OrchidBase 4.0: a database for orchid genomics and molecular biology

Yu Yun Hsiao, Chih Hsiung Fu, Sau Yee Ho, Chung I. Li, You Yi Chen, Wan Lin Wu, Jeen Shing Wang, Di Yang Zhang, Wen Qi Hu, Xia Yu, Wei Hong Sun, Zhuang Zhou, Ke Wei Liu, Laiqiang Huang, Si Ren Lan, Hong Hwa Chen, Wei Sheng Wu, Zhong Jian Liu, Wen Chieh Tsai

Research output: Contribution to journalArticlepeer-review

10 Citations (Scopus)

Abstract

Background: The Orchid family is the largest families of the monocotyledons and an economically important ornamental plant worldwide. Given the pivotal role of this plant to humans, botanical researchers and breeding communities should have access to valuable genomic and transcriptomic information of this plant. Previously, we established OrchidBase, which contains expressed sequence tags (ESTs) from different tissues and developmental stages of Phalaenopsis as well as biotic and abiotic stress-treated Phalaenopsis. The database includes floral transcriptomic sequences from 10 orchid species across all the five subfamilies of Orchidaceae. Description: Recently, the whole-genome sequences of Apostasia shenzhenica, Dendrobium catenatum, and Phalaenopsis equestris were de novo assembled and analyzed. These datasets were used to develop OrchidBase 4.0, including genomic and transcriptomic data for these three orchid species. OrchidBase 4.0 offers information for gene annotation, gene expression with fragments per kilobase of transcript per millions mapped reads (FPKM), KEGG pathways and BLAST search. In addition, assembled genome sequences and location of genes and miRNAs could be visualized by the genome browser. The online resources in OrchidBase 4.0 can be accessed by browsing or using BLAST. Users can also download the assembled scaffold sequences and the predicted gene and protein sequences of these three orchid species. Conclusions: OrchidBase 4.0 is the first database that contain the whole-genome sequences and annotations of multiple orchid species. OrchidBase 4.0 is available at http://orchidbase.itps.ncku.edu.tw/

Original languageEnglish
Article number371
JournalBMC Plant Biology
Volume21
Issue number1
DOIs
Publication statusPublished - 2021 Dec

All Science Journal Classification (ASJC) codes

  • Plant Science

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