OrchidBase 5.0: updates of the orchid genome knowledgebase
Abstract Containing the largest number of species, the orchid family provides not only materials for studying plant evolution and environmental adaptation, but economically and culturally important ornamental plants for human society. Previously, we collected genome and transcriptome information of...
| Published in: | BMC Plant Biology |
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| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , |
| Format: | Article |
| Language: | English |
| Published: |
BMC
2022-12-01
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| Online Access: | https://doi.org/10.1186/s12870-022-03955-5 |
| _version_ | 1852704302315864064 |
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| author | You-Yi Chen Chung‐I Li Yu-Yun Hsiao Sau-Yee Ho Zhe-Bin Zhang Chien-Chi Liao Bing-Ru Lee Shao-Ting Lin Wan-Lin Wu Jeen-Shing Wang Diyang Zhang Ke-Wei Liu Ding-Kun Liu Xue-Wei Zhao Yuan-Yuan Li Shi-Jie Ke Zhuang Zhou Ming-Zhong Huang Yong-Shu Wu Dong-Hui Peng Si-Ren Lan Hong-Hwa Chen Zhong-Jian Liu Wei-Sheng Wu Wen-Chieh Tsai |
| author_facet | You-Yi Chen Chung‐I Li Yu-Yun Hsiao Sau-Yee Ho Zhe-Bin Zhang Chien-Chi Liao Bing-Ru Lee Shao-Ting Lin Wan-Lin Wu Jeen-Shing Wang Diyang Zhang Ke-Wei Liu Ding-Kun Liu Xue-Wei Zhao Yuan-Yuan Li Shi-Jie Ke Zhuang Zhou Ming-Zhong Huang Yong-Shu Wu Dong-Hui Peng Si-Ren Lan Hong-Hwa Chen Zhong-Jian Liu Wei-Sheng Wu Wen-Chieh Tsai |
| author_sort | You-Yi Chen |
| collection | DOAJ |
| container_title | BMC Plant Biology |
| description | Abstract Containing the largest number of species, the orchid family provides not only materials for studying plant evolution and environmental adaptation, but economically and culturally important ornamental plants for human society. Previously, we collected genome and transcriptome information of Dendrobium catenatum, Phalaenopsis equestris, and Apostasia shenzhenica which belong to two different subfamilies of Orchidaceae, and developed user-friendly tools to explore the orchid genetic sequences in the OrchidBase 4.0. The OrchidBase 4.0 offers the opportunity for plant science community to compare orchid genomes and transcriptomes and retrieve orchid sequences for further study. In the year 2022, two whole-genome sequences of Orchidoideae species, Platanthera zijinensis and Platanthera guangdongensis, were de novo sequenced, assembled and analyzed. In addition, systemic transcriptomes from these two species were also established. Therefore, we included these datasets to develop the new version of OrchidBase 5.0. In addition, three new functions including synteny, gene order, and miRNA information were also developed for orchid genome comparisons and miRNA characterization. OrchidBase 5.0 extended the genetic information to three orchid subfamilies (including five orchid species) and provided new tools for orchid researchers to analyze orchid genomes and transcriptomes. The online resources can be accessed at https://cosbi.ee.ncku.edu.tw/orchidbase5/ |
| format | Article |
| id | doaj-art-5dee641da6ea4d6dbd99686c2c7204f2 |
| institution | Directory of Open Access Journals |
| issn | 1471-2229 |
| language | English |
| publishDate | 2022-12-01 |
| publisher | BMC |
| record_format | Article |
| spelling | doaj-art-5dee641da6ea4d6dbd99686c2c7204f22025-08-19T21:19:22ZengBMCBMC Plant Biology1471-22292022-12-0122111410.1186/s12870-022-03955-5OrchidBase 5.0: updates of the orchid genome knowledgebaseYou-Yi Chen0Chung‐I Li1Yu-Yun Hsiao2Sau-Yee Ho3Zhe-Bin Zhang4Chien-Chi Liao5Bing-Ru Lee6Shao-Ting Lin7Wan-Lin Wu8Jeen-Shing Wang9Diyang Zhang10Ke-Wei Liu11Ding-Kun Liu12Xue-Wei Zhao13Yuan-Yuan Li14Shi-Jie Ke15Zhuang Zhou16Ming-Zhong Huang17Yong-Shu Wu18Dong-Hui Peng19Si-Ren Lan20Hong-Hwa Chen21Zhong-Jian Liu22Wei-Sheng Wu23Wen-Chieh Tsai24Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung UniversityDepartment of Statistics, National Cheng Kung UniversityOrchid Research and Development Center, National Cheng Kung UniversityDepartment 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 UniversityInstitute of Tropical Plant Sciences and Microbiology, National Cheng Kung UniversityInstitute of Tropical Plant Sciences and Microbiology, National Cheng Kung UniversityDepartment of Electrical Engineering, National Cheng Kung UniversityKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry UniversityTsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua UniversityKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at 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 at 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 at 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 at 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 at 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 at College of Landscape Architecture, Fujian Agriculture and Forestry UniversityEducation Botanical Garden of Fujian Agriculture and Forestry UniversityKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at 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 at College of Landscape Architecture, Fujian Agriculture and Forestry UniversityOrchid Research and Development Center, National Cheng Kung UniversityKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry UniversityDepartment of Electrical Engineering, National Cheng Kung UniversityInstitute of Tropical Plant Sciences and Microbiology, National Cheng Kung UniversityAbstract Containing the largest number of species, the orchid family provides not only materials for studying plant evolution and environmental adaptation, but economically and culturally important ornamental plants for human society. Previously, we collected genome and transcriptome information of Dendrobium catenatum, Phalaenopsis equestris, and Apostasia shenzhenica which belong to two different subfamilies of Orchidaceae, and developed user-friendly tools to explore the orchid genetic sequences in the OrchidBase 4.0. The OrchidBase 4.0 offers the opportunity for plant science community to compare orchid genomes and transcriptomes and retrieve orchid sequences for further study. In the year 2022, two whole-genome sequences of Orchidoideae species, Platanthera zijinensis and Platanthera guangdongensis, were de novo sequenced, assembled and analyzed. In addition, systemic transcriptomes from these two species were also established. Therefore, we included these datasets to develop the new version of OrchidBase 5.0. In addition, three new functions including synteny, gene order, and miRNA information were also developed for orchid genome comparisons and miRNA characterization. OrchidBase 5.0 extended the genetic information to three orchid subfamilies (including five orchid species) and provided new tools for orchid researchers to analyze orchid genomes and transcriptomes. The online resources can be accessed at https://cosbi.ee.ncku.edu.tw/orchidbase5/https://doi.org/10.1186/s12870-022-03955-5OrchidOrchidBaseWhole-genome sequencesOrchidoideaePlatantheraSynteny |
| spellingShingle | You-Yi Chen Chung‐I Li Yu-Yun Hsiao Sau-Yee Ho Zhe-Bin Zhang Chien-Chi Liao Bing-Ru Lee Shao-Ting Lin Wan-Lin Wu Jeen-Shing Wang Diyang Zhang Ke-Wei Liu Ding-Kun Liu Xue-Wei Zhao Yuan-Yuan Li Shi-Jie Ke Zhuang Zhou Ming-Zhong Huang Yong-Shu Wu Dong-Hui Peng Si-Ren Lan Hong-Hwa Chen Zhong-Jian Liu Wei-Sheng Wu Wen-Chieh Tsai OrchidBase 5.0: updates of the orchid genome knowledgebase Orchid OrchidBase Whole-genome sequences Orchidoideae Platanthera Synteny |
| title | OrchidBase 5.0: updates of the orchid genome knowledgebase |
| title_full | OrchidBase 5.0: updates of the orchid genome knowledgebase |
| title_fullStr | OrchidBase 5.0: updates of the orchid genome knowledgebase |
| title_full_unstemmed | OrchidBase 5.0: updates of the orchid genome knowledgebase |
| title_short | OrchidBase 5.0: updates of the orchid genome knowledgebase |
| title_sort | orchidbase 5 0 updates of the orchid genome knowledgebase |
| topic | Orchid OrchidBase Whole-genome sequences Orchidoideae Platanthera Synteny |
| url | https://doi.org/10.1186/s12870-022-03955-5 |
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