Comparative genomic analysis of immune-related genes and chemosensory receptors provides insights into the evolution and adaptation of four major domesticated Asian carps
Abstract Background Ctenopharyngodon idella (grass carp), Mylopharyngodon piceus (black carp), Hypophthalmichthys nobilis (bighead carp), and Hypophthalmichthys molitrix (silver carp), collectively known as the four major domesticated Asian carp, are freshwater fish species from the family Cyprinida...
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BMC
2025-05-01
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| Online Access: | https://doi.org/10.1186/s12864-025-11719-2 |
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| author | Ling Shi Judy Kin-Wing Ng Qing Xiong Kelvin Fu-Kiu Ao Soo-Kyung Shin Cherie Tsz-Yiu Law Weixue Mu Guang-Ming Liu Shitao Rao Stephen Kwok-Wing Tsui |
| author_facet | Ling Shi Judy Kin-Wing Ng Qing Xiong Kelvin Fu-Kiu Ao Soo-Kyung Shin Cherie Tsz-Yiu Law Weixue Mu Guang-Ming Liu Shitao Rao Stephen Kwok-Wing Tsui |
| author_sort | Ling Shi |
| collection | DOAJ |
| description | Abstract Background Ctenopharyngodon idella (grass carp), Mylopharyngodon piceus (black carp), Hypophthalmichthys nobilis (bighead carp), and Hypophthalmichthys molitrix (silver carp), collectively known as the four major domesticated Asian carp, are freshwater fish species from the family Cyprinidae and are widely consumed in China. Current studies on these species primarily focus on immune system regulation and the growth and development of individual species. However, in-depth genomic investigations and comprehensive comparative analysis remained limited. Methods The complete genomes of Ctenopharyngodon idella, Mylopharyngodon piceus and Hypophthalmichthys nobilis were assembled using a hybrid approach that integrated both next- and third-generation sequencing reads, followed by annotation using the MAKER2 pipeline. Based on the high-quality genomes of Ctenopharyngodon idella, Mylopharyngodon piceus Hypophthalmichthys nobilis, and Hypophthalmichthys molitrix, a comparative genomic analysis was conducted using bioinformatic tools to investigate gene family evolution in these four domesticated Asian carp species. Results High-quality genomes of Ctenopharyngodon idella, Mylopharyngodon piceus, and Hypophthalmichthys nobilis were assembled, achieving over 90% completeness. Immune-related gene families, including MHC class I and NLRC3-like genes, have undergone rapid evolution, with Ctenopharyngodon idella exhibiting significant expansion of NLRC3-like genes. Massive tandem duplication events were identified in trace amine-associated receptors (TAARs), and rapid expansion was observed in TAAR16 and TAAR29. Additionally, a novel TAAR gene cluster was identified in all four Asian carp species. Comparative genomic analysis revealed the expansion of type 1 taste receptor genes, particularly in Ctenopharyngodon idella and Mylopharyngodon piceus. Conclusion This study has successfully constructed the high-quality genomes of Ctenopharyngodon idella, Mylopharyngodon piceus, and Hypophthalmichthys nobilis. The comparative genomic analysis revealed the evolution of immune-related genes and chemosensory receptors in the four major domesticated Asian carp species. These findings suggested the enhanced immunity and sensory perception in these species, providing valuable insights into their adaptation, survival and reproduction. |
| format | Article |
| id | doaj-art-c7bdeae04fb34637aac59e05847759f7 |
| institution | OA Journals |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj-art-c7bdeae04fb34637aac59e05847759f72025-08-20T02:39:04ZengBMCBMC Genomics1471-21642025-05-0126112110.1186/s12864-025-11719-2Comparative genomic analysis of immune-related genes and chemosensory receptors provides insights into the evolution and adaptation of four major domesticated Asian carpsLing Shi0Judy Kin-Wing Ng1Qing Xiong2Kelvin Fu-Kiu Ao3Soo-Kyung Shin4Cherie Tsz-Yiu Law5Weixue Mu6Guang-Ming Liu7Shitao Rao8Stephen Kwok-Wing Tsui9School of Biomedical Sciences, The Chinese University of Hong KongSchool of Biomedical Sciences, The Chinese University of Hong KongSchool of Biomedical Sciences, The Chinese University of Hong KongSchool of Biomedical Sciences, The Chinese University of Hong KongSchool of Biomedical Sciences, The Chinese University of Hong KongSchool of Biomedical Sciences, The Chinese University of Hong KongSchool of Biomedical Sciences, The Chinese University of Hong KongCollege of Ocean Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Jimei UniversityDepartment of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical UniversitySchool of Biomedical Sciences, The Chinese University of Hong KongAbstract Background Ctenopharyngodon idella (grass carp), Mylopharyngodon piceus (black carp), Hypophthalmichthys nobilis (bighead carp), and Hypophthalmichthys molitrix (silver carp), collectively known as the four major domesticated Asian carp, are freshwater fish species from the family Cyprinidae and are widely consumed in China. Current studies on these species primarily focus on immune system regulation and the growth and development of individual species. However, in-depth genomic investigations and comprehensive comparative analysis remained limited. Methods The complete genomes of Ctenopharyngodon idella, Mylopharyngodon piceus and Hypophthalmichthys nobilis were assembled using a hybrid approach that integrated both next- and third-generation sequencing reads, followed by annotation using the MAKER2 pipeline. Based on the high-quality genomes of Ctenopharyngodon idella, Mylopharyngodon piceus Hypophthalmichthys nobilis, and Hypophthalmichthys molitrix, a comparative genomic analysis was conducted using bioinformatic tools to investigate gene family evolution in these four domesticated Asian carp species. Results High-quality genomes of Ctenopharyngodon idella, Mylopharyngodon piceus, and Hypophthalmichthys nobilis were assembled, achieving over 90% completeness. Immune-related gene families, including MHC class I and NLRC3-like genes, have undergone rapid evolution, with Ctenopharyngodon idella exhibiting significant expansion of NLRC3-like genes. Massive tandem duplication events were identified in trace amine-associated receptors (TAARs), and rapid expansion was observed in TAAR16 and TAAR29. Additionally, a novel TAAR gene cluster was identified in all four Asian carp species. Comparative genomic analysis revealed the expansion of type 1 taste receptor genes, particularly in Ctenopharyngodon idella and Mylopharyngodon piceus. Conclusion This study has successfully constructed the high-quality genomes of Ctenopharyngodon idella, Mylopharyngodon piceus, and Hypophthalmichthys nobilis. The comparative genomic analysis revealed the evolution of immune-related genes and chemosensory receptors in the four major domesticated Asian carp species. These findings suggested the enhanced immunity and sensory perception in these species, providing valuable insights into their adaptation, survival and reproduction.https://doi.org/10.1186/s12864-025-11719-2Four major domesticated Asian carp speciesComparative genomic analysisGene family evolutionChemosensory receptorsImmune-related genes |
| spellingShingle | Ling Shi Judy Kin-Wing Ng Qing Xiong Kelvin Fu-Kiu Ao Soo-Kyung Shin Cherie Tsz-Yiu Law Weixue Mu Guang-Ming Liu Shitao Rao Stephen Kwok-Wing Tsui Comparative genomic analysis of immune-related genes and chemosensory receptors provides insights into the evolution and adaptation of four major domesticated Asian carps BMC Genomics Four major domesticated Asian carp species Comparative genomic analysis Gene family evolution Chemosensory receptors Immune-related genes |
| title | Comparative genomic analysis of immune-related genes and chemosensory receptors provides insights into the evolution and adaptation of four major domesticated Asian carps |
| title_full | Comparative genomic analysis of immune-related genes and chemosensory receptors provides insights into the evolution and adaptation of four major domesticated Asian carps |
| title_fullStr | Comparative genomic analysis of immune-related genes and chemosensory receptors provides insights into the evolution and adaptation of four major domesticated Asian carps |
| title_full_unstemmed | Comparative genomic analysis of immune-related genes and chemosensory receptors provides insights into the evolution and adaptation of four major domesticated Asian carps |
| title_short | Comparative genomic analysis of immune-related genes and chemosensory receptors provides insights into the evolution and adaptation of four major domesticated Asian carps |
| title_sort | comparative genomic analysis of immune related genes and chemosensory receptors provides insights into the evolution and adaptation of four major domesticated asian carps |
| topic | Four major domesticated Asian carp species Comparative genomic analysis Gene family evolution Chemosensory receptors Immune-related genes |
| url | https://doi.org/10.1186/s12864-025-11719-2 |
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