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 Peng; Si Ren Lan; Hong Hwa Chen; Zhong Jian Liu; Wei Sheng Wu; Wen Chieh Tsai

doi:10.1186/s12870-022-03955-5

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 journal › Article › peer-review

3 Citations (Scopus)

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.

Original language	English
Article number	557
Journal	BMC Plant Biology
Volume	22
Issue number	1
DOIs	https://doi.org/10.1186/s12870-022-03955-5
Publication status	Published - 2022 Dec

All Science Journal Classification (ASJC) codes

Plant Science

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10.1186/s12870-022-03955-5

Cite this

Chen, Y. Y., Li, CI. I., Hsiao, Y. Y., Ho, S. Y., Zhang, Z. B., Liao, C. C., Lee, B. R., Lin, S. T., Wu, W. L., Wang, J. S., Zhang, D., Liu, K. W., Liu, D. K., Zhao, X. W., Li, Y. Y., Ke, S. J., Zhou, Z., Huang, M. Z., Wu, Y. S., ... Tsai, W. C. (2022). OrchidBase 5.0: updates of the orchid genome knowledgebase. BMC Plant Biology, 22(1), Article 557. https://doi.org/10.1186/s12870-022-03955-5

@article{73348db24be1470db40a5d9786ee9273,

title = "OrchidBase 5.0: updates of the orchid genome knowledgebase",

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.",

author = "Chen, {You Yi} and Li, {Chung‐I ‐I} and Hsiao, {Yu Yun} and Ho, {Sau Yee} and Zhang, {Zhe Bin} and Liao, {Chien Chi} and Lee, {Bing Ru} and Lin, {Shao Ting} and Wu, {Wan Lin} and Wang, {Jeen Shing} and Diyang Zhang and Liu, {Ke Wei} and Liu, {Ding Kun} and Zhao, {Xue Wei} and Li, {Yuan Yuan} and Ke, {Shi Jie} and Zhuang Zhou and Huang, {Ming Zhong} and Wu, {Yong Shu} and Peng, {Dong Hui} and Lan, {Si Ren} and Chen, {Hong Hwa} and Liu, {Zhong Jian} and Wu, {Wei Sheng} and Tsai, {Wen Chieh}",

note = "Funding Information: Publication costs was funded by the Ministry of Science and Technology, Taiwan (MOST 110–2313-B-006–002-MY3, MOST 110–2221-E-006–198-MY3 and MOST-111–2221-E-006–151-MY3), National Key R&D Program of China (Grant No.2019YFD1000400), and National Natural Science Foundation of China [no. 31870199]. The funders have no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript. Publisher Copyright: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = dec,

doi = "10.1186/s12870-022-03955-5",

language = "English",

volume = "22",

journal = "BMC Plant Biology",

issn = "1471-2229",

publisher = "BioMed Central",

number = "1",

}

Chen, YY, Li, CII, Hsiao, YY, Ho, SY, Zhang, ZB, Liao, CC, Lee, BR, Lin, ST, Wu, WL, Wang, JS, Zhang, D, Liu, KW, Liu, DK, Zhao, XW, Li, YY, Ke, SJ, Zhou, Z, Huang, MZ, Wu, YS, Peng, DH, Lan, SR, Chen, HH, Liu, ZJ, Wu, WS & Tsai, WC 2022, 'OrchidBase 5.0: updates of the orchid genome knowledgebase', BMC Plant Biology, vol. 22, no. 1, 557. https://doi.org/10.1186/s12870-022-03955-5

TY - JOUR

T1 - OrchidBase 5.0

T2 - updates of the orchid genome knowledgebase

AU - Chen, You Yi

AU - Li, Chung‐I ‐I

AU - Hsiao, Yu Yun

AU - Ho, Sau Yee

AU - Zhang, Zhe Bin

AU - Liao, Chien Chi

AU - Lee, Bing Ru

AU - Lin, Shao Ting

AU - Wu, Wan Lin

AU - Wang, Jeen Shing

AU - Zhang, Diyang

AU - Liu, Ke Wei

AU - Liu, Ding Kun

AU - Zhao, Xue Wei

AU - Li, Yuan Yuan

AU - Ke, Shi Jie

AU - Zhou, Zhuang

AU - Huang, Ming Zhong

AU - Wu, Yong Shu

AU - Peng, Dong Hui

AU - Lan, Si Ren

AU - Chen, Hong Hwa

AU - Liu, Zhong Jian

AU - Wu, Wei Sheng

AU - Tsai, Wen Chieh

N1 - Funding Information: Publication costs was funded by the Ministry of Science and Technology, Taiwan (MOST 110–2313-B-006–002-MY3, MOST 110–2221-E-006–198-MY3 and MOST-111–2221-E-006–151-MY3), National Key R&D Program of China (Grant No.2019YFD1000400), and National Natural Science Foundation of China [no. 31870199]. The funders have no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript. Publisher Copyright: © 2022, The Author(s).

PY - 2022/12

Y1 - 2022/12

N2 - 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.

AB - 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.

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UR - http://www.scopus.com/inward/citedby.url?scp=85143184094&partnerID=8YFLogxK

U2 - 10.1186/s12870-022-03955-5

DO - 10.1186/s12870-022-03955-5

M3 - Article

C2 - 36456919

AN - SCOPUS:85143184094

SN - 1471-2229

VL - 22

JO - BMC Plant Biology

JF - BMC Plant Biology

IS - 1

M1 - 557

ER -

OrchidBase 5.0: updates of the orchid genome knowledgebase

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