Genome-wide identification and bioinformatics analysis of the WD40 transcription factor family and candidate gene screening for anthocyanin biosynthesis in Rhododendron simsii
Abstract WD40 transcription factors (TFs) constitute a large gene family in eukaryotes, playing diverse roles in cellular processes. However, their functions in the major ornamental plant, Rhododendron simsii, remain poorly understood. In this study, we identified 258 WD40 proteins in the R. simsii...
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| Format: | Article |
| Language: | English |
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BMC
2023-08-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09604-x |
| _version_ | 1797577948552757248 |
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| author | Cheng Wang Yafang Tang Yan Li Chao Hu Jingyi Li Ang Lyu |
| author_facet | Cheng Wang Yafang Tang Yan Li Chao Hu Jingyi Li Ang Lyu |
| author_sort | Cheng Wang |
| collection | DOAJ |
| description | Abstract WD40 transcription factors (TFs) constitute a large gene family in eukaryotes, playing diverse roles in cellular processes. However, their functions in the major ornamental plant, Rhododendron simsii, remain poorly understood. In this study, we identified 258 WD40 proteins in the R. simsii genome, which exhibited an uneven distribution across chromosomes. Based on domain compositions and phylogenetic analysis, we classified these 258 RsWD40 proteins into 42 subfamilies and 47 clusters. Comparative genomic analysis suggested that the expansion of the WD40 gene family predates the divergence of green algae and higher plants, indicating an ancient origin. Furthermore, by analyzing the duplication patterns of RsWD40 genes, we found that transposed duplication played a major role in their expansion. Notably, the majority of RsWD40 gene duplication pairs underwent purifying selection during evolution. Synteny analysis identified significant orthologous gene pairs between R. simsii and Arabidopsis thaliana, Oryza sativa, Vitis vinifera, and Malus domestica. We also investigated potential candidate genes involved in anthocyanin biosynthesis during different flower development stages in R. simsii using RNA-seq data. Specifically, we identified 10 candidate genes during the bud stage and 7 candidate genes during the full bloom stage. GO enrichment analysis of these candidate genes revealed the potential involvement of the ubiquitination process in anthocyanin biosynthesis. Overall, our findings provide a valuable foundation for further investigation and functional analysis of WD40 genes, as well as research on the molecular mechanisms underlying anthocyanin biosynthesis in Rhododendron species. |
| first_indexed | 2024-03-10T22:15:18Z |
| format | Article |
| id | doaj.art-569d6fce87e54733a1ad69f2d498203b |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-10T22:15:18Z |
| publishDate | 2023-08-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj.art-569d6fce87e54733a1ad69f2d498203b2023-11-19T12:27:48ZengBMCBMC Genomics1471-21642023-08-0124111710.1186/s12864-023-09604-xGenome-wide identification and bioinformatics analysis of the WD40 transcription factor family and candidate gene screening for anthocyanin biosynthesis in Rhododendron simsiiCheng Wang0Yafang Tang1Yan Li2Chao Hu3Jingyi Li4Ang Lyu5Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering UniversityKey Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering UniversityDepartment of Biology and Chemical Engineering, Weihai Vocational CollegeKey Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering UniversityKey Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering UniversityInstitute of Quality Standard and Testing Technology for Agro-Products, Hubei Academy of Agricultural ScienceAbstract WD40 transcription factors (TFs) constitute a large gene family in eukaryotes, playing diverse roles in cellular processes. However, their functions in the major ornamental plant, Rhododendron simsii, remain poorly understood. In this study, we identified 258 WD40 proteins in the R. simsii genome, which exhibited an uneven distribution across chromosomes. Based on domain compositions and phylogenetic analysis, we classified these 258 RsWD40 proteins into 42 subfamilies and 47 clusters. Comparative genomic analysis suggested that the expansion of the WD40 gene family predates the divergence of green algae and higher plants, indicating an ancient origin. Furthermore, by analyzing the duplication patterns of RsWD40 genes, we found that transposed duplication played a major role in their expansion. Notably, the majority of RsWD40 gene duplication pairs underwent purifying selection during evolution. Synteny analysis identified significant orthologous gene pairs between R. simsii and Arabidopsis thaliana, Oryza sativa, Vitis vinifera, and Malus domestica. We also investigated potential candidate genes involved in anthocyanin biosynthesis during different flower development stages in R. simsii using RNA-seq data. Specifically, we identified 10 candidate genes during the bud stage and 7 candidate genes during the full bloom stage. GO enrichment analysis of these candidate genes revealed the potential involvement of the ubiquitination process in anthocyanin biosynthesis. Overall, our findings provide a valuable foundation for further investigation and functional analysis of WD40 genes, as well as research on the molecular mechanisms underlying anthocyanin biosynthesis in Rhododendron species.https://doi.org/10.1186/s12864-023-09604-xRhododendron simsiiWD40Duplication analysisAnthocyanin biosynthesisCandidate genes |
| spellingShingle | Cheng Wang Yafang Tang Yan Li Chao Hu Jingyi Li Ang Lyu Genome-wide identification and bioinformatics analysis of the WD40 transcription factor family and candidate gene screening for anthocyanin biosynthesis in Rhododendron simsii BMC Genomics Rhododendron simsii WD40 Duplication analysis Anthocyanin biosynthesis Candidate genes |
| title | Genome-wide identification and bioinformatics analysis of the WD40 transcription factor family and candidate gene screening for anthocyanin biosynthesis in Rhododendron simsii |
| title_full | Genome-wide identification and bioinformatics analysis of the WD40 transcription factor family and candidate gene screening for anthocyanin biosynthesis in Rhododendron simsii |
| title_fullStr | Genome-wide identification and bioinformatics analysis of the WD40 transcription factor family and candidate gene screening for anthocyanin biosynthesis in Rhododendron simsii |
| title_full_unstemmed | Genome-wide identification and bioinformatics analysis of the WD40 transcription factor family and candidate gene screening for anthocyanin biosynthesis in Rhododendron simsii |
| title_short | Genome-wide identification and bioinformatics analysis of the WD40 transcription factor family and candidate gene screening for anthocyanin biosynthesis in Rhododendron simsii |
| title_sort | genome wide identification and bioinformatics analysis of the wd40 transcription factor family and candidate gene screening for anthocyanin biosynthesis in rhododendron simsii |
| topic | Rhododendron simsii WD40 Duplication analysis Anthocyanin biosynthesis Candidate genes |
| url | https://doi.org/10.1186/s12864-023-09604-x |
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