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OrchidBase 5.0: updates of the orchid genome knowledgebase.
Chen, You-Yi; Li, Chung-I; Hsiao, Yu-Yun; Ho, Sau-Yee; Zhang, Zhe-Bin; Liao, Chien-Chi; Lee, Bing-Ru; Lin, Shao-Ting; Wu, Wan-Lin; Wang, Jeen-Shing; Zhang, Diyang; Liu, Ke-Wei; Liu, Ding-Kun; Zhao, Xue-Wei; Li, Yuan-Yuan; Ke, Shi-Jie; Zhou, Zhuang; Huang, Ming-Zhong; Wu, Yong-Shu; Peng, Dong-Hui; Lan, Si-Ren; Chen, Hong-Hwa; Liu, Zhong-Jian; Wu, Wei-Sheng; Tsai, Wen-Chieh.
Afiliação
  • Chen YY; Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan.
  • Li CI; Department of Statistics, National Cheng Kung University, Tainan, 701, Taiwan.
  • Hsiao YY; Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan.
  • Ho SY; Department of Electrical Engineering, National Cheng Kung University, Tainan, 701, Taiwan.
  • Zhang ZB; Department of Electrical Engineering, National Cheng Kung University, Tainan, 701, Taiwan.
  • Liao CC; Department of Electrical Engineering, National Cheng Kung University, Tainan, 701, Taiwan.
  • Lee BR; Department of Electrical Engineering, National Cheng Kung University, Tainan, 701, Taiwan.
  • Lin ST; Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan.
  • Wu WL; Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan.
  • Wang JS; Department of Electrical Engineering, National Cheng Kung University, Tainan, 701, Taiwan.
  • Zhang D; Key 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 University, Fuzhou, Fujian, 350002, China.
  • Liu KW; Tsinghua-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 (i
  • Liu DK; Key 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 University, Fuzhou, Fujian, 350002, China.
  • Zhao XW; Key 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 University, Fuzhou, Fujian, 350002, China.
  • Li YY; Key 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 University, Fuzhou, Fujian, 350002, China.
  • Ke SJ; Key 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 University, Fuzhou, Fujian, 350002, China.
  • Zhou Z; Key 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 University, Fuzhou, Fujian, 350002, China.
  • Huang MZ; Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005, China.
  • Wu YS; Key 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 University, Fuzhou, Fujian, 350002, China.
  • Peng DH; Education Botanical Garden of Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
  • Lan SR; Key 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 University, Fuzhou, Fujian, 350002, China.
  • Chen HH; Key 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 University, Fuzhou, Fujian, 350002, China.
  • Liu ZJ; Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan.
  • Wu WS; Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
  • Tsai WC; Key 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 University, Fuzhou, Fujian, 350002, China. zjliu@fafu.edu.cn.
BMC Plant Biol ; 22(1): 557, 2022 Dec 02.
Article em En | MEDLINE | ID: mdl-36456919
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/.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Orchidaceae / MicroRNAs Idioma: En Ano de publicação: 2022 Tipo de documento: Article
Texto completo
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Orchidaceae / MicroRNAs Idioma: En Ano de publicação: 2022 Tipo de documento: Article