Evidence map›Paper›PMID 36456919›Full record

ArticleBMC plant biology2022

OrchidBase 5.0: updates of the orchid genome knowledgebase.

You-Yi Chen, Chung-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 and 15 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC plant biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Review
  2. Article
  3. Evolution ofFrontiers in plant science · 2024
    Article
  4. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

25 authors.

You-Yi ChenInstitute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan.
Chung-I LiDepartment of Statistics, National Cheng Kung University, Tainan, 701, Taiwan.
Yu-Yun HsiaoOrchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan.
Sau-Yee HoDepartment of Electrical Engineering, National Cheng Kung University, Tainan, 701, Taiwan.
Zhe-Bin ZhangDepartment of Electrical Engineering, National Cheng Kung University, Tainan, 701, Taiwan.
Chien-Chi LiaoDepartment of Electrical Engineering, National Cheng Kung University, Tainan, 701, Taiwan.
Bing-Ru LeeDepartment of Electrical Engineering, National Cheng Kung University, Tainan, 701, Taiwan.
Shao-Ting LinInstitute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan.
Wan-Lin WuInstitute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan.
Jeen-Shing WangDepartment of Electrical Engineering, National Cheng Kung University, Tainan, 701, Taiwan.
Diyang ZhangKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
Ke-Wei LiuTsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine, 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.
Ding-Kun LiuKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
Xue-Wei ZhaoKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
Yuan-Yuan LiKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
Shi-Jie KeKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
Zhuang ZhouKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
Ming-Zhong HuangKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
Yong-Shu WuEducation Botanical Garden of Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
Dong-Hui PengKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
Si-Ren LanKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
Hong-Hwa ChenOrchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan.
Zhong-Jian LiuKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China. zjliu@fafu.edu.cn.
Wei-Sheng WuDepartment of Electrical Engineering, National Cheng Kung University, Tainan, 701, Taiwan. wessonwu@mail.ncku.edu.tw.ORCID http://orcid.org/0000-0002-9919-9579
Wen-Chieh TsaiInstitute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan. tsaiwc@mail.ncku.edu.tw.

Funding

Ministry of Science and Technology, Taiwan MOST 110-2313-B-006-002-MY3National Natural Science Foundation of China no. 31870199
6 · The paper itself

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. The online resources can be accessed at https://cosbi.ee.ncku.edu.tw/orchidbase5/.

Indexed as

MicroRNAsOrchidaceaeGene OrderKnowledge BasesSyntenyMicroRNAsGene ordermiRNAOrchidOrchidBaseOrchidoideaePlatantheraSyntenyWhole-genome sequences

Identifiers

PMID36456919
PMCPMC9717476

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.