Evolutionary analysis of the DHHCs in Saccharinae
Abstract The DHHC domain genes are crucial for protein lipid modification, a key post-translational modification influencing membrane targeting, subcellular trafficking, and protein function. Despite their significance, the DHHC gene family in Saccharinae remains understudied. Here, we identified 32...
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Nature Portfolio
2025-01-01
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| Online Access: | https://doi.org/10.1038/s41598-025-86463-4 |
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| author | Hao Wen Xinyu Liu Xueting Zhao Tingting Zhao Cuilian Feng Hailong Chang Jungang Wang Jishan Lin |
| author_facet | Hao Wen Xinyu Liu Xueting Zhao Tingting Zhao Cuilian Feng Hailong Chang Jungang Wang Jishan Lin |
| author_sort | Hao Wen |
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| description | Abstract The DHHC domain genes are crucial for protein lipid modification, a key post-translational modification influencing membrane targeting, subcellular trafficking, and protein function. Despite their significance, the DHHC gene family in Saccharinae remains understudied. Here, we identified 32 (110 alleles), 28, 53, and 48 DHHC genes in Saccharum spontaneum Np-X, Erianthus rufipilus, Miscanthus sinensis, and Miscanthus lutarioriparius, respectively. Collinearity analysis uncovered the loss of two M. lutarioriparius genes, homologues of EruDHHC1C and EruDHHC3A. Phylogenetic and classification analyses categorized DHHC family members into six subgroups (A-F). Ka/Ks ratio analysis indicated that gene duplication in these species was primarily driven by whole-genome duplication (WGD) and dispersed duplication (DSD), with DHHC genes evolving under strong purifying selection. Gene expression and trait correlation analysis revealed a significant negative correlation between SspDHHC28A expression in S. spontaneum and sucrose content, suggesting a role in photosynthesis product transport during rapid growth. This study deepens our understanding of the DHHC gene family’s functional dynamics and evolutionary path in Saccharinae, laying a foundation for future research. |
| format | Article |
| id | doaj-art-cff648ddc2f74f11b7b2d4f2b63a8c27 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
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| spelling | doaj-art-cff648ddc2f74f11b7b2d4f2b63a8c272025-01-26T12:31:29ZengNature PortfolioScientific Reports2045-23222025-01-0115111410.1038/s41598-025-86463-4Evolutionary analysis of the DHHCs in SaccharinaeHao Wen0Xinyu Liu1Xueting Zhao2Tingting Zhao3Cuilian Feng4Hailong Chang5Jungang Wang6Jishan Lin7Center for Genomics and Biotechnology, Fujian Agriculture and Forestry UniversityCenter for Genomics and Biotechnology, Fujian Agriculture and Forestry UniversitySanya Institute of Chinese Academy of Tropical Agricultural SciencesNational Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesNational Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesInstitute of Nanfan & Seed Industry, Zhanjiang Research Center，Guangdong Academy of SciencesNational Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesCenter for Genomics and Biotechnology, Fujian Agriculture and Forestry UniversityAbstract The DHHC domain genes are crucial for protein lipid modification, a key post-translational modification influencing membrane targeting, subcellular trafficking, and protein function. Despite their significance, the DHHC gene family in Saccharinae remains understudied. Here, we identified 32 (110 alleles), 28, 53, and 48 DHHC genes in Saccharum spontaneum Np-X, Erianthus rufipilus, Miscanthus sinensis, and Miscanthus lutarioriparius, respectively. Collinearity analysis uncovered the loss of two M. lutarioriparius genes, homologues of EruDHHC1C and EruDHHC3A. Phylogenetic and classification analyses categorized DHHC family members into six subgroups (A-F). Ka/Ks ratio analysis indicated that gene duplication in these species was primarily driven by whole-genome duplication (WGD) and dispersed duplication (DSD), with DHHC genes evolving under strong purifying selection. Gene expression and trait correlation analysis revealed a significant negative correlation between SspDHHC28A expression in S. spontaneum and sucrose content, suggesting a role in photosynthesis product transport during rapid growth. This study deepens our understanding of the DHHC gene family’s functional dynamics and evolutionary path in Saccharinae, laying a foundation for future research.https://doi.org/10.1038/s41598-025-86463-4SaccharinaeDHHCGene duplicationsSucrose storageEvolutionary |
| spellingShingle | Hao Wen Xinyu Liu Xueting Zhao Tingting Zhao Cuilian Feng Hailong Chang Jungang Wang Jishan Lin Evolutionary analysis of the DHHCs in Saccharinae Scientific Reports Saccharinae DHHC Gene duplications Sucrose storage Evolutionary |
| title | Evolutionary analysis of the DHHCs in Saccharinae |
| title_full | Evolutionary analysis of the DHHCs in Saccharinae |
| title_fullStr | Evolutionary analysis of the DHHCs in Saccharinae |
| title_full_unstemmed | Evolutionary analysis of the DHHCs in Saccharinae |
| title_short | Evolutionary analysis of the DHHCs in Saccharinae |
| title_sort | evolutionary analysis of the dhhcs in saccharinae |
| topic | Saccharinae DHHC Gene duplications Sucrose storage Evolutionary |
| url | https://doi.org/10.1038/s41598-025-86463-4 |
| work_keys_str_mv | AT haowen evolutionaryanalysisofthedhhcsinsaccharinae AT xinyuliu evolutionaryanalysisofthedhhcsinsaccharinae AT xuetingzhao evolutionaryanalysisofthedhhcsinsaccharinae AT tingtingzhao evolutionaryanalysisofthedhhcsinsaccharinae AT cuilianfeng evolutionaryanalysisofthedhhcsinsaccharinae AT hailongchang evolutionaryanalysisofthedhhcsinsaccharinae AT jungangwang evolutionaryanalysisofthedhhcsinsaccharinae AT jishanlin evolutionaryanalysisofthedhhcsinsaccharinae |