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

doi:10.1186/s12870-021-03140-0

OrchidBase 4.0: a database for orchid genomics and molecular biology

BMC Plant Biol. 2021 Aug 12;21(1):371. doi: 10.1186/s12870-021-03140-0.

Authors

Yu-Yun Hsiao¹, Chih-Hsiung Fu^{1

2}, Sau-Yee Ho², Chung-I Li³, You-Yi Chen⁴, Wan-Lin Wu^{1

5}, Jeen-Shing Wang², Di-Yang Zhang⁶, Wen-Qi Hu⁶, Xia Yu⁶, Wei-Hong Sun⁶, Zhuang Zhou^{6

7}, Ke-Wei Liu^{8

9}, Laiqiang Huang^{8

9}, Si-Ren Lan⁶, Hong-Hwa Chen^{1

4}, Wei-Sheng Wu¹⁰, Zhong-Jian Liu^{11

12

13

14}, Wen-Chieh Tsai^{15

16

17}

Affiliations

¹ Orchid Research and Development Center, National Cheng Kung University, Tainan, 70101, Taiwan.
² Department of Electrical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan.
³ Department of Statistics, National Cheng Kung University, Tainan, 70101, Taiwan.
⁴ Department of Life Sciences, National Cheng Kung University, Tainan, 70101, Taiwan.
⁵ Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 70101, Taiwan.
⁶ Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
⁷ Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005, China.
⁸ School of Life Sciences, Tsinghua University, Beijing, 100084, China.
⁹ Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine and 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 University, Shenzhen, 518055, China.
¹⁰ Department of Electrical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan. [email protected].
¹¹ Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. [email protected].
¹² Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005, China. [email protected].
¹³ Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine and 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 University, Shenzhen, 518055, China. [email protected].
¹⁴ Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, China. [email protected].
¹⁵ Orchid Research and Development Center, National Cheng Kung University, Tainan, 70101, Taiwan. [email protected].
¹⁶ Department of Life Sciences, National Cheng Kung University, Tainan, 70101, Taiwan. [email protected].
¹⁷ Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 70101, Taiwan. [email protected].

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/.

Keywords: Apostasia shenzhenica; Database; Dendrobium catenatum; Orchid; Phalaenopsis equestris; Whole-genome sequences.

MeSH terms

Databases, Genetic*
Genome, Plant
Orchidaceae / genetics*

Grants and funding

107-2313-B-006-002-MY3/Ministry of Science and Technology, Taiwan