OrchidBase 6.0: increasing the number of Cymbidium (Orchidaceae) genomes and new bioinformatic tools for orchid genome analysis
Abstract Background Orchids are well-known for their rich diversity of species as well as wide range habitats. Their floral structures are so unique in angiosperms that many of orchids are economically and culturally important in human society. Orchids pollination strategy and evolutionary trajector...
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2025-01-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-024-06024-1 |
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| author | You-Yi Chen Ye Sun Chung-I Li Shao-Ting Lin Hao-Chen Zheng Zhe-Bin Zhang Bing-Ru Lee Chun-Lin Hsieh Yu-Yun Hsiao Chi-Nga Chow Chien-Wen Yang Wen-Chi Chang Heming Chen Feng-Xi Yang Gen-Fa Zhu Qinyao Zheng Cheng-Yuan Zhou Zhuang Zhao Ye Ai Lin-Ying Wang Deqiang Chen Xin He Ming-Zhong Huang Dong-Hui Peng Hao Yu Siren Lan Zhong-Jian Liu Wei-Sheng Wu Wen-Chieh Tsai |
| author_facet | You-Yi Chen Ye Sun Chung-I Li Shao-Ting Lin Hao-Chen Zheng Zhe-Bin Zhang Bing-Ru Lee Chun-Lin Hsieh Yu-Yun Hsiao Chi-Nga Chow Chien-Wen Yang Wen-Chi Chang Heming Chen Feng-Xi Yang Gen-Fa Zhu Qinyao Zheng Cheng-Yuan Zhou Zhuang Zhao Ye Ai Lin-Ying Wang Deqiang Chen Xin He Ming-Zhong Huang Dong-Hui Peng Hao Yu Siren Lan Zhong-Jian Liu Wei-Sheng Wu Wen-Chieh Tsai |
| author_sort | You-Yi Chen |
| collection | DOAJ |
| description | Abstract Background Orchids are well-known for their rich diversity of species as well as wide range habitats. Their floral structures are so unique in angiosperms that many of orchids are economically and culturally important in human society. Orchids pollination strategy and evolutionary trajectory are also fantastic human for centuries. Previously, OrchidBase was created not only for storage and management of orchid genomic and transcriptomic information including Apostasia shenzhenica, Dendrobium catenatum, Phalaenopsis equestris, and two species of Platanthera that belong to three different subfamilies of Orchidaceae, but explored orchid genetic sequences for their function. The OrchidBase offers an opportunity for the plant science community to compare orchid genomes and transcriptomes, and retrieve orchid sequences for further study. Description Recently, three whole-genome sequences of the Epidendroideae species, Cymbidium sinense, C. ensifolium and C. goeringii, were sequenced de novo, assembled, and analyzed. In addition, the systemic transcriptomes of these three species have been established. We included these datasets to develop a new version of OrchidBase 6.0. Furthermore, four new analytical methods, namely regulation, updated transcriptome, advanced BLAST, and domain search, were developed for orchid genome analyses. Conclusion OrchidBase 6.0 extended genetic information to that of eight orchid species and created new tools for an expanded community curation in response to the ever-increasing volume and complexity of data. |
| format | Article |
| id | doaj-art-32f524ff812642a4be207b17da16a693 |
| institution | Kabale University |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
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| series | BMC Plant Biology |
| spelling | doaj-art-32f524ff812642a4be207b17da16a6932025-01-05T12:13:04ZengBMCBMC Plant Biology1471-22292025-01-0125111310.1186/s12870-024-06024-1OrchidBase 6.0: increasing the number of Cymbidium (Orchidaceae) genomes and new bioinformatic tools for orchid genome analysisYou-Yi Chen0Ye Sun1Chung-I Li2Shao-Ting Lin3Hao-Chen Zheng4Zhe-Bin Zhang5Bing-Ru Lee6Chun-Lin Hsieh7Yu-Yun Hsiao8Chi-Nga Chow9Chien-Wen Yang10Wen-Chi Chang11Heming Chen12Feng-Xi Yang13Gen-Fa Zhu14Qinyao Zheng15Cheng-Yuan Zhou16Zhuang Zhao17Ye Ai18Lin-Ying Wang19Deqiang Chen20Xin He21Ming-Zhong Huang22Dong-Hui Peng23Hao Yu24Siren Lan25Zhong-Jian Liu26Wei-Sheng Wu27Wen-Chieh Tsai28Department of Agronomy, National Chiayi UniversityJiangsu Lixiahe District Institute of Agricultural SciencesDepartment of Statistics, National Cheng Kung UniversityGraduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia SinicaDepartment of Electrical Engineering, National Cheng Kung UniversityDepartment of Electrical Engineering, National Cheng Kung UniversityDepartment of Electrical Engineering, National Cheng Kung UniversityDepartment of Electrical Engineering, National Cheng Kung UniversityOrchid Research and Development Center, National Cheng Kung UniversityInstitute of Tropical Plant Sciences and Microbiology, National Cheng Kung UniversityGraduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia SinicaInstitute of Tropical Plant Sciences and Microbiology, National Cheng Kung UniversityGuangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Institute of Environmental Horticulture, Guangdong Academy of AgriculturalGuangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Institute of Environmental Horticulture, Guangdong Academy of AgriculturalGuangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Institute of Environmental Horticulture, Guangdong Academy of AgriculturalKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center, College of Landscape Architecture, Fujian Agriculture and Forestry UniversityKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center, College of Landscape Architecture, Fujian Agriculture and Forestry UniversityKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center, College of Landscape Architecture, Fujian Agriculture and Forestry UniversityKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center, College of Landscape Architecture, Fujian Agriculture and Forestry UniversityKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center, College of Landscape Architecture, Fujian Agriculture and Forestry UniversityCollege of Forestry, Fujian Agriculture and Forestry UniversityCollege of Forestry, Fujian Agriculture and Forestry UniversityCollege of Forestry, Fujian Agriculture and Forestry UniversityKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center, College of Landscape Architecture, Fujian Agriculture and Forestry UniversityDepartment of Biological Sciences, National University of SingaporeKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center, College of Landscape Architecture, Fujian Agriculture and Forestry UniversityKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center, College of Landscape Architecture, Fujian Agriculture and Forestry UniversityDepartment of Electrical Engineering, National Cheng Kung UniversityGraduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia SinicaAbstract Background Orchids are well-known for their rich diversity of species as well as wide range habitats. Their floral structures are so unique in angiosperms that many of orchids are economically and culturally important in human society. Orchids pollination strategy and evolutionary trajectory are also fantastic human for centuries. Previously, OrchidBase was created not only for storage and management of orchid genomic and transcriptomic information including Apostasia shenzhenica, Dendrobium catenatum, Phalaenopsis equestris, and two species of Platanthera that belong to three different subfamilies of Orchidaceae, but explored orchid genetic sequences for their function. The OrchidBase offers an opportunity for the plant science community to compare orchid genomes and transcriptomes, and retrieve orchid sequences for further study. Description Recently, three whole-genome sequences of the Epidendroideae species, Cymbidium sinense, C. ensifolium and C. goeringii, were sequenced de novo, assembled, and analyzed. In addition, the systemic transcriptomes of these three species have been established. We included these datasets to develop a new version of OrchidBase 6.0. Furthermore, four new analytical methods, namely regulation, updated transcriptome, advanced BLAST, and domain search, were developed for orchid genome analyses. Conclusion OrchidBase 6.0 extended genetic information to that of eight orchid species and created new tools for an expanded community curation in response to the ever-increasing volume and complexity of data.https://doi.org/10.1186/s12870-024-06024-1OrchidOrchidBaseCymbidiumWhole-genome sequencingGenomeTranscriptome |
| spellingShingle | You-Yi Chen Ye Sun Chung-I Li Shao-Ting Lin Hao-Chen Zheng Zhe-Bin Zhang Bing-Ru Lee Chun-Lin Hsieh Yu-Yun Hsiao Chi-Nga Chow Chien-Wen Yang Wen-Chi Chang Heming Chen Feng-Xi Yang Gen-Fa Zhu Qinyao Zheng Cheng-Yuan Zhou Zhuang Zhao Ye Ai Lin-Ying Wang Deqiang Chen Xin He Ming-Zhong Huang Dong-Hui Peng Hao Yu Siren Lan Zhong-Jian Liu Wei-Sheng Wu Wen-Chieh Tsai OrchidBase 6.0: increasing the number of Cymbidium (Orchidaceae) genomes and new bioinformatic tools for orchid genome analysis BMC Plant Biology Orchid OrchidBase Cymbidium Whole-genome sequencing Genome Transcriptome |
| title | OrchidBase 6.0: increasing the number of Cymbidium (Orchidaceae) genomes and new bioinformatic tools for orchid genome analysis |
| title_full | OrchidBase 6.0: increasing the number of Cymbidium (Orchidaceae) genomes and new bioinformatic tools for orchid genome analysis |
| title_fullStr | OrchidBase 6.0: increasing the number of Cymbidium (Orchidaceae) genomes and new bioinformatic tools for orchid genome analysis |
| title_full_unstemmed | OrchidBase 6.0: increasing the number of Cymbidium (Orchidaceae) genomes and new bioinformatic tools for orchid genome analysis |
| title_short | OrchidBase 6.0: increasing the number of Cymbidium (Orchidaceae) genomes and new bioinformatic tools for orchid genome analysis |
| title_sort | orchidbase 6 0 increasing the number of cymbidium orchidaceae genomes and new bioinformatic tools for orchid genome analysis |
| topic | Orchid OrchidBase Cymbidium Whole-genome sequencing Genome Transcriptome |
| url | https://doi.org/10.1186/s12870-024-06024-1 |
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