Identification and characterization of a male-specific region in largemouth bass (Micropterus Salmoides) by whole-genome sequencing, resequencing and genomics comparison
IntroductionCompared to mammals and birds, sex-determining genes differ in most fish species. Largemouth bass (Micropterus Salmoides) is one of the most important cultured fish species in China, and there are growth differences between males and females. However, its sex-determining genes and mechan...
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Frontiers Media S.A.
2025-05-01
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| Series: | Frontiers in Marine Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmars.2025.1586534/full |
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| author | Xinhui Zhang Xinhui Zhang Xinhui Zhang Junjian Dong Zhiqiang Ruan Fengying Gao Wenchuan Zhou Xinxin You Jieming Chen Qiong Shi Qiong Shi Xing Ye Chengfei Sun |
| author_facet | Xinhui Zhang Xinhui Zhang Xinhui Zhang Junjian Dong Zhiqiang Ruan Fengying Gao Wenchuan Zhou Xinxin You Jieming Chen Qiong Shi Qiong Shi Xing Ye Chengfei Sun |
| author_sort | Xinhui Zhang |
| collection | DOAJ |
| description | IntroductionCompared to mammals and birds, sex-determining genes differ in most fish species. Largemouth bass (Micropterus Salmoides) is one of the most important cultured fish species in China, and there are growth differences between males and females. However, its sex-determining genes and mechanisms currently remain unknown.MethodsWe explored the sex-determination mechanism by integrating whole-genome sequencing, resequencing and comparative genomics approaches.ResultsIn this study, we employed HiFi and Hi-C sequencing technologies to construct a chromosome-level haplotypic genome assembly for male largemouth bass, with a genome size of 875.69 Mb. The assembled genome contains 23 chromosomes, covering 95.31% of the complete sequences with a high scaffold N50 of 35.93 Mb. A genome-wide association study (GWAS) of sex was performed with four populations consisting of 62 males and 58 females. For the sex trait, a total of 3,838 SNP loci were identified to be significantly associated with sexual discrepancy. Interestingly, almost all these significant SNPs (3,825) were clustered on chromosome 10 (Chr10), within a 3.5-Mb sex-determination region (SDR). They were homozygous in females while heterozygous in males. We therefore speculate that largemouth bass owns a XX/XY sex determination system. By comparing genomics data and examining coverage depth of resequencing reads, we revealed a ~51-kb male-specific region (MSR) on Chr10. Gene annotation discovered a coding sequence (msy) within MSR-1, which may contribute to sex determination of largemouth bass. By differential expression analysis, two candidate sex-determining genes (ccdc103 and jockey) were predicted within the target SDR. Moreover, we applied two male-specific non-coding fragments (within MSR-2 and MSR-3) to design specific sex markers, successfully obtaining universal gender identity in examined largemouth bass.DiscussionOverall, our findings improve our understanding of the molecular basis for sex determination in largemouth bass, which will thereby promote the mono-sexual breeding progress in the aquaculture industry. |
| format | Article |
| id | doaj-art-5bcc3c75700d4b1c8ba06e6448010378 |
| institution | OA Journals |
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| language | English |
| publishDate | 2025-05-01 |
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| series | Frontiers in Marine Science |
| spelling | doaj-art-5bcc3c75700d4b1c8ba06e64480103782025-08-20T02:16:50ZengFrontiers Media S.A.Frontiers in Marine Science2296-77452025-05-011210.3389/fmars.2025.15865341586534Identification and characterization of a male-specific region in largemouth bass (Micropterus Salmoides) by whole-genome sequencing, resequencing and genomics comparisonXinhui Zhang0Xinhui Zhang1Xinhui Zhang2Junjian Dong3Zhiqiang Ruan4Fengying Gao5Wenchuan Zhou6Xinxin You7Jieming Chen8Qiong Shi9Qiong Shi10Xing Ye11Chengfei Sun12Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, ChinaCollege of Life Sciences and Oceanography, Shenzhen University, Shenzhen, ChinaShenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, ChinaKey Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, ChinaShenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, ChinaKey Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, ChinaShenzhen Ocean Development Promotion Center, Shenzhen, ChinaShenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, ChinaShenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, ChinaCollege of Life Sciences and Oceanography, Shenzhen University, Shenzhen, ChinaShenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, ChinaKey Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, ChinaKey Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, ChinaIntroductionCompared to mammals and birds, sex-determining genes differ in most fish species. Largemouth bass (Micropterus Salmoides) is one of the most important cultured fish species in China, and there are growth differences between males and females. However, its sex-determining genes and mechanisms currently remain unknown.MethodsWe explored the sex-determination mechanism by integrating whole-genome sequencing, resequencing and comparative genomics approaches.ResultsIn this study, we employed HiFi and Hi-C sequencing technologies to construct a chromosome-level haplotypic genome assembly for male largemouth bass, with a genome size of 875.69 Mb. The assembled genome contains 23 chromosomes, covering 95.31% of the complete sequences with a high scaffold N50 of 35.93 Mb. A genome-wide association study (GWAS) of sex was performed with four populations consisting of 62 males and 58 females. For the sex trait, a total of 3,838 SNP loci were identified to be significantly associated with sexual discrepancy. Interestingly, almost all these significant SNPs (3,825) were clustered on chromosome 10 (Chr10), within a 3.5-Mb sex-determination region (SDR). They were homozygous in females while heterozygous in males. We therefore speculate that largemouth bass owns a XX/XY sex determination system. By comparing genomics data and examining coverage depth of resequencing reads, we revealed a ~51-kb male-specific region (MSR) on Chr10. Gene annotation discovered a coding sequence (msy) within MSR-1, which may contribute to sex determination of largemouth bass. By differential expression analysis, two candidate sex-determining genes (ccdc103 and jockey) were predicted within the target SDR. Moreover, we applied two male-specific non-coding fragments (within MSR-2 and MSR-3) to design specific sex markers, successfully obtaining universal gender identity in examined largemouth bass.DiscussionOverall, our findings improve our understanding of the molecular basis for sex determination in largemouth bass, which will thereby promote the mono-sexual breeding progress in the aquaculture industry.https://www.frontiersin.org/articles/10.3389/fmars.2025.1586534/fulllargemouth bass (Micropterus salmoides)chromosome-level genome assemblyGWASmale-specific regionsex markers |
| spellingShingle | Xinhui Zhang Xinhui Zhang Xinhui Zhang Junjian Dong Zhiqiang Ruan Fengying Gao Wenchuan Zhou Xinxin You Jieming Chen Qiong Shi Qiong Shi Xing Ye Chengfei Sun Identification and characterization of a male-specific region in largemouth bass (Micropterus Salmoides) by whole-genome sequencing, resequencing and genomics comparison Frontiers in Marine Science largemouth bass (Micropterus salmoides) chromosome-level genome assembly GWAS male-specific region sex markers |
| title | Identification and characterization of a male-specific region in largemouth bass (Micropterus Salmoides) by whole-genome sequencing, resequencing and genomics comparison |
| title_full | Identification and characterization of a male-specific region in largemouth bass (Micropterus Salmoides) by whole-genome sequencing, resequencing and genomics comparison |
| title_fullStr | Identification and characterization of a male-specific region in largemouth bass (Micropterus Salmoides) by whole-genome sequencing, resequencing and genomics comparison |
| title_full_unstemmed | Identification and characterization of a male-specific region in largemouth bass (Micropterus Salmoides) by whole-genome sequencing, resequencing and genomics comparison |
| title_short | Identification and characterization of a male-specific region in largemouth bass (Micropterus Salmoides) by whole-genome sequencing, resequencing and genomics comparison |
| title_sort | identification and characterization of a male specific region in largemouth bass micropterus salmoides by whole genome sequencing resequencing and genomics comparison |
| topic | largemouth bass (Micropterus salmoides) chromosome-level genome assembly GWAS male-specific region sex markers |
| url | https://www.frontiersin.org/articles/10.3389/fmars.2025.1586534/full |
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