Evidence map›Paper›PMID 39748253›Full record

ArticleBMC plant biology2025

OrchidBase 6.0: increasing the number of Cymbidium (Orchidaceae) genomes and new bioinformatic tools for orchid genome analysis.

You-Yi Chen, Ye Sun, Chung-I Li, Shao-Ting Lin, Hao-Chen Zheng, Zhe-Bin Zhang, Bing-Ru Lee, Chun-Lin Hsieh, Yu-Yun Hsiao, Chi-Nga Chow and 19 more

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Article in BMC plant biology, 2025. 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

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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
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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

29 authors.

You-Yi Chen *Department of Agronomy, National Chiayi University, Chaiyi, 600, Taiwan.
Ye Sun *Jiangsu Lixiahe District Institute of Agricultural Sciences, Yangzhou, 225007, China.
Chung-I LiDepartment of Statistics, National Cheng Kung University, Tainan City, 701, Taiwan.
Shao-Ting LinGraduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Tainan City, Taiwan.
Hao-Chen ZhengDepartment of Electrical Engineering, National Cheng Kung University, Tainan City, 701, Taiwan.
Zhe-Bin ZhangDepartment of Electrical Engineering, National Cheng Kung University, Tainan City, 701, Taiwan.
Bing-Ru LeeDepartment of Electrical Engineering, National Cheng Kung University, Tainan City, 701, Taiwan.
Chun-Lin HsiehDepartment of Electrical Engineering, National Cheng Kung University, Tainan City, 701, Taiwan.
Yu-Yun HsiaoOrchid Research and Development Center, National Cheng Kung University, Tainan City, 701, Taiwan.
Chi-Nga ChowInstitute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan City, 701, Taiwan.
Chien-Wen YangGraduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Tainan City, Taiwan.
Wen-Chi ChangInstitute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan City, 701, Taiwan.
Heming ChenGuangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Institute of Environmental Horticulture, Guangdong Academy of Agricultural, Guangzhou, 510640, China.
Feng-Xi YangGuangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Institute of Environmental Horticulture, Guangdong Academy of Agricultural, Guangzhou, 510640, China.
Gen-Fa ZhuGuangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Institute of Environmental Horticulture, Guangdong Academy of Agricultural, Guangzhou, 510640, China.
Qinyao ZhengKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
Cheng-Yuan ZhouKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
Zhuang ZhaoKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
Ye AiKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
Lin-Ying WangKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
Deqiang ChenCollege of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
Xin HeCollege of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
Ming-Zhong HuangCollege of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
Dong-Hui PengKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
Hao YuDepartment of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
Siren LanKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China. lkzx@fafu.edu.cn.
Zhong-Jian LiuKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center, 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 City, 701, Taiwan. wessonwu@mail.ncku.edu.tw.
Wen-Chieh TsaiGraduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Tainan City, Taiwan. tsaiwc@mail.ncku.edu.tw.

Funding

National Key Research and Development Program of China 2023YFD1600504National Science and Technology Council 110-2221-E-006-198-MY3National Science and Technology Council 110-2313-B-006-002-MY3National Science and Technology Council, Taiwan 111-2313-B-006-003
6 · The paper itself

Abstract

backgroundOrchids are well-known for their rich diversity of species as well as wide range habitats. Their floral structures are so unique in angiosperms that many of orchids are economically and culturally important in human society. Orchids pollination strategy and evolutionary trajectory are also fantastic human for centuries. Previously, OrchidBase was created not only for storage and management of orchid genomic and transcriptomic information including Apostasia shenzhenica, Dendrobium catenatum, Phalaenopsis equestris, and two species of Platanthera that belong to three different subfamilies of Orchidaceae, but explored orchid genetic sequences for their function. The OrchidBase offers an opportunity for the plant science community to compare orchid genomes and transcriptomes, and retrieve orchid sequences for further study. DESCRIPTION: Recently, three whole-genome sequences of the Epidendroideae species, Cymbidium sinense, C. ensifolium and C. goeringii, were sequenced de novo, assembled, and analyzed. In addition, the systemic transcriptomes of these three species have been established. We included these datasets to develop a new version of OrchidBase 6.0. Furthermore, four new analytical methods, namely regulation, updated transcriptome, advanced BLAST, and domain search, were developed for orchid genome analyses.

conclusionOrchidBase 6.0 extended genetic information to that of eight orchid species and created new tools for an expanded community curation in response to the ever-increasing volume and complexity of data.

Indexed as

Computational BiologyGenome, PlantOrchidaceaeDatabases, GeneticGenomicsTranscriptomeCymbidiumGenomeOrchidOrchidBaseTranscriptomeWhole-genome sequencing

Identifiers

PMID39748253
PMCPMC11697506

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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.