Exploring the cobia (Rachycentron canadum) genome: Unveiling putative male heterogametic regions and identification sex-specific markers
Role
Principal Investigator
Description
GigaScience is a peer-reviewed scientific journal that was established in 2012. It covers research and large data-sets that result from work in the life sciences. Making it open access (OA) allows me to post this relevant paper in social media channels, broadening the viewership in the aquaculture industry and getting more exposure of what we do in TFI. Open access papers have a greater citation score than paid papers*, as also the case for my most cited papers. This is particular important for disseminating the works of our TFI in Singapore. Abstract 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 species are completely unknown. Results: Here, we reported two 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 (GWAS) and sequencing depth analysis identified three 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 two only 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 two genes playing a potential role in the sex determination of the species, and provides further support for the rapid evolution of sex-determining mechanisms in teleost fish.
Date
01 Jun 2024 - 30 Aug 2024
Project Type
PUBLICATION_SUPPORT
Keywords
Chromosome-level genome;Cobia;Molecular sex markers
Funding Body
JCU Singapore
Amount
0
Project Team
N/A