OrchidBase 5.0: updates of the orchid genome knowledgebase

You Yi Chen, Chung‐I ‐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 PengSi Ren Lan, Hong Hwa Chen, Zhong Jian Liu, Wei Sheng Wu, Wen Chieh Tsai

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)


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.

Original languageEnglish
Article number557
JournalBMC Plant Biology
Issue number1
Publication statusPublished - 2022 Dec

All Science Journal Classification (ASJC) codes

  • Plant Science


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