請用此 Handle URI 來引用此文件：
http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/97597完整後設資料紀錄
| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 董致韡 | zh_TW |
| dc.contributor.advisor | Chih-Wei Tung | en |
| dc.contributor.author | 古欣穎 | zh_TW |
| dc.contributor.author | Joyce Koh Xin Ying | en |
| dc.date.accessioned | 2025-07-03T16:10:54Z | - |
| dc.date.available | 2025-07-04 | - |
| dc.date.copyright | 2025-07-03 | - |
| dc.date.issued | 2025 | - |
| dc.date.submitted | 2025-06-19 | - |
| dc.identifier.citation | References
Abdelrahman, H., ElHady, M., Alcivar-Warren, A., Allen, S., Al-Tobasei, R., Bao, L., Beck, B., Blackburn, H., Bosworth, B., Buchanan, J., Chappell, J., Daniels, W., Dong, S., Dunham, R., Durland, E., Elaswad, A., Gomez-Chiarri, M., Gosh, K., Guo, X.,…Zhou, T. (2017). Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research. BMC Genomics 2017 18:1, 18(1). https://doi.org/10.1186/s12864-017-3557-1 Adolfi, M. C., Du, K., Kneitz, S., Cabau, C., Zahm, M., Klopp, C., Feron, R., Paixão, R. V., Varela, E. S., De Almeida, F. L., De Oliveira, M. A., Nóbrega, R. H., Lopez-Roques, C., Iampietro, C., Lluch, J., Kloas, W., Wuertz, S., Schaefer, F., Stöck, M.,…Schartl, M. (2021). A duplicated copy of id2b is an unusual sex-determining candidate gene on the Y chromosome of arapaima (Arapaima gigas). Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-01066-z Adzigbli, L., Wang, Z., Lai, Z., Li, J., & Deng, Y. (2019). Sex determination in pearl oyster: A mini review. Aquaculture Reports, 15. https://doi.org/10.1016/j.aqrep.2019.100214 Akagi, T., Henry, I. M., Tao, R., & Comai, L. (2014). A Y-chromosome–encoded small RNA acts as a sex determinant in persimmons. Science, 346(6209), 646-650. https://doi.org/10.1126/science.1257225 Allendorf, F. W., & Thorgaard, G. H. (1984). Tetraploidy and the Evolution of Salmonid Fishes. Evolutionary Genetics of Fishes. https://doi.org/10.1007/978-1-4684-4652-4_1 Anderson, J. L., Marí, A. R., Braasch, I., Amores, A., Hohenlohe, P., Batzel, P., & Postlethwait, J. H. (2012). Multiple Sex-Associated Regions and a Putative Sex Chromosome in Zebrafish Revealed by RAD Mapping and Population Genomics. PLoS ONE, 7(7). https://doi.org/10.1371/journal.pone.0040701 Anitha, A., & Senthilkumaran, B. (2021). Role of sox family genes in teleostean reproduction-an overview. Reproduction and Breeding, 1(1). https://doi.org/10.1016/j.repbre.2021.02.004 Arick, M. A., Grover, C. E., Hsu, C.-Y., Magbanua, Z., Pechanova, O., Miller, E. R., Thrash, A., Youngblood, R. C., Ezzell, L., Alam, M. S., Benzie, J. A. H., Hamilton, M. G., Karsi, A., Lawrence, M. L., & Peterson, D. G. (2023). A high-quality chromosome-level genome assembly of rohu carp, Labeo rohita, and its utilization in SNP-based exploration of gene flow and sex determination. G3 Genes|Genomes|Genetics, 13(3). https://doi.org/10.1093/g3journal/jkad009 Arkhipov, A. A., Pushkova, E. N., Bolsheva, N. L., Rozhmina, T. A., Borkhert, E. V., Zhernova, D. A., Rybakova, T. Y., Barsukov, N. M., Moskalenko, O. D., Sigova, E. A., Dvorianinova, E. M., Melnikova, N. V., Dmitriev, A. A., Arkhipov, A. A., Pushkova, E. N., Bolsheva, N. L., Rozhmina, T. A., Borkhert, E. V., Zhernova, D. A.,…Dmitriev, A. A. (2024). Nanopore Data-Driven Chromosome-Level Assembly of Flax Genome. Plants 2024, Vol. 13, Page 3465, 13(24). https://doi.org/10.3390/plants13243465 Astashyn, A., Tvedte, E. S., Sweeney, D., Sapojnikov, V., Bouk, N., Joukov, V., Mozes, E., Strope, P. K., Sylla, P. M., Wagner, L., Bidwell, S. L., Brown, L. C., Clark, K., Davis, E. W., Smith-White, B., Hlavina, W., Pruitt, K. D., Schneider, V. A., Murphy, T. D.,…Murphy, T. D. (2024). Rapid and sensitive detection of genome contamination at scale with FCS-GX. Genome Biology 2024 25:1, 25(1). https://doi.org/10.1186/s13059-024-03198-7 Austin, C. M., Tan, M. H., Harrisson, K. A., Lee, Y. P., Croft, L. J., Sunnucks, P., Pavlova, A., & Gan, H. M. (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). https://doi.org/10.1093/gigascience/gix063 Bachtrog, D., Kirkpatrick, M., Mank, J. E., McDaniel, S. F., Pires, J. C., Rice, W., & Valenzuela, N. (2011). Are all sex chromosomes created equal? Trends in Genetics, 27(9). https://doi.org/10.1016/j.tig.2011.05.005 Basavaraju, Y. (2023). Monosex population in aquaculture. Frontiers in Aquaculture Biotechnology. https://doi.org/10.1016/B978-0-323-91240-2.00012-9 Beardmore, J. A., Mair, G. C., & Lewis, R. I. (2001). Monosex male production in finfish as exemplified by tilapia: applications, problems, and prospects. Reproductive Biotechnology in Finfish Aquaculture. https://doi.org/10.1016/B978-0-444-50913-0.50015-1 Blix, T. B., Dalmo, R. A., Wargelius, A., & Myhr, A. I. (2021). Genome editing on finfish: Current status and implications for sustainability. Reviews in Aquaculture, 13(4). https://doi.org/10.1111/raq.12571 Bonenfant, Q., Noé, L., & Touzet, H. (2023). Porechop_ABI: discovering unknown adapters in Oxford Nanopore Technology sequencing reads for downstream trimming. Bioinformatics Advances, 3(1). https://doi.org/10.1093/bioadv/vbac085 Boughattas, S., Albatesh, D., Al-Khater, A., Giraldes, B. W., Althani, A. A., & Benslimane, F. M. (2021). Whole genome sequencing of marine organisms by Oxford Nanopore Technologies: Assessment and optimization of HMW‐DNA extraction protocols. Ecology and Evolution, 11(24). https://doi.org/10.1002/ece3.8447 Braasch, I. (2020). Genome Evolution: Domestication of the Allopolyploid Goldfish. Current Biology, 30(14). https://doi.org/10.1016/j.cub.2020.05.073 Bradley, K. M., Breyer, J. P., Melville, D. B., Broman, K. W., Knapik, E. W., & Smith, J. R. (2011). An SNP-Based Linkage Map for Zebrafish Reveals Sex Determination Loci. G3 Genes|Genomes|Genetics, 1(1). https://doi.org/10.1534/g3.111.000190 Brunet, F. d. r. G., Crollius, H. R., Paris, M., Aury, J.-M., Gibert, P., Jaillon, O., Laudet, V., & Robinson-Rechavi, M. (2006). Gene Loss and Evolutionary Rates Following Whole-Genome Duplication in Teleost Fishes. Molecular Biology and Evolution, 23(9). https://doi.org/10.1093/molbev/msl049 Budd, A., Banh, Q., Domingos, J., & Jerry, D. (2015). Sex Control in Fish: Approaches, Challenges and Opportunities for Aquaculture. Journal of Marine Science and Engineering, 3(2), 329-355. https://doi.org/10.3390/jmse3020329 Cai, M., Zou, Y., Xiao, S., Li, W., Han, Z., Han, F., Xiao, J., Liu, F., Wang, Z., Cai, M., Zou, Y., Xiao, S., Li, W., Han, Z., Han, F., Xiao, J., Liu, F., & Wang, Z. (2019). Chromosome assembly of Collichthys lucidus, a fish of Sciaenidae with a multiple sex chromosome system. Scientific Data 2019 6:1, 6(1). https://doi.org/10.1038/s41597-019-0139-x Carey, S. B., Aközbek, L., Lovell, J. T., Jenkins, J., Healey, A. L., Shu, S., Grabowski, P., Yocca, A., Stewart, A., Jones, T., Barry, K., Rajasekar, S., Talag, J., Scutt, C., Lowry, P. P., Munzinger, J., Knox, E. B., Soltis, D. E., Soltis, P. S.,…Harkess, A. (2024). ZW sex chromosome structure in Amborella trichopoda. Nature Plants 2024 10:12, 10(12). https://doi.org/10.1038/s41477-024-01858-x Carey, S. B., Lovell, J. T., Jenkins, J., Leebens-Mack, J., Schmutz, J., Wilson, M. A., & Harkess, A. (2022). Representing sex chromosomes in genome assemblies. Cell Genomics, 2(5). https://doi.org/10.1016/j.xgen.2022.100132 Catanach, A., Ruigrok, M., Bowatte, D., Davy, M., Storey, R., Valenza-Troubat, N., López-Girona, E., Hilario, E., Wylie, M. J., Chagné, D., Wellenreuther, M., Catanach, A., Ruigrok, M., Bowatte, D., Davy, M., Storey, R., Valenza-Troubat, N., López-Girona, E., Hilario, E.,…Wellenreuther, M. (2021). The genome of New Zealand trevally (Carangidae: Pseudocaranx georgianus) uncovers a XY sex determination locus. BMC Genomics 2021 22:1, 22(1). https://doi.org/10.1186/s12864-021-08102-2 Cavalcante, R. L. D., Ortega, J. M., de Souza, J. E. S., & Sakamoto, T. (2020). Assessing the Sex-Related Genomic Composition Difference Using a k-mer. Advances in Bioinformatics and Computational Biology. https://doi.org/10.1007/978-3-030-65775-8_5 Cavileer, T. D., Hunter, S. S., Olsen, J., Wenburg, J., & Nagler, J. J. (2015). A Sex‐Determining Gene (sdY) Assay Shows Discordance between Phenotypic and Genotypic Sex in Wild Populations of Chinook Salmon. Transactions of the American Fisheries Society, 144(2). https://doi.org/10.1080/00028487.2014.993479 Chakraborty, M., Baldwin-Brown, J. G., Long, A. D., & Emerson, J. J. (2016). Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage. Nucleic Acids Research, 44(19). https://doi.org/10.1093/nar/gkw654 Chakraborty, M., Baldwin-Brown, J. G., Long, A. D., & J. (2016). Contiguous and accuratede novoassembly of metazoan genomes with modest long read coverage. Nucleic Acids Research, gkw654. https://doi.org/10.1093/nar/gkw654 Charlesworth, B. (1991). The Evolution of Sex Chromosomes. Science, 251(4997). https://doi.org/10.1126/science.1998119 Charlesworth, B., & Charlesworth, D. (2000). The degeneration of Y chromosomes. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 355(1403). https://doi.org/10.1098/rstb.2000.0717 Chen, J., Zhu, Z., & Hu, W. (2022). Progress in research on fish sex determining genes. Water Biology and Security, 1(1), 100008. https://doi.org/https://doi.org/10.1016/j.watbs.2022.100008 Chen, L., Zhou, Z., Zhou, Z., Yang, J., Deng, Y., Bai, Y., Pu, F., Zhou, T., & Xu, P. (2024). Chromosome-level assembly and gene annotation of Decapterus maruadsi genome using Nanopore and Hi-C technologies. Scientific Data, 11(1). https://doi.org/10.1038/s41597-024-02912-1 Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018). fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34(17). https://doi.org/10.1093/bioinformatics/bty560 Chen, Y., Nie, F., Xie, S.-Q., Zheng, Y.-F., Dai, Q., Bray, T., Wang, Y.-X., Xing, J.-F., Huang, Z.-J., Wang, D.-P., He, L.-J., Luo, F., Wang, J.-X., Liu, Y.-Z., Xiao, C.-L., Chen, Y., Nie, F., Xie, S.-Q., Zheng, Y.-F.,…Xiao, C.-L. (2021). Efficient assembly of nanopore reads via highly accurate and intact error correction. Nature Communications 2021 12:1, 12(1). https://doi.org/10.1038/s41467-020-20236-7 Chen, Z., Omori, Y., Koren, S., Shirokiya, T., Kuroda, T., Miyamoto, A., Wada, H., Fujiyama, A., Toyoda, A., Zhang, S., Wolfsberg, T. G., Kawakami, K., Phillippy, A. M., Program, N. C. S., Mullikin, J. C., & Burgess, S. M. (2019). De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication. Science Advances, 5(6). https://doi.org/10.1126/sciadv.aav0547 Chernyavskaya, Y., Zhang, X., Liu, J., Blackburn, J., Chernyavskaya, Y., Zhang, X., Liu, J., & Blackburn, J. (2022). Long-read sequencing of the zebrafish genome reorganizes genomic architecture. BMC Genomics 2022 23:1, 23(1). https://doi.org/10.1186/s12864-022-08349-3 Cnaani, A., & Levavi-Sivan, B. (2009). Sexual Development in Fish, Practical Applications for Aquaculture. Sexual Development, 3(2-3). https://doi.org/10.1159/000223080 Cui, Z., Liu, Y., Wang, W., Wang, Q., Zhang, N., Lin, F., Wang, N., Shao, C., Dong, Z., Li, Y., Yang, Y., Hu, M., Li, H., Gao, F., Wei, Z., Meng, L., Liu, Y., Wei, M., Zhu, Y.,…Chen, S. (2017). Genome editing reveals dmrt1 as an essential male sex-determining gene in Chinese tongue sole (Cynoglossus semilaevis). Scientific Reports 2017 7:1, 7(1). https://doi.org/10.1038/srep42213 Curzon, A. Y., Shirak, A., Ron, M., & Seroussi, E. (2023). Master-Key Regulators of Sex Determination in Fish and Other Vertebrates—A Review. International Journal of Molecular Sciences, 24(3), 2468. https://doi.org/10.3390/ijms24032468 Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., McCarthy, S. A., Davies, R. M., & Li, H. (2021). Twelve years of SAMtools and BCFtools. GigaScience, 10(2). https://doi.org/10.1093/gigascience/giab008 Dauar, M. T., Picard, C., Labonte, A., & Poirier, J. (2023). Evaluation of HIVEP3 polymorphic variants and gene expression in Alzheimer’s disease. Alzheimer's & Dementia, 19(S12). https://doi.org/10.1002/alz.078629 David, L., Blum, S., Feldman, M. W., Lavi, U., & Hillel, J. (2003). Recent Duplication of the Common Carp (Cyprinus carpio L.) Genome as Revealed by Analyses of Microsatellite Loci. Molecular Biology and Evolution, 20(9). https://doi.org/10.1093/molbev/msg173 De Coster, W., & Rademakers, R. (2023). NanoPack2: population-scale evaluation of long-read sequencing data. Bioinformatics, 39(5). https://doi.org/10.1093/bioinformatics/btad311 DeAngelis, M. M., Wang, D. G., & Hawkins, T. L. (1995). Solid-phase reversible immobilization for the isolation of PCR products. Nucleic Acids Research, 23(22). https://doi.org/10.1093/nar/23.22.4742 Devlin, R. H., & Nagahama, Y. (2002). Sex determination and sex differentiation in fish: an overview of genetic, physiological, and environmental influences. Aquaculture, 208(3), 191-364. https://doi.org/https://doi.org/10.1016/S0044-8486(02)00057-1 Di Genova, A., Buena-Atienza, E., Ossowski, S., Sagot, M.-F., Di Genova, A., Buena-Atienza, E., Ossowski, S., & Sagot, M.-F. (2020). Efficient hybrid de novo assembly of human genomes with WENGAN. Nature Biotechnology 2020 39:4, 39(4). https://doi.org/10.1038/s41587-020-00747-w Diakos, E., Chevalier, C., Shahjahan, M., Hardy, A., Lambert, S., Kestemont, P., Fontaine, P., Pasquet, A., Lecocq, T., Diakos, E., Chevalier, C., Shahjahan, M., Hardy, A., Lambert, S., Kestemont, P., Fontaine, P., Pasquet, A., & Lecocq, T. (2024). Early impact of domestication on aggressiveness, activity, and stress behaviors in zebrafish (Danio rerio) using mirror test and automated videotracking. Scientific Reports 2024 14:1, 14(1). https://doi.org/10.1038/s41598-024-71451-x Dong, J., Albertinit, D. F., Nishimori, K., Kumar, T. R., Lu, N., & Matzuk, M. M. (1996). Growth differentiation factor-9 is required during early ovarian folliculogenesis. Nature, 383(6600). https://doi.org/10.1038/383531a0 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, S., Postlethwait, J., Meyer, A., Guiguen, Y., Schartl, M., Du, K.,…Schartl, M. (2019). The genome of the arapaima (Arapaima gigas) provides insights into gigantism, fast growth and chromosomal sex determination system. Scientific Reports 2019 9:1, 9(1). https://doi.org/10.1038/s41598-019-41457-x Feller, A. F., Ogi, V., Seehausen, O., Meier, J. I., Feller, A. F., Ogi, V., Seehausen, O., & Meier, J. I. (2021). Identification of a novel sex determining chromosome in cichlid fishes that acts as XY or ZW in different lineages. Hydrobiologia 2021 848:16, 848(16). https://doi.org/10.1007/s10750-021-04560-7 Feron, R., & Jaron, K. S. (2021). SexGenomicsToolkit/PSASS: 3.1.0 (3.1.0). Zenodo. https://doi.org/https://doi.org/10.5281/zenodo.4442702 Feron, R., Zahm, M., Cabau, C., Klopp, C., Roques, C., Bouchez, O., Eché, C., Valière, S., Donnadieu, C., Haffray, P., Bestin, A., Morvezen, R., Acloque, H., Euclide, P. T., Wen, M., Jouano, E., Schartl, M., Postlethwait, J. H., Schraidt, C.,…Guiguen, Y. (2020). Characterization of a Y‐specific duplication/insertion of the anti‐Mullerian hormone type II receptor gene based on a chromosome‐scale genome assembly of yellow perch, Perca flavescens. Molecular Ecology Resources, 20(2). https://doi.org/10.1111/1755-0998.13133 Fisher, S., Barry, A., Abreu, J., Minie, B., Nolan, J., Delorey, T. M., Young, G., Fennell, T. J., Allen, A., Ambrogio, L., Berlin, A. M., Blumenstiel, B., Cibulskis, K., Friedrich, D., Johnson, R., Juhn, F., Reilly, B., Shammas, R., Stalker, J.,…Nusbaum, C. (2011). A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biology 2011 12:1, 12(1). https://doi.org/10.1186/gb-2011-12-1-r1 Gand, M., Bloemen, B., Vanneste, K., Roosens, N. H. C., De Keersmaecker, S. C. J., Gand, M., Bloemen, B., Vanneste, K., Roosens, N. H. C., & De Keersmaecker, S. C. J. (2023). Comparison of 6 DNA extraction methods for isolation of high yield of high molecular weight DNA suitable for shotgun metagenomics Nanopore sequencing to detect bacteria. BMC Genomics 2023 24:1, 24(1). https://doi.org/10.1186/s12864-023-09537-5 Gao, Z.-X., & Draper, B. W. (2018). Gene Knockout and Its Principle and Application in Sex Control of Fish Species. Sex Control in Aquaculture. https://doi.org/10.1002/9781119127291.ch5 Gatins, R., Arias, C. F., Sánchez, C., Bernardi, G., & De León, L. F. (2024). Whole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific. Gigabyte, 2024, 1-18. https://doi.org/10.46471/gigabyte.115 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, 19(6). https://doi.org/10.1111/1755-0998.13064 Geffroy, B., Guilbaud, F., Amilhat, E., Beaulaton, L., Vignon, M., Huchet, E., Rives, J., Bobe, J., Fostier, A., Guiguen, Y., Bardonnet, A., Geffroy, B., Guilbaud, F., Amilhat, E., Beaulaton, L., Vignon, M., Huchet, E., Rives, J., Bobe, J.,…Bardonnet, A. (2016). Sexually dimorphic gene expressions in eels: useful markers for early sex assessment in a conservation context. Scientific Reports 2016 6:1, 6(1). https://doi.org/10.1038/srep34041 Gidmark, N. J., & Simons, A. M. (2014). Cyprinidae: carps and minnows. Freshwater Fishes of North America, 1, 354-450. Glasauer, S. M. K., Neuhauss, S. C. F., Glasauer, S. M. K., & Neuhauss, S. C. F. (2014). Whole-genome duplication in teleost fishes and its evolutionary consequences. Molecular Genetics and Genomics 2014 289:6, 289(6). https://doi.org/10.1007/s00438-014-0889-2 Godwin, J., & Roberts, R. (2018). Environmental and Genetic Sex Determining Mechanisms in Fishes. In (pp. 311-344). Springer International Publishing. https://doi.org/10.1007/978-3-319-94139-4_11 Gomelsky, B. (2003). Chromosome set manipulation and sex control in common carp: a review. Aquatic Living Resources, 16(5). https://doi.org/10.1016/S0990-7440(03)00085-8 Goto-Kazeto, R., Abe, Y., Masai, K., Yamaha, E., Adachi, S., & Yamauchi, K. (2006). Temperature-dependent sex differentiation in goldfish: Establishing the temperature-sensitive period and effect of constant and fluctuating water temperatures. Aquaculture, 254(1-4). https://doi.org/10.1016/j.aquaculture.2005.10.009 Guerrero-Tortolero, D. A., & Campos-Ramos, R. (2018). Sex Reversal and Determination and Sex Control in Shrimp and Prawn. Sex Control in Aquaculture. https://doi.org/10.1002/9781119127291.ch36 Guiguen, Y., Bertho, S., Herpin, A., & Fostier, A. (2018). Sex Determination and Sex Control in Salmonidae. Sex Control in Aquaculture. https://doi.org/10.1002/9781119127291.ch11 Haga, Y., Sakamoto, Y., Arai, M., Suzuki, Y., & Suzuki, A. (2023). Long-Read Whole-Genome Sequencing Using a Nanopore Sequencer and Detec. Methods in Molecular Biology. https://doi.org/10.1007/978-1-0716-2996-3_13 Hanson, K. C., Gravel, M. A., Graham, A., Shoji, A., & Cooke, S. J. (2008). Sexual Variation in Fisheries Research and Management: When Does Sex Matter? Reviews in Fisheries Science, 16(4). https://doi.org/10.1080/10641260802013866 Hedgpeth, J. W. (1962). The Physiology of Crustacea. BioScience, 12(1). https://doi.org/10.2307/1293068 Herrán, R. d. l., Hermida, M., Rubiolo, J. A., Gómez-Garrido, J., Cruz, F., Robles, F., Navajas-Pérez, R., Blanco, A., Villamayor, P. R., Torres, D., Sánchez-Quinteiro, P., Ramirez, D., Rodríguez, M. E., Arias-Pérez, A., Cross, I., Duncan, N., Martínez-Peña, T., Riaza, A., Millán, A.,…Martínez, P. (2023). A chromosome‐level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex‐determining gene in the flatfish Solea senegalensis. Molecular Ecology Resources, 23(4). https://doi.org/10.1111/1755-0998.13750 Hoegg, S., Brinkmann, H., Taylor, J. S., Meyer, A., Hoegg, S., Brinkmann, H., Taylor, J. S., & Meyer, A. (2004). Phylogenetic Timing of the Fish-Specific Genome Duplication Correlates with the Diversification of Teleost Fish. Journal of Molecular Evolution 2004 59:2, 59(2). https://doi.org/10.1007/s00239-004-2613-z Hontela, A., & Stacey, N. (2019). Cyprinidae. In Reproductive seasonality in teleosts (pp. 53-78). CRC press. Howe, K., Clark, M. D., Torroja, C. F., Torrance, J., Berthelot, C., Muffato, M., Collins, J. E., Humphray, S., McLaren, K., Matthews, L., McLaren, S., Sealy, I., Caccamo, M., Churcher, C., Scott, C., Barrett, J. C., Koch, R., Rauch, G.-J., White, S.,…Stemple, D. L. (2013). The zebrafish reference genome sequence and its relationship to the human genome. Nature 2013 496:7446, 496(7446). https://doi.org/10.1038/nature12111 Hu, J., Fan, J., Sun, Z., & Liu, S. (2020). NextPolish: a fast and efficient genome polishing tool for long-read assembly. Bioinformatics, 36(7). https://doi.org/10.1093/bioinformatics/btz891 Hu, J., Wang, Z., Sun, Z., Hu, B., Ayoola, A. O., Liang, F., Li, J., Sandoval, J. R., Cooper, D. N., Ye, K., Ruan, J., Xiao, C.-L., Wang, D., Wu, D.-D., Wang, S., Hu, J., Wang, Z., Sun, Z., Hu, B.,…Wang, S. (2024). NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads. Genome Biology 2024 25:1, 25(1). https://doi.org/10.1186/s13059-024-03252-4 Hu, X., Li, H., Lin, Y., Wang, Z., Feng, H., Zhou, M., Shi, L., Cao, H., & Ren, Y. (2022). Genomic deciphering of sex determination and unique immune system of a potential model species rare minnow (Gobiocypris rarus). Science Advances, 8(5). https://doi.org/10.1126/sciadv.abl7253 Huang, M. C., Huang, M. C., Ye, H., Ye, H., Kuan, Y. K., Kuan, Y. K., Li, M.-H., Li, M.-H., Ying, J. Y., & Ying, J. Y. (2009). Integrated two-step gene synthesis in a microfluidic device. Lab on a Chip, 9(2). https://doi.org/10.1039/B807688J Imarazene, B., Du, K., Beille, S., Jouanno, E., Feron, R., Pan, Q., Torres-Paz, J., Lopez-Roques, C., Castinel, A., Gil, L., Kuchly, C., Donnadieu, C., Parrinello, H., Journot, L., Cabau, C., Zahm, M., Klopp, C., Pavlica, T., Al-Rikabi, A.,…Guiguen, Y. (2021). A supernumerary “B-sex” chromosome drives male sex determination in the Pachón cavefish, Astyanax mexicanus. Current Biology, 31(21). https://doi.org/10.1016/j.cub.2021.08.030 Ingram, B., Sungan, S., Gooley, G., Sim, S. Y., Tinggi, D., & Silva, S. S. D. (2005). Induced spawning, larval development and rearing of two indigenous Malaysian mahseer, Tor tambroides and T. douronensis. Aquaculture Research, 36(10). https://doi.org/10.1111/j.1365-2109.2005.01309.x Islam, S., & Watanabe, H. (2020). Versican: A Dynamic Regulator of the Extracellular Matrix. Journal of Histochemistry and Cytochemistry, 68(11). https://doi.org/10.1369/0022155420953922 Jaafar, F., Na-Nakorn, U., Srisapoome, P., Amornsakun, T., Duong, T.-Y., Gonzales-Plasus, M. M., Hoang, D.-H., Parhar, I. S., Jaafar, F., Na-Nakorn, U., Srisapoome, P., Amornsakun, T., Duong, T.-Y., Gonzales-Plasus, M. M., Hoang, D.-H., & Parhar, I. S. (2021). A Current Update on the Distribution, Morphological Features, and Genetic Identity of the Southeast Asian Mahseers, Tor Species. Biology 2021, Vol. 10, Page 286, 10(4). https://doi.org/10.3390/biology10040286 Jasonowicz, A. J., Simeon, A., Zahm, M., Cabau, C., Klopp, C., Roques, C., Iampietro, C., Lluch, J., Donnadieu, C., Parrinello, H., Drinan, D. P., Hauser, L., Guiguen, Y., & Planas, J. V. (2022). Generation of a chromosome‐level genome assembly for Pacific halibut (Hippoglossus stenolepis) and characterization of its sex‐determining genomic region. Molecular Ecology Resources, 22(7). https://doi.org/10.1111/1755-0998.13641 Johnson, L. K., Sahasrabudhe, R., Gill, J. A., Roach, J. L., Froenicke, L., Brown, C. T., & Whitehead, A. (2020). Draft genome assemblies using sequencing reads from Oxford Nanopore Technology and Illumina platforms for four species of North American Fundulus killifish. GigaScience, 9(6). https://doi.org/10.1093/gigascience/giaa067 Johnston, I. A., Kent, M. P., Boudinot, P., Looseley, M., Bargelloni, L., Faggion, S., Merino, G. A., Ilsley, G. R., Bobe, J., Tsigenopoulos, C. S., Robertson, J., Harrison, P. W., Martinez, P., Robledo, D., Macqueen, D. J., & Lien, S. (2024). Advancing fish breeding in aquaculture through genome functional annotation. Aquaculture, 583. https://doi.org/10.1016/j.aquaculture.2024.740589 Kamiya, T., Kai, W., Tasumi, S., Oka, A., Matsunaga, T., Mizuno, N., Fujita, M., Suetake, H., Suzuki, S., Hosoya, S., Tohari, S., Brenner, S., Miyadai, T., Venkatesh, B., Suzuki, Y., & Kikuchi, K. (2012). A Trans-Species Missense SNP in Amhr2 Is Associated with Sex Determination in the Tiger Pufferfish, Takifugu rubripes (Fugu). PLOS Genetics, 8(7). https://doi.org/10.1371/journal.pgen.1002798 Khatei, A., Ganie, P. A., Sidiq, M. J., Posti, R., & Pandey, P. K. (2025). Genomic Insights into Fisheries and Aquaculture: A Bioinformatics Appr. Information Technology in Fisheries and Aquaculture. https://doi.org/10.1007/978-981-97-8553-7_11 Kikuchi, K., & Hamaguchi, S. (2013). Novel sex‐determining genes in fish and sex chromosome evolution. Developmental Dynamics, 242(4). https://doi.org/10.1002/dvdy.23927 Kim, B. Y., Gellert, H. R., Church, S. H., Suvorov, A., Anderson, S. S., Barmina, O., Beskid, S. G., Comeault, A. A., Crown, K. N., Diamond, S. E., Dorus, S., Fujichika, T., Hemker, J. A., Hrcek, J., Kankare, M., Katoh, T., Magnacca, K. N., Martin, R. A., Matsunaga, T.,…Petrov, D. A. (2024). Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life. PLoS Biology, 22(7). https://doi.org/10.1371/journal.pbio.3002697 Kirubakaran, T. G., Andersen, Ø., De Rosa, M. C., Andersstuen, T., Hallan, K., Kent, M. P., Lien, S., Kirubakaran, T. G., Andersen, Ø., De Rosa, M. C., Andersstuen, T., Hallan, K., Kent, M. P., & Lien, S. (2019). Characterization of a male specific region containing a candidate sex determining gene in Atlantic cod. Scientific Reports 2019 9:1, 9(1). https://doi.org/10.1038/s41598-018-36748-8 Kirubakaran, T. G., Andersen, Ø., Moser, M., Árnyasi, M., McGinnity, P., Lien, S., & Kent, M. (2020). A Nanopore Based Chromosome-Level Assembly Representing Atlantic Cod from the Celtic Sea. G3 Genes|Genomes|Genetics, 10(9). https://doi.org/10.1534/g3.120.401423 Kitano, J., Ansai, S., Takehana, Y., Yamamoto, Y., Kitano, J., Ansai, S., Takehana, Y., & Yamamoto, Y. (2024). Diversity and Convergence of Sex-Determination Mechanisms in Teleost Fish. Annual Review of Animal Biosciences, 12(Volume 12, 2024). https://doi.org/10.1146/annurev-animal-021122-113935 Kobayashi, T. (2024). Involvement of gonadal soma-derived factor in the reproduction of teleosts. Aquaculture and Fisheries, 9(3). https://doi.org/10.1016/j.aaf.2023.04.002 Kobayashi, Y. (2022). Control of gonadal maturation and sex in grouper. Aquaculture and Fisheries, 7(5). https://doi.org/10.1016/j.aaf.2022.03.008 Kocour, M., Linhart, O., Gela, D., & Rodina, M. (2005). Growth Performance of All‐Female and Mixed‐Sex Common Carp Cyprinus Carpio L. Populations in the Central Europe Climatic Conditions. Journal of the World Aquaculture Society, 36(1). https://doi.org/10.1111/j.1749-7345.2005.tb00136.x Kokot, M., Długosz, M., & Deorowicz, S. (2017). KMC 3: counting and manipulating k-mer statistics. Bioinformatics, 33(17). https://doi.org/10.1093/bioinformatics/btx304 Kolmogorov, M., Yuan, J., Lin, Y., Pevzner, P. A., Kolmogorov, M., Yuan, J., Lin, Y., & Pevzner, P. A. (2019). Assembly of long, error-prone reads using repeat graphs. Nature Biotechnology 2019 37:5, 37(5). https://doi.org/10.1038/s41587-019-0072-8 Kottelat, M. (2013). THE FISHES OF THE INLAND WATERS OF SOUTHEAST ASIA : A CATALOGUE AND CORE BIBLIOGRAPHY OF THE FISHES KNOWN TO OCCUR IN FRESHWATERS, MANGROVES AND ESTUARIES. Raffles Bulletin of Zoology, 1-663. https://research.ebsco.com/linkprocessor/plink?id=9208ac3f-4ddf-3d5d-913e-ee32b1de9eec Koyama, T., Nakamoto, M., Morishima, K., Yamashita, R., Yamashita, T., Sasaki, K., Kuruma, Y., Mizuno, N., Suzuki, M., Okada, Y., Ieda, R., Uchino, T., Tasumi, S., Hosoya, S., Uno, S., Koyama, J., Toyoda, A., Kikuchi, K., & Sakamoto, T. (2019). A SNP in a Steroidogenic Enzyme Is Associated with Phenotypic Sex in Seriola Fishes. Current Biology, 29(11). https://doi.org/10.1016/j.cub.2019.04.069 Kuhl, H., Du, K., Schartl, M., Kalous, L., Stöck, M., Lamatsch, D. K., Kuhl, H., Du, K., Schartl, M., Kalous, L., Stöck, M., & Lamatsch, D. K. (2022). Equilibrated evolution of the mixed auto-/allopolyploid haplotype-resolved genome of the invasive hexaploid Prussian carp. Nature Communications 2022 13:1, 13(1). https://doi.org/10.1038/s41467-022-31515-w L, C., RL, W., J, W., V, N., & I, B. (2023). ntLink: A Toolkit for De Novo Genome Assembly Scaffolding and Mapping Using Long Reads - PubMed. Current protocols, 3(4). https://doi.org/10.1002/cpz1.733 Lau, M. M. L., Lim, L. W. K., Chung, H. H., & Gan, H. M. (2023). The first draft genome assembly and data analysis of the Malaysian mahseer (Tor tambroides). Aquaculture and Fisheries, 8(5), 481-491. https://doi.org/10.1016/j.aaf.2022.05.002 Levy Karin, E., Mirdita, M., Söding, J., Levy Karin, E., Mirdita, M., & Söding, J. (2020). MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics. Microbiome 2020 8:1, 8(1). https://doi.org/10.1186/s40168-020-00808-x Li, D., Zeng, L., Zhang, W., Wang, Q., Wu, J., Zhu, C., & Meng, Z. (2025). Multi-omics study of sex in greater amberjack (Seriola dumerili): Identifying related genes, analyzing sex-biased expression, and developing sex-specific markers. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 53. https://doi.org/10.1016/j.cbd.2024.101364 Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. https://doi.org/10.48550/arXiv.1303.3997 Li, J.-T., Hou, G.-Y., Kong, X.-F., Li, C.-Y., Zeng, J.-M., Li, H.-D., Xiao, G.-B., Li, X.-M., Sun, X.-W., Li, J.-T., Hou, G.-Y., Kong, X.-F., Li, C.-Y., Zeng, J.-M., Li, H.-D., Xiao, G.-B., Li, X.-M., & Sun, X.-W. (2015). The fate of recent duplicated genes following a fourth-round whole genome duplication in a tetraploid fish, common carp (Cyprinus carpio). Scientific Reports 2015 5:1, 5(1). https://doi.org/10.1038/srep08199 Li, N., Stein, R. S. L., He, W., Komives, E., & Wang, W. (2013). Identification of Methyllysine Peptides Binding to Chromobox Protein Homolog 6 Chromodomain in the Human Proteome. Molecular & Cellular Proteomics, 12(10). https://doi.org/10.1074/mcp.O112.025015 Li, X.-Y., Mei, J., Ge, C.-T., Liu, X.-L., Gui, J.-F., Li, X.-Y., Mei, J., Ge, C.-T., Liu, X.-L., & Gui, J.-F. (2022). Sex determination mechanisms and sex control approaches in aquaculture animals. Science China Life Sciences 2022 65:6, 65(6). https://doi.org/10.1007/s11427-021-2075-x Li, Y., Wang, D., Wang, W., Yang, W., Gao, J., Zhang, W., Shan, L., Kang, M., Chen, Y., & Ma, T. (2023). A chromosome‐level Populus qiongdaoensis genome assembly provides insights into tropical adaptation and a cryptic turnover of sex determination. Molecular Ecology, 32(6), 1366-1380. https://doi.org/10.1111/mec.16566 Liao, Q., Du, R., Gou, J., Guo, L., Shen, H., Liu, H., Nguyen, J. K., Ming, R., Yin, T., Huang, S., & Yan, J. (2020). The genomic architecture of the sex‐determining region and sex‐related metabolic variation in Ginkgo biloba. The Plant Journal, 104(5), 1399-1409. https://doi.org/10.1111/tpj.15009 Liao, Q., Gong, G., Wang, J., Xie, Y., Guo, W., & Mei, J. (2023). Identification of sex-linked codominant markers and development of a rapid LAMP-based genetic sex identification method in channel catfish (Ictalurus punctatus). Aquaculture, 572. https://doi.org/10.1016/j.aquaculture.2023.739556 Lien, S., Koop, B. F., Sandve, S. R., Miller, J. R., Kent, M. P., Nome, T., Hvidsten, T. R., Leong, J. S., Minkley, D. R., Zimin, A., Grammes, F., Grove, H., Gjuvsland, A., Walenz, B., Hermansen, R. A., von Schalburg, K., Rondeau, E. B., Di Genova, A., Samy, J. K. A.,…Davidson, W. S. (2016). The Atlantic salmon genome provides insights into rediploidization. Nature 2016 533:7602, 533(7602). https://doi.org/10.1038/nature17164 Liew, W. C., Bartfai, R., Lim, Z., Sreenivasan, R., Siegfried, K. R., & Orban, L. (2012). Polygenic Sex Determination System in Zebrafish. PLoS ONE, 7(4). https://doi.org/10.1371/journal.pone.0034397 Liew, W. C., & Orbán, L. (2014). Zebrafish sex: a complicated affair. Briefings in Functional Genomics, 13(2). https://doi.org/10.1093/bfgp/elt041 Lim, L. W. K., Chung, H. H., Lau, M. M. L., Aziz, F., & Gan, H. M. (2021). Improving the phylogenetic resolution of Malaysian and Javan mahseer (Cyprinidae), Tor tambroides and Tor tambra: Whole mitogenomes sequencing, phylogeny and potential mitogenome markers. Gene, 791. https://doi.org/10.1016/j.gene.2021.145708 Lin, W., Zhu, X., Gao, L., Mao, M., Gao, D., Huang, Z., Lin, W., Zhu, X., Gao, L., Mao, M., Gao, D., & Huang, Z. (2021). Osteomodulin positively regulates osteogenesis through interaction with BMP2. Cell Death & Disease 2021 12:2, 12(2). https://doi.org/10.1038/s41419-021-03404-5 Lis, J. T., & Schleif, R. (1975). Size fractionation of double-stranded DNA by precipitation with polyethylene glycol. Nucleic Acids Research, 2(3). https://doi.org/10.1093/nar/2.3.383 Liu, H., Pang, M., Yu, X., Zhou, Y., Tong, J., & Fu, B. (2018). Sex-specific markers developed by next-generation sequencing confirmed an XX/XY sex determination system in bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix). DNA Research, 25(3). https://doi.org/10.1093/dnares/dsx054 Liu, H., Xia, W., Li, B., Liu, L., Wang, Y., Luo, Q., Ou, M., Zhu, X., Chen, K., & Zhao, J. (2023). Sex-specific markers developed by 2b-RAD and genome sequencing reveal an XX/XY sex-determination system in mud carp (Cirrhinus molitorella). Aquaculture, 565. https://doi.org/10.1016/j.aquaculture.2022.739131 Liu, X., Tang, X., Chen, M., Ni, G., & Yang, Y. (2024). Development and application of molecular markers in fisheries, aquaculture, and industry of representative temperate and tropical sea cucumbers: a review. Frontiers in Marine Science, 11. https://doi.org/10.3389/fmars.2024.1423096 Lu, D., Liu, C., Ji, W., Xia, R., Li, S., Liu, Y., Liu, N., Liu, Y., Deng, X. W., & Li, B. (2024). Nanopore ultra-long sequencing and adaptive sampling spur plant complete telomere-to-telomere genome assembly. Molecular Plant, 17(11). https://doi.org/10.1016/j.molp.2024.10.008 Lu, G., & Luo, M. (2020). Genomes of major fishes in world fisheries and aquaculture: Status, application and perspective. Aquaculture and Fisheries, 5(4), 163-173. https://doi.org/10.1016/j.aaf.2020.05.004 Lü, Z., Yu, Z., Luo, W., Liu, T., Wang, Y., Liu, Y., Liu, J., Liu, B., Gong, L., Liu, L., & Li, Y. (2024). Chromosome-level genome assembly and annotation of eel goby (Odontamblyopus rebecca). Scientific Data, 11(1). https://doi.org/10.1038/s41597-024-02997-8 Maghini, D. G., Moss, E. L., Vance, S. E., Bhatt, A. S., Maghini, D. G., Moss, E. L., Vance, S. E., & Bhatt, A. S. (2020). Improved high-molecular-weight DNA extraction, nanopore sequencing and metagenomic assembly from the human gut microbiome. Nature Protocols 2020 16:1, 16(1). https://doi.org/10.1038/s41596-020-00424-x Mank, J. E., & Avise, J. C. (2009). Evolutionary Diversity and Turn-Over of Sex Determination in Teleost Fishes. Sexual Development, 3(2-3). https://doi.org/10.1159/000223071 Mank, J. E., Promislow, D. E. L., & Avise, J. C. (2006). Evolution of alternative sex-determining mechanisms in teleost fishes. Biological Journal of the Linnean Society, 87(1), 83-93. https://doi.org/10.1111/j.1095-8312.2006.00558.x Manni, M., Berkeley, M. R., Seppey, M., Simão, F. A., & Zdobnov, E. M. (2021). BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Molecular Biology and Evolution, 38(10). https://doi.org/10.1093/molbev/msab199 Marçais, G., & Kingsford, C. (2011). A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics, 27(6). https://doi.org/10.1093/bioinformatics/btr011 Martínez, P., Robledo, D., Taboada, X., Blanco, A., Moser, M., Maroso, F., Hermida, M., Gómez-Tato, A., Álvarez-Blázquez, B., Cabaleiro, S., Piferrer, F., Bouza, C., Lien, S., & Viñas, A. M. (2021). A genome-wide association study, supported by a new chromosome-level genome assembly, suggests sox2 as a main driver of the undifferentiatiated ZZ/ZW sex determination of turbot (Scophthalmus maximus). Genomics, 113(4). https://doi.org/10.1016/j.ygeno.2021.04.007 Martínez, P., Viñas, A. M., Sánchez, L., Díaz, N., Ribas, L., & Piferrer, F. (2014). Genetic architecture of sex determination in fish: applications to sex ratio control in aquaculture. Frontiers in Genetics, 5. https://doi.org/10.3389/fgene.2014.00340 Mascali, F. C., Mastrochirico-Filho, V. A., Posner, V. M., Rubiolo, J. A., Hashimoto, D. T., Villanova, G. V., Mascali, F. C., Mastrochirico-Filho, V. A., Posner, V. M., Rubiolo, J. A., Hashimoto, D. T., & Villanova, G. V. (2024). High-quality genome assembly and annotation of the pacu Piaractus mesopotamicus: an aquatic genetic resource of South American aquaculture. Aquaculture International 2024 32:7, 32(7). https://doi.org/10.1007/s10499-024-01601-5 Michael, T. P., Jupe, F., Bemm, F., Motley, S. T., Sandoval, J. P., Lanz, C., Loudet, O., Weigel, D., Ecker, J. R., Michael, T. P., Jupe, F., Bemm, F., Motley, S. T., Sandoval, J. P., Lanz, C., Loudet, O., Weigel, D., & Ecker, J. R. (2018). High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell. Nature Communications 2018 9:1, 9(1). https://doi.org/10.1038/s41467-018-03016-2 Ming, R., Bendahmane, A., Renner, S. S., Ming, R., Bendahmane, A., & Renner, S. S. (2011). Sex Chromosomes in Land Plants. Annual Review of Plant Biology, 62(Volume 62, 2011). https://doi.org/10.1146/annurev-arplant-042110-103914 Moran, M. N., Jones, D. B., Jensen, S. A., Marcoli, R., & Jerry, D. R. (2024). Optimising commercial traits through gene editing in aquaculture: Strategies for accelerating genetic improvement. Reviews in Aquaculture, 16(3). https://doi.org/10.1111/raq.12889 Mu, J., Hu, W., Chen, R., Yang, Y., Li, H., Li, W., Yin, X., & Xu, D. (2024). Production of neomale and neofemale large yellow croaker (Larimichthys crocea) and establishment of all-female populations. Aquaculture, 590. https://doi.org/10.1016/j.aquaculture.2024.741010 Nagabhushana, A., Mishra, R. K., Nagabhushana, A., & Mishra, R. K. (2016). Finding clues to the riddle of sex determination in zebrafish. Journal of Biosciences 2016 41:1, 41(1). https://doi.org/10.1007/s12038-016-9593-1 Nanda, I., Kondo, M., Hornung, U., Asakawa, S., Winkler, C., Shimizu, A., Shan, Z., Haaf, T., Shimizu, N., Shima, A., Schmid, M., Schartl, M., Nanda, I., Kondo, M., Hornung, U., Asakawa, S., Winkler, C., Shimizu, A., Shan, Z.,…Schartl, M. (2002). A duplicated copy of DMRT1 in the sex-determining region of the Y chromosome of the medaka, Oryzias latipes. Proceedings of the National Academy of Sciences, 99(18). https://doi.org/10.1073/pnas.182314699 Nelson, J. S., Grande, T. C., & Wilson, M. V. (2016). Fishes of the World. John Wiley & Sons. Neves, C. T. J., Matzrafi, M., Thiele, M., Lorant, A., Mesgaran, M. B., & Stetter, M. G. (2020a). Male Linked Genomic Region Determines Sex in Dioecious Amaranthus palmeri. Journal of Heredity, 111(7), 606-612. https://doi.org/10.1093/jhered/esaa047 Neves, C. t. J., Matzrafi, M., Thiele, M., Lorant, A., Mesgaran, M. B., & Stetter, M. G. (2020b). Male Linked Genomic Region Determines Sex in Dioecious Amaranthus palmeri. Journal of Heredity, 111(7). https://doi.org/10.1093/jhered/esaa047 Nguyen, N. H., & Nguyen, N. H. (2024). Genetics and Genomics of Infectious Diseases in Key Aquaculture Species. Biology 2024, Vol. 13, Page 29, 13(1). https://doi.org/10.3390/biology13010029 Okayasu, R., & Iliakis, G. (1989). Linear DNA Elution Dose Response Curves Obtained in CHO Cells with Non-unwinding Filter Elution after Appropriate Selection of the Lysis Conditions. International Journal of Radiation Biology, 55(4). https://doi.org/10.1080/09553008914550621 Opazo, J. C., Butts, G. T., Nery, M. F., Storz, J. F., & Hoffmann, F. G. (2013). Whole-Genome Duplication and the Functional Diversification of Teleost Fish Hemoglobins. Molecular Biology and Evolution, 30(1). https://doi.org/10.1093/molbev/mss212 Pan, Q., Feron, R., Yano, A., Guyomard, R., Jouanno, E., Vigouroux, E., Wen, M., Busnel, J.-M., Bobe, J., Concordet, J.-P., Parrinello, H., Journot, L., Klopp, C., Lluch, J., Roques, C., Postlethwait, J., Schartl, M., Herpin, A., & Guiguen, Y. (2019). Identification of the master sex determining gene in Northern pike (Esox lucius) reveals restricted sex chromosome differentiation. PLOS Genetics, 15(8). https://doi.org/10.1371/journal.pgen.1008013 Pan, Q., Kay, T., Depincé, A., Adolfi, M., Schartl, M., Guiguen, Y., & Herpin, A. (2021). Evolution of master sex determiners: TGF-β signalling pathways at regulatory crossroads. Philosophical Transactions of the Royal Society B: Biological Sciences, 376(1832), 20200091. https://doi.org/10.1098/rstb.2020.0091 Pasquier, J., Cabau, C., Nguyen, T., Jouanno, E., Severac, D., Braasch, I., Journot, L., Pontarotti, P., Klopp, C., Postlethwait, J. H., Guiguen, Y., Bobe, J., Pasquier, J., Cabau, C., Nguyen, T., Jouanno, E., Severac, D., Braasch, I., Journot, L.,…Bobe, J. (2016). Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. BMC Genomics 2016 17:1, 17(1). https://doi.org/10.1186/s12864-016-2709-z Peichel, C. L., McCann, S. R., Ross, J. A., Naftaly, A. F. S., Urton, J. R., Cech, J. N., Grimwood, J., Schmutz, J., Myers, R. M., Kingsley, D. M., White, M. A., Peichel, C. L., McCann, S. R., Ross, J. A., Naftaly, A. F. S., Urton, J. R., Cech, J. N., Grimwood, J., Schmutz, J.,…White, M. A. (2020). Assembly of the threespine stickleback Y chromosome reveals convergent signatures of sex chromosome evolution. Genome Biology 2020 21:1, 21(1). https://doi.org/10.1186/s13059-020-02097-x Prost, S., Petersen, M., Grethlein, M., Hahn, S. J., Kuschik-Maczollek, N., Olesiuk, M. E., Reschke, J.-O., Schmey, T. E., Zimmer, C., Gupta, D. K., Schell, T., Coimbra, R., De Raad, J., Lammers, F., Winter, S., & Janke, A. (2020). Improving the Chromosome-Level Genome Assembly of the Siamese Fighting Fish (Betta splendens) in a University Master’s Course. G3 Genes|Genomes|Genetics, 10(7). https://doi.org/10.1534/g3.120.401205 Purushothaman, S., Meola, M., Roloff, T., Rooney, A. M., Egli, A., Purushothaman, S., Meola, M., Roloff, T., Rooney, A. M., & Egli, A. (2024). Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection. Scientific Reports 2024 14:1, 14(1). https://doi.org/10.1038/s41598-024-80660-3 Rajendiran, P., Jaafar, F., Kar, S., Sudhakumari, C., Senthilkumaran, B., & Parhar, I. S. (2021). Sex Determination and Differentiation in Teleost: Roles of Genetics, Environment, and Brain. Biology, 10(10), 973. https://doi.org/10.3390/biology10100973 Redhwan, A. I., & Komilus, C. F. (2021). Mahsheers in Malaysia: A Review on Feed for Tor tambroides (Empurau) Cultured in Captivity. 1st Postgraduate Seminar on Agriculture and Forestry, Redhwan, A. I., Rao, S., Mohamad-Zuki, N., Kari, A., Kamarudin, A., Ismail, N., Nguang, S., Ha, H., Yong, W., & Yong, F. (2022). Mahseer in Malaysia: A review of feed for cultured Tor tambroides and Tor tambra. Bioscience Research, 19(1), 349-359. Regan, T., Hori, T. S., & Bean, T. P. (2024). A chromosome-scale Mytilus edulis genome assembly for aquaculture, marine ecology, and evolution. G3 Genes|Genomes|Genetics, 14(8). https://doi.org/10.1093/g3journal/jkae138 Rhie, A., Nurk, S., Cechova, M., Hoyt, S. J., Taylor, D. J., Altemose, N., Hook, P. W., Koren, S., Rautiainen, M., Alexandrov, I. A., Allen, J., Asri, M., Bzikadze, A. V., Chen, N.-C., Chin, C.-S., Diekhans, M., Flicek, P., Formenti, G., Fungtammasan, A.,…Phillippy, A. M. (2023). The complete sequence of a human Y chromosome. Nature 2023 621:7978, 621(7978). https://doi.org/10.1038/s41586-023-06457-y Rhoads, A., & Au, K. F. (2015). PacBio Sequencing and its Applications. Genomics, Proteomics & Bioinformatics, 13(5). https://doi.org/10.1016/j.gpb.2015.08.002 Ribas, L., Valdivieso, A., Díaz, N., & Piferrer, F. (2017). Appropriate rearing density in domesticated zebrafish to avoid masculinization: links with the stress response. Journal of Experimental Biology, 220(6). https://doi.org/10.1242/jeb.144980 Rice, W. R. (1984). Sex Chromosomes and the Evolution of Sexual Dimorphism. Evolution, 38(4), 735-742. https://doi.org/10.2307/2408385 Richter, A., Mörl, H., Thielemann, M., Kleemann, M., Geißen, R., Schwarz, R., Albertz, C., Koch, P., Petzold, A., Kroll, T., Groth, M., Hartmann, N., Herpin, A., Englert, C., Richter, A., Mörl, H., Thielemann, M., Kleemann, M., Geißen, R.,…Englert, C. (2025). The master male sex determinant Gdf6Y of the turquoise killifish arose through allelic neofunctionalization. Nature Communications 2025 16:1, 16(1). https://doi.org/10.1038/s41467-025-55899-7 Roach, M. J., Schmidt, S. A., Borneman, A. R., Roach, M. J., Schmidt, S. A., & Borneman, A. R. (2018). Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies. BMC Bioinformatics 2018 19:1, 19(1). https://doi.org/10.1186/s12859-018-2485-7 Roberts, M. D., Davis, O., Josephs, E. B., & Williamson, R. J. (2025). K-mer-based Approaches to Bridging Pangenomics and Population Genetics. Molecular Biology and Evolution, 42(3). https://doi.org/10.1093/molbev/msaf047 Robledo, D., Palaiokostas, C., Bargelloni, L., Martínez, P., & Houston, R. (2018). Applications of genotyping by sequencing in aquaculture breeding and genetics. Reviews in Aquaculture, 10(3), 670-682. https://doi.org/10.1111/raq.12193 Rodríguez-Marí, A., Yan, Y.-L., BreMiller, R. A., Wilson, C., Cañestro, C., & Postlethwait, J. H. (2005). Characterization and expression pattern of zebrafish anti-Müllerian hormone (amh) relative to sox9a, sox9b, and cyp19a1a, during gonad development. Gene Expression Patterns, 5(5). https://doi.org/10.1016/j.modgep.2005.02.008 Ruan, J., Li, H., Ruan, J., & Li, H. (2019). Fast and accurate long-read assembly with wtdbg2. Nature Methods 2019 17:2, 17(2). https://doi.org/10.1038/s41592-019-0669-3 Ruan, R., Feng, T., Li, Y., Yue, H., Ye, H., Du, H., Liu, Q., Ruan, J., Li, C., & Wei, Q. (2021). Screening and identification of female-specific DNA sequences in octaploid sturgeon using comparative genomics with high-throughput sequencing. Genomics, 113(6). https://doi.org/10.1016/j.ygeno.2021.11.012 Sacchi, S., D’Ippolito, G., Sena, P., Marsella, T., Tagliasacchi, D., Maggi, E., Argento, C., Tirelli, A., Giulini, S., La Marca, A., Sacchi, S., D’Ippolito, G., Sena, P., Marsella, T., Tagliasacchi, D., Maggi, E., Argento, C., Tirelli, A., Giulini, S., & La Marca, A. (2015). The anti-Müllerian hormone (AMH) acts as a gatekeeper of ovarian steroidogenesis inhibiting the granulosa cell response to both FSH and LH. Journal of Assisted Reproduction and Genetics 2015 33:1, 33(1). https://doi.org/10.1007/s10815-015-0615-y Schlötterer, C., Tobler, R., Kofler, R., Nolte, V., Schlötterer, C., Tobler, R., Kofler, R., & Nolte, V. (2014). Sequencing pools of individuals — mining genome-wide polymorphism data without big funding. Nature Reviews Genetics 2014 15:11, 15(11). https://doi.org/10.1038/nrg3803 Sember, A., Nguyen, P., Perez, M. F., Altmanová, M., Ráb, P., & Cioffi, M. D. B. (2021a). Multiple sex chromosomes in teleost fishes from a cytogenetic perspective: state of the art and future challenges. Philosophical Transactions of the Royal Society B: Biological Sciences, 376(1833), 20200098. https://doi.org/10.1098/rstb.2020.0098 Sember, A., Nguyen, P., Perez, M. F., Altmanová, M., Ráb, P., & Cioffi, M. d. B. (2021b). Multiple sex chromosomes in teleost fishes from a cytogenetic perspective: state of the art and future challenges. Philosophical Transactions of the Royal Society B, 376(1833). https://doi.org/10.1098/rstb.2020.0098 Senol Cali, D., Kim, J. S., Ghose, S., Alkan, C., & Mutlu, O. (2019). Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions. Briefings in Bioinformatics, 20(4). https://doi.org/10.1093/bib/bby017 Ser, J. R., Roberts, R. B., & Kocher, T. D. (2010). Multiple interacting loci control sex determination in Lake Malawi cichlid fish. Evolution, 64(2). https://doi.org/10.1111/j.1558-5646.2009.00871.x Sereika, M., Kirkegaard, R. H., Karst, S. M., Michaelsen, T. Y., Sørensen, E. A., Wollenberg, R. D., Albertsen, M., Sereika, M., Kirkegaard, R. H., Karst, S. M., Michaelsen, T. Y., Sørensen, E. A., Wollenberg, R. D., & Albertsen, M. (2022). Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing. Nature Methods 2022 19:7, 19(7). https://doi.org/10.1038/s41592-022-01539-7 SF, A., W, G., W, M., EW, M., & DJ, L. (1990). Basic local alignment search tool. Journal of molecular biology, 215(3). https://doi.org/10.1016/S0022-2836(05)80360-2 Shafin, K., Pesout, T., Lorig-Roach, R., Haukness, M., Olsen, H. E., Bosworth, C., Armstrong, J., Tigyi, K., Maurer, N., Koren, S., Sedlazeck, F. J., Marschall, T., Mayes, S., Costa, V., Zook, J. M., Liu, K. J., Kilburn, D., Sorensen, M., Munson, K. M.,…Paten, B. (2020). Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nature Biotechnology 2020 38:9, 38(9). https://doi.org/10.1038/s41587-020-0503-6 Shan, X., Xu, T., Ma, Z., Zhang, X., Ruan, Z., Chen, J., Shi, Q., & You, X. (2021). Genome-wide association improves genomic selection for ammonia tolerance in the orange-spotted grouper (Epinephelus coioides). Aquaculture, 533. https://doi.org/10.1016/j.aquaculture.2020.736214 Shen, W., Le, S., Li, Y., & Hu, F. (2016). SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLoS ONE, 11(10). https://doi.org/10.1371/journal.pone.0163962 Skaletsky, H., Kuroda-Kawaguchi, T., Minx, P. J., Cordum, H. S., Hillier, L., Brown, L. G., Repping, S., Pyntikova, T., Ali, J., Bieri, T., Chinwalla, A., Delehaunty, A., Delehaunty, K., Du, H., Fewell, G., Fulton, L., Fulton, R., Graves, T., Hou, S.-F.,…Page, D. C. (2003). The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 2003 423:6942, 423(6942). https://doi.org/10.1038/nature01722 Song, H., Dong, T., Yan, X., Wang, W., Tian, Z., Sun, A., Dong, Y., Zhu, H., & Hu, H. (2023). Genomic selection and its research progress in aquaculture breeding. Reviews in Aquaculture, 15(1). https://doi.org/10.1111/raq.12716 Stanley, J. G. (2011). Female Homogamety in Grass Carp (Ctenopharyngodon idella) Determined by Gynogenesis. Journal of the Fisheries Board of Canada, 33(6). https://doi.org/10.1139/f76-175 Stanojević, D., Lin, D., Nurk, S., Sessions, P. F. d., & Šikić, M. (2024). Telomere-to-Telomere Phased Genome Assembly Using HERRO-Corrected Simplex Nanopore Reads. bioRxiv. https://doi.org/10.1101/2024.05.18.594796 Stanojević, D., Lin, D., Sessions, P. F. d., & Šikić, M. (2024). Telomere-to-telomere phased genome assembly using error-corrected Simplex nanopore reads. bioRxiv. https://doi.org/10.1101/2024.05.18.594796 Sun, L., Gao, T., Wang, F., Qin, Z., Yan, L., Tao, W., Li, M., Jin, C., Ma, L., Kocher, T. D., & Wang, D. (2020). Chromosome‐level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of nanopore sequencing, Bionano and Hi‐C technology. Molecular Ecology Resources, 20(5). https://doi.org/10.1111/1755-0998.13190 Sundaray, J. K., Dixit, S., Rather, A., Rasal, K. D., & Sahoo, L. (2022). Aquaculture omics: An update on the current status of research and data analysis. Marine Genomics, 64. https://doi.org/10.1016/j.margen.2022.100967 Surachat, K., Deachamag, P., & Wonglapsuwan, M. (2022). The first de novo genome assembly and sex marker identification of Pluang Chomphu fish (Tor tambra) from Southern Thailand. Computational and Structural Biotechnology Journal, 20. https://doi.org/10.1016/j.csbj.2022.03.021 Suurväli, J., Whiteley, A. R., Zheng, Y., Gharbi, K., Leptin, M., & Wiehe, T. (2020). The Laboratory Domestication of Zebrafish: From Diverse Populations to Inbred Substrains. Molecular Biology and Evolution, 37(4). https://doi.org/10.1093/molbev/msz289 Swain, P. P., Sahoo, L., Kumar, R., & Sundaray, J. K. (2021). Applications of Next-Generation Sequencing in Aquaculture and Fisherie. Advances in Fisheries Biotechnology. https://doi.org/10.1007/978-981-16-3215-0_3 Tan, M. H., Austin, C. M., Hammer, M. P., Lee, Y. P., Croft, L. J., & Gan, H. M. (2018). Finding Nemo: hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the clownfish (Amphiprion ocellaris) genome assembly. GigaScience, 7(3). https://doi.org/10.1093/gigascience/gix137 Taslima, K., Kikuchi, K., & Hosoya, S. (2024). Genomic architecture and sex chromosome systems of commercially important fish species in Asia – Current status, knowledge gaps and future prospects. Reviews in Aquaculture, 16(4). https://doi.org/10.1111/raq.12939 Tomaszkiewicz, M., Medvedev, P., & Makova, K. D. (2017). Y and W Chromosome Assemblies: Approaches and Discoveries. Trends in Genetics, 33(4). https://doi.org/10.1016/j.tig.2017.01.008 Tu, G., Yan, Z., Zhang, L., Liu, Z., Lv, Y., Li, Z., He, J., Weng, S., He, J., Wang, M., Tu, G., Yan, Z., Zhang, L., Liu, Z., Lv, Y., Li, Z., He, J., Weng, S., He, J., & Wang, M. (2025). A chromosome-level genome assembly of the mud carp (Cirrhinus molitorella). Scientific Data 2025 12:1, 12(1). https://doi.org/10.1038/s41597-025-04615-7 Vaser, R., Sović, I., Nagarajan, N., & Šikić, M. (2017). Fast and accurate de novo genome assembly from long uncorrected reads. Genome Research, 27(5). https://doi.org/10.1101/gr.214270.116 Venkatesh, B. (2003). Evolution and diversity of fish genomes. Current Opinion in Genetics & Development, 13(6). https://doi.org/10.1016/j.gde.2003.09.001 Ventura, T. (2018). Monosex in Aquaculture. Results and Problems in Cell Differentiation. https://doi.org/10.1007/978-3-319-92486-1_6 Voldoire, E., Brunet, F., Naville, M., Volff, J.-N., & Galiana, D. (2017). Expansion by whole genome duplication and evolution of the sox gene family in teleost fish. PLoS ONE, 12(7). https://doi.org/10.1371/journal.pone.0180936 Volff, J.-N., & Volff, J.-N. (2004). Genome evolution and biodiversity in teleost fish. Heredity 2005 94:3, 94(3). https://doi.org/10.1038/sj.hdy.6800635 Wang, H.-P., & Shen, Z.-G. (2018). Sex Control in Aquaculture. Sex Control in Aquaculture. https://doi.org/10.1002/9781119127291.ch1 Wang, H., Wan, H. T., Wu, B., Jian, J., Ng, A. H. M., Chung, C. Y.-L., Chow, E. Y.-C., Zhang, J., Wong, A. O. L., Lai, K. P., Chan, T. F., Zhang, E. L., & Wong, C. K.-C. (2022). A Chromosome-level assembly of the Japanese eel genome, insights into gene duplication and chromosomal reorganization. GigaScience, 11. https://doi.org/10.1093/gigascience/giac120 Wang, J.-T., Li, J.-T., Zhang, X.-F., Sun, X.-W., Wang, J.-T., Li, J.-T., Zhang, X.-F., & Sun, X.-W. (2012). Transcriptome analysis reveals the time of the fourth round of genome duplication in common carp (Cyprinus carpio). BMC Genomics 2012 13:1, 13(1). https://doi.org/10.1186/1471-2164-13-96 Wang, J., Tao, W., Kocher, T. D., & Wang, D. (2024). Sex chromosome turnover and biodiversity in fishes. Journal of Genetics and Genomics, 51(12). https://doi.org/10.1016/j.jgg.2024.08.008 Wang, L., Sun, F., Wan, Z. Y., Yang, Z., Tay, Y. X., Lee, M., Ye, B., Wen, Y., Meng, Z., Fan, B., Alfiko, Y., Shen, Y., Piferrer, F., Meyer, A., Schartl, M., Yue, G. H., Wang, L., Sun, F., Wan, Z. Y.,…Yue, G. H. (2022). Transposon-induced epigenetic silencing in the X chromosome as a novel form of dmrt1 expression regulation during sex determination in the fighting fish. BMC Biology 2021 20:1, 20(1). https://doi.org/10.1186/s12915-021-01205-y Wang, Y., Wen, X., Zhang, X., Fu, S., Liu, J., Tan, W., Luo, M., Liu, L., Huang, H., You, X., Luo, J., & Chen, F. (2020). Chromosome Genome Assembly of the Leopard Coral Grouper (Plectropomus leopardus) With Nanopore and Hi-C Sequencing Data. Frontiers in Genetics, 11. https://doi.org/10.3389/fgene.2020.00876 Wang, Y., Zhao, Y., Bollas, A., Wang, Y., Au, K. F., Wang, Y., Zhao, Y., Bollas, A., Wang, Y., & Au, K. F. (2021). Nanopore sequencing technology, bioinformatics and applications. Nature Biotechnology 2021 39:11, 39(11). https://doi.org/10.1038/s41587-021-01108-x Wei, W.-Y., Gong, Y., Guo, X.-F., Liu, M., Zhou, Y.-L., Li, Z., Zhou, L., Wang, Z.-W., Gui, J.-F., Wei, W.-Y., Gong, Y., Guo, X.-F., Liu, M., Zhou, Y.-L., Li, Z., Zhou, L., Wang, Z.-W., & Gui, J.-F. (2023). Gonadal transcriptomes reveal sex-biased expression genes associated with sex determination and differentiation in red-tail catfish (Hemibagrus wyckioides). BMC Genomics 2023 24:1, 24(1). https://doi.org/10.1186/s12864-023-09264-x Wen, M., Feron, R., Pan, Q., Guguin, J., Jouanno, E., Herpin, A., Klopp, C., Cabau, C., Zahm, M., Parrinello, H., Journot, L., Burgess, S. M., Omori, Y., Postlethwait, J. H., Schartl, M., Guiguen, Y., Wen, M., Feron, R., Pan, Q.,…Guiguen, Y. (2020). Sex chromosome and sex locus characterization in goldfish, Carassius auratus (Linnaeus, 1758). BMC Genomics 2020 21:1, 21(1). https://doi.org/10.1186/s12864-020-06959-3 Wen, M., Zhang, Y., Wang, S., Hu, F., Tang, C., Li, Q., Qin, Q., Tao, M., Zhang, C., Zhao, R., Wang, S., Liu, Q., Tang, C., & Liu, S. (2022). Sex locus and sex markers identification using whole genome pool-sequencing approach in the largemouth bass (Micropterus Salmoides L.). Aquaculture, 559. https://doi.org/10.1016/j.aquaculture.2022.738375 Wen, M., Zhang, Y., Wang, S., Hu, F., Tang, C., Li, Q., Qin, Q., Tao, M., Zhang, C., Zhao, R., Wang, S., Liu, Q., Tang, C., & Liu, S. (2022). Sex locus and sex markers identification using whole genome pool-sequencing approach in the largemouth bass (Micropterus Salmoides L.). Aquaculture, 559, 738375. https://doi.org/https://doi.org/10.1016/j.aquaculture.2022.738375 Wen, M., Zhang, Y., Wang, S., Wang, Y., Qin, Q., Tao, M., Zhang, C., Zhao, R., Wang, S., Hu, F., Liu, Q., Wei, Z., Gu, Q., Tang, C., & Liu, S. (2022a). Characterization of sex locus and sex-specific sequences in the mandarin fishes. Aquaculture, 561, 738650. https://doi.org/https://doi.org/10.1016/j.aquaculture.2022.738650 Wen, M., Zhang, Y., Wang, S., Wang, Y., Qin, Q., Tao, M., Zhang, C., Zhao, R., Wang, S., Hu, F., Liu, Q., Wei, Z., Gu, Q., Tang, C., & Liu, S. (2022b). Characterization of sex locus and sex-specific sequences in the mandarin fishes. Aquaculture, 561. https://doi.org/10.1016/j.aquaculture.2022.738650 Wilson, C. A., High, S. K., McCluskey, B. M., Amores, A., Yan, Y.-l., Titus, T. A., Anderson, J. L., Batzel, P., Carvan, M. J., Schartl, M., & Postlethwait, J. H. (2014). Wild Sex in Zebrafish: Loss of the Natural Sex Determinant in Domesticated Strains. Genetics, 198(3). https://doi.org/10.1534/genetics.114.169284 Winfield, I. J., & Nelson, J. S. (2012). Cyprinid fishes: systematics, biology and exploitation (Vol. 3). Springer Science & Business Media. Wootton, R. J. (2012). Ecology of teleost fishes (Vol. 1). Springer Science & Business Media. Wu, C.-S., Ma, Z.-Y., Zheng, G.-D., Zou, S.-M., Zhang, X.-J., Zhang, Y.-A., Wu, C.-S., Ma, Z.-Y., Zheng, G.-D., Zou, S.-M., Zhang, X.-J., & Zhang, Y.-A. (2022). Chromosome-level genome assembly of grass carp (Ctenopharyngodon idella) provides insights into its genome evolution. BMC Genomics 2022 23:1, 23(1). https://doi.org/10.1186/s12864-022-08503-x Wu, X., Zhao, L., Fan, Z., Lu, B., Chen, J., Tan, D., Jiang, D., Tao, W., & Wang, D. (2021). Screening and characterization of sex-linked DNA markers and marker-assisted selection in blue tilapia (Oreochromis aureus). Aquaculture, 530. https://doi.org/10.1016/j.aquaculture.2020.735934 Xin-hui, Z., Ze-xia, G., Wei, L., Jiu-fu, W., Wen, S., & Wei-min, W. (2015). Studies on morphological characteristics and genetic analysis of the gynogenesis blunt snout bream (Megalobrama amblycephala). Acta hydrobiologica sinica, 39(1), 126-132. Xu, M., Guo, L., Gu, S., Wang, O., Zhang, R., Peters, B. A., Fan, G., Liu, X., Xu, X., Deng, L., & Zhang, Y. (2020). TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads. GigaScience, 9(9). https://doi.org/10.1093/gigascience/giaa094 Xu, P., Xu, J., Liu, G., Chen, L., Zhou, Z., Peng, W., Jiang, Y., Zhao, Z., Jia, Z., Sun, Y., Wu, Y., Chen, B., Pu, F., Feng, J., Luo, J., Chai, J., Zhang, H., Wang, H., Dong, C.,…Sun, X. (2019). The allotetraploid origin and asymmetrical genome evolution of the common carp Cyprinus carpio. Nature Communications 2019 10:1, 10(1). https://doi.org/10.1038/s41467-019-12644-1 Xu, P., Zhang, X., Wang, X., Li, J., Liu, G., Kuang, Y., Xu, J., Zheng, X., Ren, L., Wang, G., Zhang, Y., Huo, L., Zhao, Z., Cao, D., Lu, C., Li, C., Zhou, Y., Liu, Z., Fan, Z.,…Sun, X. (2014). Genome sequence and genetic diversity of the common carp, Cyprinus carpio. Nature Genetics, 46(11), 1212-1219. https://doi.org/10.1038/ng.3098 Xu, T., Li, Y., Zheng, W., & Sun, Y. (2024). A chromosome-level genome assembly of the miiuy croaker (Miichthys miiuy) using nanopore sequencing and Hi-C. Aquaculture and Fisheries, 9(2). https://doi.org/10.1016/j.aaf.2021.06.001 Xue, L., Gao, Y., Wu, M., Tian, T., Fan, H., Huang, Y., Huang, Z., Li, D., Xu, L., Xue, L., Gao, Y., Wu, M., Tian, T., Fan, H., Huang, Y., Huang, Z., Li, D., & Xu, L. (2021). Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair. Genome Biology 2021 22:1, 22(1). https://doi.org/10.1186/s13059-021-02430-y Yamamoto, T.-O., & Kajishima, T. (1968). Sex hormone induction of sex reversal in the goldfish and evidence for male heterogamity. Journal of Experimental Zoology, 168(2). https://doi.org/10.1002/jez.1401680209 Yáñez, J. M., Barría, A., López, M. E., Moen, T., Garcia, B. F., Yoshida, G. M., & Xu, P. (2023). Genome‐wide association and genomic selection in aquaculture. Reviews in Aquaculture, 15(2). https://doi.org/10.1111/raq.12750 Yang, C., Huang, R., Ou, M., Gui, B., Zhao, J., He, L., Li, Y., Liao, L., Chen, K., & Wang, Y. (2020a). A rapid method of sex-specific marker discovery based on NGS and determination of the XX / XY sex-determination system in Channa maculata. Aquaculture, 528. https://doi.org/10.1016/j.aquaculture.2020.735499 Yang, C., Huang, R., Ou, M., Gui, B., Zhao, J., He, L., Li, Y., Liao, L., Chen, K., & Wang, Y. (2020b). A rapid method of sex-specific marker discovery based on NGS and determination of the XX / XY sex-determination system in Channa maculata. Aquaculture, 528, 735499. https://doi.org/10.1016/j.aquaculture.2020.735499 Yang, Z., Fu, G., Lee, M., Yeo, S., & Yue, G. H. (2025). Genes for editing to improve economic traits in aquaculture fish species. Aquaculture and Fisheries, 10(1). https://doi.org/10.1016/j.aaf.2024.05.005 Yang, Z., Yu, Y., Tay, Y. X., & Yue, G. H. (2022). Genome editing and its applications in genetic improvement in aquaculture. Reviews in Aquaculture, 14(1). https://doi.org/10.1111/raq.12591 Yano, A., Nicol, B., Jouanno, E., Quillet, E., Fostier, A., Guyomard, R., & Guiguen, Y. (2013). The sexually dimorphic on the Y‐chromosome gene (sdY) is a conserved male‐specific Y‐chromosome sequence in many salmonids. Evolutionary Applications, 6(3). https://doi.org/10.1111/eva.12032 Yu, C., Tang, H., Jiang, Y., Lu, H., Chen, Q., Gui, L., Qiu, J., Xu, X., Li, J., & Shen, Y. (2024). Growth performance and selection signatures revealed by whole-genome resequencing in genetically selected grass carp (Ctenopharyngodon idella). Aquaculture, 587. https://doi.org/10.1016/j.aquaculture.2024.740885 Zarkower, D., & Murphy, M. W. (2021). DMRT1: an ancient sexual regulator required for human gonadogenesis. Sexual development : genetics, molecular biology, evolution, endocrinology, embryology, and pathology of sex determination and differentiation, 16(2-3). https://doi.org/10.1159/000518272 Zhang, H. H., Xu, M. R. X., Wang, P. L., Zhu, Z. G., Nie, C. F., Xiong, X. M., Wang, L., Xie, Z. Z., Wen, X., Zeng, Q. X., Zhang, X. G., & Dai, F. Y. (2020). High‐quality genome assembly and transcriptome of Ancherythroculter nigrocauda, an endemic Chinese cyprinid species. Molecular Ecology Resources, 20(4), 882-891. https://doi.org/10.1111/1755-0998.13158 Zhang, L., Chen, T., Wang, Y., Zhang, S., Lv, Q., Kong, D., Jiang, H., Zheng, Y., Ren, Y., Huang, W., Liu, P., & Jiang, Y. (2022). Comparison Analysis of Different DNA Extraction Methods on Suitability for Long-Read Metagenomic Nanopore Sequencing. Frontiers in Cellular and Infection Microbiology, 12. https://doi.org/10.3389/fcimb.2022.919903 Zhang, X., Li, M., Ma, H., Liu, X., Shi, H., Li, M., & Wang, D. (2017). Mutation of foxl2 or cyp19a1a Results in Female to Male Sex Reversal in XX Nile Tilapia. Endocrinology, 158(8). https://doi.org/10.1210/en.2017-00127 Zimin, A. V., Marçais, G., Puiu, D., Roberts, M., Salzberg, S. L., & Yorke, J. A. (2013). The MaSuRCA genome assembler. Bioinformatics, 29(21). https://doi.org/10.1093/bioinformatics/btt476 | - |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/97597 | - |
| dc.description.abstract | none | zh_TW |
| dc.description.abstract | The Thai, or Javan, mahseer (Tor tambra) is a freshwater cyprinid of ecological and economic significance, yet its genomic architecture and mechanisms of sex determination remain poorly understood. This study presents the first long-read only genome assembly for T. tambra using Oxford Nanopore sequencing, revealing indications of a fourth round of whole genome duplication based on genome metrics and Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness. Sex-specific genomic regions were investigated through both k-mer–based and allele frequency–based approaches, with findings supporting an XX/XY sex determination system. A high number of male-specific 60-mers enabled the assembly of putative male-linked contigs. BLASTn analysis of sex-specific contigs uncovered several predicted genes potentially related to development or sex differentiation; however, the absence of canonical sex-determining genes and limited query coverage suggest that these findings should be interpreted with caution. Allele frequency analysis further identified six male-associated scaffolds, suggesting putative Y-linked regions. This study also demonstrates the importance of selecting appropriate k-mer lengths for marker discovery. While the findings provide initial insights into sex-linked genomic features in T. tambra, the exact localization of sex-determining loci remains unresolved. Overall, this research offers a genomic foundation for future studies on sex determination and genome evolution in T. tambra, with potential applications in aquaculture, including non-invasive sex identification and selective breeding strategies. | en |
| dc.description.provenance | Submitted by admin ntu (admin@lib.ntu.edu.tw) on 2025-07-03T16:10:54Z No. of bitstreams: 0 | en |
| dc.description.provenance | Made available in DSpace on 2025-07-03T16:10:54Z (GMT). No. of bitstreams: 0 | en |
| dc.description.tableofcontents | Table of Contents
Acknowledgements ii Abstract iv Table of Contents v List of Figures vii List of Tables viii List of Appendices x Abbreviations xi Chapter 1: Introduction 1 1.1 Development of Genomic Resources for Fish: Applications for Aquaculture and Fisheries 1 1.2 Application of Oxford Nanopore Technologies for Genome Assembly in Fish 2 1.3 Sex Determination in Teleosts 4 1.4 Importance of Sex Determination for Aquaculture, Fisheries and Conservation 6 1.5 Sex Determining Genes and Master-Key Regulators 8 1.6 Current Approaches to Identification of Sex Determining Genes and Regions 10 1.7 The Thai Mahseer: Biology, Aquaculture, and Genomic Research 13 1.8 Cyprinidae Family: Genomic Resources & Sex Determination 15 1.9 Research Aim 17 Chapter 2: Materials and Methods 18 2.1 Sample Collection and Sequencing 18 2.2 Assembly of YALA5 Female T. tambra Genome 25 2.3 Re-assembly of Published Male T. tambroides Genome 28 2.4 Genomic Variation Between Females and Males 29 Chapter 3: Results 35 3.1 YALA5F Female T. tambra Genome Assembly 35 3.2 Re-Assembled Published Male T. tambroides Genome 37 3.3 Sex-Associated Genomic Variations Identified through K-mer Comparison 38 3.4 Differences in Genome-Wide Allele Frequency Between Females and Males 43 Chapter 4: Discussion 45 4.1 YALA5 Female T. tambra Genome Assembly 45 4.2 Quality Assessment of the Male Genome T. tambroides Re-Assembly Relative to the Published Assembly 48 4.3 Comparative K-mer (35- vs 60-mer) Analysis Identified Sex-Associated Genomic Variations 49 4.4 Patterns of Genome-Wide Sex-Specific Allele Frequency Revealed from Pool-Seq and YALA5 Female T. tambra Genome Assembly 54 4.5 Discrepancies in Sex Determination Findings from Previous Publication: XX/XY vs. ZZ/ZW in T. tambra 56 Chapter 5: Conclusion 59 References 60 Figures 80 Tables 88 Appendices 109 | - |
| dc.language.iso | en | - |
| dc.subject | Tor tambra | zh_TW |
| dc.subject | allele frequency analysis | en |
| dc.subject | Tor tambra | en |
| dc.subject | genome assembly | en |
| dc.subject | Oxford Nanopore | en |
| dc.subject | sex determination | en |
| dc.subject | k-mer analysis | en |
| dc.title | 透過基因組分析揭示泰國金馬鱗魚 （Tor tambra）的性別相關區域 | zh_TW |
| dc.title | Uncovering the Sex-Associated Regions in the Thai Mahseer (Tor tambra) through Genomic Analysis | en |
| dc.type | Thesis | - |
| dc.date.schoolyear | 113-2 | - |
| dc.description.degree | 碩士 | - |
| dc.contributor.oralexamcommittee | 伊藤剛;于宏燦;Monwadee Wonglapsuwan | zh_TW |
| dc.contributor.oralexamcommittee | Takeshi Itoh;Hon-Tsen Yu;Monwadee Wonglapsuwan | en |
| dc.subject.keyword | Tor tambra, | zh_TW |
| dc.subject.keyword | Tor tambra,genome assembly,Oxford Nanopore,sex determination,k-mer analysis,allele frequency analysis, | en |
| dc.relation.page | 115 | - |
| dc.identifier.doi | 10.6342/NTU202501200 | - |
| dc.rights.note | 同意授權(全球公開) | - |
| dc.date.accepted | 2025-06-19 | - |
| dc.contributor.author-college | 共同教育中心 | - |
| dc.contributor.author-dept | 全球農業科技與基因體科學碩士學位學程 | - |
| dc.date.embargo-lift | 2030-06-18 | - |
| 顯示於系所單位： | 全球農業科技與基因體科學碩士學位學程 | |
文件中的檔案：
| 檔案 | 大小 | 格式 | |
|---|---|---|---|
| ntu-113-2.pdf 此日期後於網路公開 2030-06-18 | 9.26 MB | Adobe PDF |
系統中的文件，除了特別指名其著作權條款之外，均受到著作權保護，並且保留所有的權利。