OrchidBase 4.0: a database for orchid genomics and molecular biology

文献类型： 外文期刊

第一作者： Hsiao, Yu-Yun

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

作者机构：

关键词： Orchid; Whole-genome sequences; Apostasia shenzhenica; Dendrobium catenatum; Phalaenopsis equestris; Database

期刊名称：BMC PLANT BIOLOGY （ 影响因子：4.215； 五年影响因子：4.96 ）

ISSN： 1471-2229

年卷期： 2021 年 21 卷 1 期

页码：

收录情况： SCI

摘要： 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/

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