Acknowledgement
This research was financially supported in part by a Ph.D. Scholarship for Chalermprakiat 70 years of reign under the Agricultural Research Development Agency (Public Organization) (ARDA) and the Royal Golden Jubilee PhD program under the Thailand Research Fund (TRF) and Agricultural Research Development Agency (Public Organization): The Seventieth Anniversary Celebrations of His Majesty's Accession to the Throne Ph.D. Scholarship Programme (HRD6401028) awarded to V.C. (6317400245) and K.S. The High-Quality Research Graduate Development Cooperation Project between Kasetsart University and the National Science and Technology Development Agency (NSTDA) was awarded to T.P. (6417400247) and K.S. The Center of Excellence on Agricultural Biotechnology, Office of the Permanent Secretary, Ministry of Higher Education, Science, Research and Innovation (AG-BIO/MHESI no. 60-003-005) was awarded to K.S. The National Research Council of Thailand (NRCT) (N42A650233); National Research Council of Thailand: High-Potential Research Team Grant Program (N42A660605) awarded to V.C., W.S., S.F.A., E.K., N.M., P.D., and K.S. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. We thank the Pathum Thani Aquatic Animal Genetics Research and Development Center, Aquatic Animal Genetics Research and Development Division (Department of Fisheries, Thailand) for supplying the silver barb specimens.
References
- Food and Agricultrue Organization of the United Nations. The State of World Fisheries and Aquaculture 2022: Towards Blue Transformation. Rome: Food and Agriculture Organization of the United Nations, 2022.
- Food and Agricultrue Organization of the United Nations. The State of World Fisheries and Aquaculture 2020: Sustainability in Action. Rome: Food and Agriculture Organization of the United Nations, 2020.
- 3.Jahan H, Ema NS, Hossain MS, Pervin MA, Akter R, Hossain Z. Growth performance study of silver barb (Barbonymus gonionotus) by replacing fishmeal with soybean meal in the diet. Asian J Med Biol Res 2020;6:149-154. https://doi.org/10.3329/ajmbr.v6i2.48045
- Department of Fisheries, Fisheries Statistics of Thailand 2018. Bangkok: Department of Fisheries, Ministry of Agriculture and Cooperatives, 2020.
- Gupta MV, Rab MA. Adoption and Economies of Sliver Barb (Puntius gonionotus) Culture in Seasonal Waters in Bangladesh. Dhaka: International Center for Living Aquatic Resources Management, 1994.
- Rahman MR, Nishat AA, Sarder MR, Islam R. Comparison of growth performance of gynogenetic female, gynogenetic neomale and normal mixed-sex silver barb (Barbonymus gonionotus) in earthen ponds. Bangladesh J Fish Res 2018;30:11-18. https://doi.org/10.3329/bjsr.v30i1-2.36116
- Wang HP, Shen ZG. Sex control in aquaculture: concept to practice. In: Sex Control in Aquaculture (Wang HP, Piferrer F, Chen SL, Shen ZG, eds.). Oxford: John Wiley & Sons, Ltd., 2018. pp. 1-34.
- Pongthana N, Penman DJ, Baoprasertkul P, Hussain MG, Shahidul Islam M, Powell SF, et al. Monosex female production in the silver barb (Puntius gonionotus Bleeker). Aquaculture 1999;173:247-256. https://doi.org/10.1016/S0044-8486(98)00449-9
- Pongthana N, Penman DJ, Karnasuta J, McAndrew BJ. Induced gynogenesis in the silver barb (Puntius gonionotus Bleeker) and evidence for female homogamety. Aquaculture 1995;135:267-276. https://doi.org/10.1016/0044-8486(95)01033-5
- Na-Nakorn U, Legrand E. Induction of triploidy in Puntius gonionotus (Bleeker) by cold shock. Kasetsart Univ Fish Res Bull 1992;18:1-10. https://doi.org/10.1016/0044-8486(93)90088-G
- Arganda-Carreras I, Kaynig V, Rueden C, Eliceiri KW, Schindelin J, Cardona A, et al. Trainable weka segmentation: a machine learning tool for microscopy pixel classification. Bioinformatics 2017;33:2424-2426. https://doi.org/10.1093/bioinformatics/btx180
- Robledo D, Palaiokostas C, Bargelloni L, Martinez P, Houston R. Applications of genotyping by sequencing in aquaculture breeding and genetics. Rev Aquac 2018;10:670-682. https://doi.org/10.1111/raq.12193
- Sopniewski J, Shams F, Scheele BC, Kefford BJ, Ezaz T. Identifying sex-linked markers in Litoria aurea: a novel approach to understanding sex chromosome evolution in an amphibian. Sci Rep 2019;9:16591.
- Wessels I, Maywald M, Rink L. Zinc as a gatekeeper of immune function. Nutrients 2017;9:1286.
- Nguyen DH, Panthum T, Ponjarat J, Laopichienpong N, Kraichak E, Singchat W, et al. An investigation of ZZ/ZW and XX/XY sex determination systems in North African catfish (Clarias gariepinus). Front Genet 2020;11:562856.
- Nguyen DH, Ponjarat J, Laopichienpong N, Kraichak E, Panthum T, Singchat W, et al. Genome-wide SNP analysis suggests male heterogamety in bighead catfish (Clarias macrocephalus, Gunther, 1864). Aquaculture 2021;543:737005.
- Panthum T, Jaisamut K, Singchat W, Ahmad SF, Kongkaew L, Wongloet W, et al. Something fishy about siamese fighting fish (Betta splendens) sex: polygenic sex determination or a newly emerged sex-determining region? Cells 2022;11:1764.
- Panthum T, Laopichienpong N, Kraichak E, Singchat W, Nguyen DH, Ariyaraphong N, et al. The snakeskin gourami (Trichopodus pectoralis) tends to exhibit XX/XY sex determination. Fishes 2021;6:43. https://doi.org/10.3390/fishes6040043
- Supikamolseni A, Ngaoburanawit N, Sumontha M, Chanhome L, Suntrarachun S, Peyachoknagul S, et al. Molecular barcoding of venomous snakes and species-specific multiplex PCR assay to identify snake groups for which antivenom is available in Thailand. Genet Mol Res 2015;14:13981-13997. https://doi.org/10.4238/2015.October.29.18
- Jaccoud D, Peng K, Feinstein D, Kilian A. Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res 2001;29:E25.
- Kilian A, Wenzl P, Huttner E, Carling J, Xia L, Blois H, et al. Diversity arrays technology: a generic genome profiling technology on open platforms. In: Data Production and Analysis in Population Genomics: Methods and Protocols (Pompanon F, Bonin A, eds.). Totowa: Humana Press, 2012. pp. 67-89.
- R Core Team. R: A language and environment for statistical computing. Vienna: R Foundation for Statistical Computing, 2022.
- Knueppel S, Rohde K. HapEstXXR: multi-locus stepwise regression. R Package Documentation, 2019.
- Koomgun T, Laopichienpong N, Singchat W, Panthum T, Phatcharakullawarawat R, Kraichak E, et al. Genome complexity reduction high-throughput genome sequencing of green iguana (Iguana iguana) reveal a paradigm shift in understanding sex-chromosomal linkages on homomorphic X and Y sex chromosomes. Front Genet 2020;11:556267.
- Pavan-Kumar A, Raman S, Koringa PG, Patel N, Shah T, Singh RK, et al. Complete mitochondrial genome of threatened mahseer Tor tor (Hamilton 1822) and its phylogenetic relationship within Cyprinidae family. J Genet 2016;95:853-863. https://doi.org/10.1007/s12041-016-0706-2
- Kasahara M, Naruse K, Sasaki S, Nakatani Y, Qu W, Ahsan B, et al. The medaka draft genome and insights into vertebrate genome evolution. Nature 2007;447:714-719. https://doi.org/10.1038/nature05846
- Broughton RE, Milam JE, Roe BA. The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA. Genome Res 2001;11:1958-1967. https://doi.org/10.1101/gr.156801
- Elmerot C, Arnason U, Gojobori T, Janke A. The mitochondrial genome of the pufferfish, Fugu rubripes, and ordinal teleostean relationships. Gene 2002;295:163-172. https://doi.org/10.1016/S0378-1119(02)00688-1
- Bao W, Kojima KK, Kohany O. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA 2015;6:11.
- O'Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res 2016;44:D733-D745. https://doi.org/10.1093/nar/gkv1189
- Lima T, Auchincloss AH, Coudert E, Keller G, Michoud K, Rivoire C, et al. HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. Nucleic Acids Res 2009;37: D471-D478. https://doi.org/10.1093/nar/gkn661
- Ge SX, Jung D, Yao R. ShinyGO: a graphical gene-set enrichment tool for animals and plants. Bioinformatics 2020;36:2628-2629. https://doi.org/10.1093/bioinformatics/btz931
- Arai MN. Pelagic coelenterates and eutrophication: a review. Hydrobiologia 2001;451:69-87. https://doi.org/10.1023/A:1011840123140
- Felip A, Zanuy S, Carrillo M, Piferrer F. Induction of triploidy and gynogenesis in teleost fish with emphasis on marine species. Genetica 2001;111:175-195. https://doi.org/10.1023/A:1013724322169
- Pandian TJ, Koteeswaran R. Lability of sex differentiation in fish. Curr Sci 1999;76:580-583.
- Arai K, Fujimoto T. Chromosome manipulation techniques and applications to aquaculture. In: Sex Control in Aquaculture (Wang HP, Piferrer F, Chen SL, Shen ZG, eds.). Oxford: John Wiley & Sons, Ltd., 2018. pp. 137-162.
- Ditcharoen S, Antonio Carlos Bertollo L, Rab P, Hnatkova E, Franco Molina W, Liehr T, et al. Genomic organization of repetitive DNA elements and extensive karyotype diversity of silurid catfishes (Teleostei: Siluriformes): a comparative cytogenetic approach. Int J Mol Sci 2019;20:3545.
- Maneechot N, Yano CF, Bertollo LA, Getlekha N, Molina WF, Ditcharoen S, et al. Genomic organization of repetitive DNAs highlights chromosomal evolution in the genus Clarias (Clariidae, Siluriformes). Mol Cytogenet 2016;9:4.
- Saenjundaeng P, Supiwong W, Sassi FM, Bertollo LA, Rab P, Kretschmer R, et al. Chromosomes of Asian cyprinid fishes: variable karyotype patterns and evolutionary trends in the genus Osteochilus (Cyprinidae, Labeoninae, "Osteochilini"). Genet Mol Biol 2020;43:e20200195.
- Lambert B, Vandeputte J, Remacle S, Bergiers I, Simonis N, Twizere JC, et al. Protein interactions of the transcription factor Hoxa1. BMC Dev Biol 2012;12:29.
- Zhang L, Ren F, Zhang Q, Chen Y, Wang B, Jiang J. The TEAD/TEF family of transcription factor Scalloped mediates Hippo signaling in organ size control. Dev Cell 2008;14:377-387. https://doi.org/10.1016/j.devcel.2008.01.006
- Pant J, Giovinazzo JA, Tuka LS, Pena D, Raper J, Thomson R. Apolipoproteins L1-6 share key cation channel-regulating residues but have different membrane insertion and ion conductance properties. J Biol Chem 2021;297:100951.
- Vaughn LS, Bragg DC, Sharma N, Camargos S, Cardoso F, Patel RC. Altered activation of protein kinase PKR and enhanced apoptosis in dystonia cells carrying a mutation in PKR activator protein PACT. J Biol Chem 2015;290:22543-22557 https://doi.org/10.1074/jbc.M115.669408
- Nakaya T. Dissection of FUS domains involved in regulation of SnRNP70 gene expression. FEBS Lett 2020;594:3518-3529. https://doi.org/10.1002/1873-3468.13924
- Motose H, Takatani S, Ikeda T, Takahashi T. NIMA-related kinases regulate directional cell growth and organ development through microtubule function in Arabidopsis thaliana. Plant Signal Behav 2012;7:1552-1555. https://doi.org/10.4161/psb.22412
- Gamble T, Coryell J, Ezaz T, Lynch J, Scantlebury DP, Zarkower D. Restriction site-associated DNA sequencing (RAD-seq) reveals an extraordinary number of transitions among gecko sex-determining systems. Mol Biol Evol 2015;32:1296-1309. https://doi.org/10.1093/molbev/msv023
- Ezaz T, Srikulnath K, Graves JA. Origin of amniote sex chromosomes: an ancestral super-sex chromosome, or common requirements? J Hered 2017;108:94-105. https://doi.org/10.1093/jhered/esw053
- Singchat W, Sillapaprayoon S, Muangmai N, Baicharoen S, Indananda C, Duengkae P, et al. Do sex chromosomes of snakes, monitor lizards, and iguanian lizards result from multiple fission of an "ancestral amniote super-sex chromosome"? Chromosome Res 2020;28:209-228. https://doi.org/10.1007/s10577-020-09631-4
- Chalopin D, Naville M, Plard F, Galiana D, Volff JN. Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates. Genome Biol Evol 2015;7:567-580. https://doi.org/10.1093/gbe/evv005
- Laopichienpong N, Kraichak E, Singchat W, Sillapaprayoon S, Muangmai N, Suntrarachun S, et al. Genome-wide SNP analysis of Siamese cobra (Naja kaouthia) reveals the molecular basis of transitions between Z and W sex chromosomes and supports the presence of an ancestral super-sex chromosome in amniotes. Genomics 2021;113:624-636. https://doi.org/10.1016/j.ygeno.2020.09.058
- Srikulnath K, Ahmad SF, Singchat W, Panthum T. Do Ty3/Gypsy transposable elements play preferential roles in sex chromosome differentiation? Life (Basel) 2022;12:522.
- Ahmad SF, Singchat W, Jehangir M, Panthum T, Srikulnath K. Consequence of paradigm shift with repeat landscapes in reptiles: powerful facilitators of chromosomal rearrangements for diversity and evolution. Genes (Basel) 2020;11:827.
- Carducci F, Barucca M, Canapa A, Carotti E, Biscotti MA. Mobile elements in ray-finned fish genomes. Life (Basel) 2020;10:221.
- Dechaud C, Volff JN, Schartl M, Naville M. Sex and the TEs: transposable elements in sexual development and function in animals. Mob DNA 2019;10:42.
- Yoshido A, Sichova J, Pospisilova K, Nguyen P, Volenikova A, Safar J, et al. Evolution of multiple sex-chromosomes associated with dynamic genome reshuffling in Leptidea wood-white butterflies. Heredity (Edinb) 2020;125:138-154. https://doi.org/10.1038/s41437-020-0325-9
- Charlesworth D. Evolution of recombination rates between sex chromosomes. Philos Trans R Soc Lond B Biol Sci 2017;372:20160456.
- Penman DJ, Piferrer F. Fish gonadogenesis. Part I: Genetic and environmental mechanisms of sex determination. Rev Fish Sci Aquac 2008;16:16-34. https://doi.org/10.1080/10641260802324610
- Ospina-Alvarez N, Piferrer F. Temperature-dependent sex determination in fish revisited: prevalence, a single sex ratio response pattern, and possible effects of climate change. PLoS One 2008;3:e2837.
- Gamble T, Castoe TA, Nielsen SV, Banks JL, Card DC, Schield DR, et al. The discovery of XY sex chromosomes in a Boa and Python. Curr Biol 2017;27:2148-2153. https://doi.org/10.1016/j.cub.2017.06.010
- Budd AM, Banh QQ, Domingos JA, Jerry DR. Sex control in fish: approaches, challenges and opportunities for aquaculture. J Mar Sci Eng 2015;3:329-355. https://doi.org/10.3390/jmse3020329
- Jiang S, Ma X, Li T, Zhu C, You X. Developing single nucleotide polymorphisms for identification of cod products by RAD-Seq. Animals (Basel) 2020;10:423.
- Gamble T. Using RAD-seq to recognize sex-specific markers and sex chromosome systems. Mol Ecol 2016;25:2114-2116. https://doi.org/10.1111/mec.13648
- Mattarucchi E, Marsoni M, Binelli G, Passi A, Lo Curto F, Pasquali F, et al. Different real time PCR approaches for the fine quantification of SNP's alleles in DNA pools: assays development, characterization and pre-validation. J Biochem Mol Biol 2005;38:555-562. https://doi.org/10.5483/BMBRep.2005.38.5.555