Exploring the cobia (Rachycentron canadum) genome: unveiling putative male heterogametic regions and identification of sex-specific markers.

Autor:	Shen X; Tropical Futures Institute, James Cook University Singapore, 387380, Singapore., Hu J; BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China., Yáñez JM; Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, 8820808 Santiago, Chile., Bastos Gomes G; Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore., Poon ZWJ; James Cook University, 387380, Singapore., Foster D; Open Blue Sea Farms, Panama City, Panama., Alarcon JF; Open Blue Sea Farms, Panama City, Panama., Shao L; BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China., Guo X; BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China., Shao Y; China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong 518120, China.; State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China.; Geogia Tech Shenzhen Institute (GTSI), Tianjin University, Shen Zhen 518067, China., Huerlimann R; Marine Climate Change Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, 904-0495, Japan., Li C; Marine Climate Change Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, 904-0495, Japan., Goulden E; Department of Agriculture and Fisheries, Queensland Government, Bribie Island Research Centre, Woorim, QLD 4507, Australia., Anderson K; Department of Agriculture and Fisheries, Queensland Government, Bribie Island Research Centre, Woorim, QLD 4507, Australia., Fan G; BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China.; China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong 518120, China.; BGI-Shenzhen, Shenzhen, Guangdong 518083, China., Domingos JA; Tropical Futures Institute, James Cook University Singapore, 387380, Singapore.; Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville QLD 4811, Australia.
Jazyk:	angličtina
Zdroj:	GigaScience [Gigascience] 2024 Jan 02; Vol. 13.
DOI:	10.1093/gigascience/giae034
Abstrakt:	Background: Cobia (Rachycentron canadum) is the only member of the Rachycentridae family and exhibits considerable sexual dimorphism in growth rate. Sex determination in teleosts has been a long-standing basic biological question, and the molecular mechanisms of sex determination/differentiation in cobia are completely unknown. Results: Here, we reported 2 high-quality, chromosome-level annotated male and female cobia genomes with assembly sizes of 586.51 Mb (contig/scaffold N50: 86.0 kb/24.3 Mb) and 583.88 Mb (79.9 kb/22.5 Mb), respectively. Synteny inference among perciform genomes revealed that cobia and the remora Echeneis naucrates were sister groups. Further, whole-genome resequencing of 31 males and 60 females, genome-wide association study, and sequencing depth analysis identified 3 short male-specific regions within a 10.7-kb continuous genomic region on male chromosome 18, which hinted at an undifferentiated sex chromosome system with a putative XX/XY mode of sex determination in cobia. Importantly, the only 2 genes within/between the male-specific regions, epoxide hydrolase 1 (ephx1, renamed cephx1y) and transcription factor 24 (tcf24, renamed ctcf24y), showed testis-specific/biased gene expression, whereas their counterparts cephx1x and ctf24x, located in female chromosome 18, were similarly expressed in both sexes. In addition, male-specific PCR targeting the cephx1y gene revealed that this genomic feature is conserved in cobia populations from Panama, Brazil, Australia, and Japan. Conclusion: The first comprehensive genomic survey presented here is a valuable resource for future studies on cobia population structure and dynamics, conservation, and evolutionary history. Furthermore, it establishes evidence of putative male heterogametic regions with 2 genes playing a potential role in the sex determination of the species, and it provides further support for the rapid evolution of sex-determining mechanisms in teleost fish. (© The Author(s) 2024. Published by Oxford University Press GigaScience.)
Databáze:	MEDLINE
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