continuous genome assembly of eurasian perch (Perca fluviatilis) using linked-read sequencing. G3: Genes, Genomes, Genetics, 8(12): 3737−3743.
    Pardal-Fernández JM, Carrascosa-Romero MC, Álvarez S, Medina-Monzón MC, Caamaño MB, De Cabo C. 2018. A new severe mutation in the SLC5A7 gene related to congenital myasthenic syndrome type 20. Neuromuscular Disorders, 28(10): 881−884. doi: 10.1016/j.nmd.2018.06.020
    Pryszcz LP, Gabaldón T. 2016. Redundans: an assembly pipeline for highly heterozygous genomes. Nucleic Acids Research, 44(12): e113. doi: 10.1093/nar/gkw294
    Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y. 2012. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics, 13(1): 341. doi: 10.1186/1471-2164-13-341
    Rimmer MA, Glamuzina B. 2019. A review of grouper (Family Serranidae: Subfamily Epinephelinae) aquaculture from a sustainability science perspective. Reviews in Aquaculture, 11(1): 58−87. doi: 10.1111/raq.12226
    Ritchie ME, Phipson B, Wu D, Hu YF, Law CW, Shi W, Smyth GK. 2015. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research, 43(7): e47. doi: 10.1093/nar/gkv007
    Robinson MD, McCarthy DJ, Smyth GK. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26(1): 139−140. doi: 10.1093/bioinformatics/btp616
    Shao CW, Li C, Wang N, Qin YT, Xu WT, Liu Q, Zhou Q, Zhao Y, Li XH, Liu SS, Chen XW, Mahboob S, Liu X, Chen SL. 2018. Chromosome-level genome assembly of the spotted sea bass, Lateolabrax maculatus. GigaScience, 7(11): giy114.
    Sreejit G, Ahmed A, Parveen N, Jha V, Valluri VL, Ghosh S, Mukhopadhyay S. 2014. The ESAT-6 protein of Mycobacterium tuberculosis interacts with Beta-2-Microglobulin (β2M) affecting antigen presentation function of macrophage. PLoS Pathogens, 10(10): e1004446. doi: 10.1371/journal.ppat.1004446
    Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B. 2006. Augustus: ab initio prediction of alternative transcripts. Nucleic Acids Research, 34(S2): W435−W439.
    Strychalski J, Brym P, Czarnik U, Gugołek A. 2015. A novel AAT-deletion mutation in the coding sequence of the BCO2 gene in yellow-fat rabbits. Journal of Applied Genetics, 56(4): 535−537. doi: 10.1007/s13353-015-0290-9
    Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25(9): 1105−1111. doi: 10.1093/bioinformatics/btp120
    Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. 2012. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols, 7(3): 562−578. doi: 10.1038/nprot.2012.016
    Våge DI, Boman IA. 2010. A nonsense mutation in the beta-carotene oxygenase 2 (BCO2) gene is tightly associated with accumulation of carotenoids in adipose tissue in sheep (Ovis aries). BMC Genetics, 11(1): 10. doi: 10.1186/1471-2156-11-10
    Van Dyken SJ, Locksley RM. 2018. Chitins and chitinase activity in airway diseases. Journal of Allergy and Clinical Immunology, 142(2): 364−369. doi: 10.1016/j.jaci.2018.06.017
    Van Herwerden L, Howard Choat J, Newman SJ, Leray M, Hillersøy G. 2009. Complex patterns of population structure and recruitment of Plectropomus leopardus (Pisces: Epinephelidae) in the Indo-West Pacific: implications for fisheries management. Marine Biology, 156(8): 1595−1607. doi: 10.1007/s00227-009-1195-0
    Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng QD, Wortman J, Young SK, Earl AM. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One, 9(11): e112963. doi: 10.1371/journal.pone.0112963
    Wang L, Yu CP, Guo L, Lin HR, Meng ZN. 2015a. In silico comparative transcriptome analysis of two color morphs of the common coral trout (Plectropomus leopardus). PLoS One, 10(12): e0145868. doi: 10.1371/journal.pone.0145868
    Wang S, Zhang JB, Jiao WQ, Li J, Xun XG, Sun Y, Guo XM, Huan P, Dong B, Zhang LL, Hu XL, Sun XQ, Wang J, Zhao CT, Wang YF, Wang DW, Huang XT, Wang RJ, Lv J, Li YL, Zhang ZF, Liu BZ, Lu W, Hui YY, Liang J, Zhou ZC, Hou R, Li X, Liu YC, Li HD, Ning XH, Lin Y, Zhao L, Xing Q, Dou JZ, Li YP, Mao JX, Guo HB, Dou HQ, Li TQ, Mu C, Jiang WK, Fu Q, Fu XT, Miao Y, Liu J, Yu Q, Li RJ, Liao H, Li X, Kong YF, Jiang Z, Chourrout D, Li RQ, Bao ZM. 2017. Scallop genome provides insights into evolution of bilaterian karyotype and development. Nature Ecology & Evolution, 1(5): 0120.
    Wang YP, Lu Y, Zhang Y, Ning ZM, Li Y, Zhao Q, Lu HY, Huang R, Xia XQ, Feng Q, Liang XF, Liu KY, Zhang L, Lu TT, Huang T, Fan DL, Weng QJ, Zhu CR, Lu YQ, Li WJ, Wen ZR, Zhou CC, Tian QL, Kang XJ, Shi MJ, Zhang WT, Jang SH, Du FK, He S, Liao LJ, Li YM, Gui B, He HH, Ning Z, Yang C, He L, Luo LF, Yang R, Luo Q, Liu XC, Li SS, Huang W, Xiao L, Lin HR, Han B, Zhu ZY. 2015b. The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation. Nature Genetics, 47(6): 625−631. doi: 10.1038/ng.3280
    Xie ZZ, Yu CP, Guo L, Li MM, Yong Z, Liu XC, Meng ZN, Lin HR. 2016. Ion Torrent next-generation sequencing reveals the complete mitochondrial genome of black and reddish morphs of the Coral Trout Plectropomus leopardus. Mitochondrial DNA, 27(1): 609−612. doi: 10.3109/19401736.2014.908369
    Xu L, Zhang Y, Su Y, Liu L, Yang J, Zhu YY, Li CY. 2010. Structure and evolution of full-length LTR retrotransposons in rice genome. Plant Systematics and Evolution, 287(1): 19−28.
    Yang XF, Liu HP, Ma ZH, Zou Y, Zou M, Mao YZ, Li XM, Wang H, Chen TS, Wang WM, Yang RB. 2019a. Chromosome-level genome assembly of Triplophysa tibetana, a fish adapted to the harsh high-altitude environment of the Tibetan Plateau. Molecular Ecology Resources, 19(4): 1027−1036. doi: 10.1111/1755-0998.13021
    Yang Y, Wu LN, Wu X, Li BJ, Huang WH, Weng ZY, Lin ZX, Song LL, Guo Y, Meng ZN, Liu XC, Xia JH. 2020. Identification of candidate growth-related SNPs and genes using GWAS in brown-marbled grouper (Epinephelus fuscoguttatus). Marine Biotechnology, 22(2): 153−166. doi: 10.1007/s10126-019-09940-8
    Yang Y, Zhou HQ, Hou LP, Xing K, Shu H. 2019b. Transcriptional profiling of skeletal muscle reveals starvation response and compensatory growth in Spinibarbus hollandi. BMC Genomics, 20(1): 938. doi: 10.1186/s12864-019-6345-2
    Yang ZH. 1997. Paml: a program package for phylogenetic analysis by maximum likelihood. Bioinformatics, 13(5): 555−556. doi: 10.1093/bioinformatics/13.5.555
    Yu W, Wen GL, Lin HZ, Yang YK, Huang XL, Zhou CP, Zhang ZW, Duan YF, Huang Z, Li T. 2018. Effects of dietary Spirulina platensis on growth performance, hematological and serum biochemical parameters, hepatic antioxidant status, immune responses and disease resistance of Coral trout Plectropomus leopardus (Lacepede, 1802). Fish & Shellfish Immunology, 74: 649−655.
    Zhou Q, Gao HY, Zhang Y, Fan GY, Xu H, Zhai JM, Xu WT, Chen ZF, Zhang H, Liu SS, Niu YP, Li WS, Li WM, Lin HR, Chen SL. 2019a. A chromosome-level genome assembly of the giant grouper (Epinephelus lanceolatus) provides insights into its innate immunity and rapid growth. Molecular Ecology Resources, 19(5): 1322−1332. doi: 10.1111/1755-0998.13048
    Zhou S, Song DL, Zhou XF, Mao XL, Zhou XF, Wang SL, Wei JG, Huang YH, Wang WX, Xiao SM, Qin QW. 2019b. Characterization of Bacillus subtilis from gastrointestinal tract of hybrid Hulong grouper (Epinephelus fuscoguttatus × E. lanceolatus) and its effects as probiotic additives. Fish & Shellfish Immunology, 84: 1115−1124.
    Zhou ZX, Chen L, Dong CJ, Peng WZ, Kong SN, Sun JS, Pu F, Chen BH, Feng JX, Xu P. 2018. Genome-scale association study of abnormal scale pattern in Yellow River carp identified previously known causative gene in European Mirror Carp. Marine Biotechnology, 20(5): 573−583. doi: 10.1007/s10126-018-9827-3
    Zhuang X, Qu M, Zhang X, Ding SX. 2013. A comprehensive description and evolutionary analysis of 22 grouper (Perciformes, Epinephelidae) mitochondrial genomes with emphasis on two novel genome organizations. PLoS One, 8(8): e73561. doi: 10.1371/journal.pone.0073561
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