Evidence map›Paper›PMID 34384382›Full record

ArticleBMC plant biology2021

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 and 9 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC plant biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
13.1field-weighted citation impact, top 1% of its field
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

7 citing papers in PubMed, 17 citations in OpenAlex.

  1. Article
  2. Identification and Analysis ofInternational journal of molecular sciences · 2024
    Article
  3. Article
  4. Article
  5. Article
  6. 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

19 authors at 6 institutions in 2 countries.

Yu-Yun HsiaoOrchid Research and Development Center, National Cheng Kung University, Tainan, 70101, Taiwan.
Chih-Hsiung FuOrchid Research and Development Center, National Cheng Kung University, Tainan, 70101, Taiwan.
Sau-Yee HoDepartment of Electrical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan.
Chung-I LiDepartment of Statistics, National Cheng Kung University, Tainan, 70101, Taiwan.
You-Yi ChenDepartment of Life Sciences, National Cheng Kung University, Tainan, 70101, Taiwan.
Wan-Lin WuOrchid Research and Development Center, National Cheng Kung University, Tainan, 70101, Taiwan.
Jeen-Shing WangDepartment of Electrical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan.
Di-Yang ZhangKey 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.
Wen-Qi HuKey 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.
Xia YuKey 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.
Wei-Hong SunKey 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.
Zhuang ZhouKey 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.
Ke-Wei LiuSchool of Life Sciences, Tsinghua University, Beijing, 100084, China.
Laiqiang HuangSchool of Life Sciences, Tsinghua University, Beijing, 100084, China.
Si-Ren LanKey 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.
Hong-Hwa ChenOrchid Research and Development Center, National Cheng Kung University, Tainan, 70101, Taiwan.
Wei-Sheng WuDepartment of Electrical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan. wessonwu@mail.ncku.edu.tw.ORCID http://orcid.org/0000-0002-9919-9579
Zhong-Jian LiuKey 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. zjliu@fafu.edu.cn.
Wen-Chieh TsaiOrchid Research and Development Center, National Cheng Kung University, Tainan, 70101, Taiwan. tsaiwc@mail.ncku.edu.tw.
National Cheng Kung University · TWFujian Agriculture and Forestry University · CNTsinghua–Berkeley Shenzhen Institute · CNNational Chengchi University · TWShaoguan University · CNZheJiang Academy of Agricultural Sciences · CN

Funding

Ministry of Science and Technology, Taiwan 107-2313-B-006-002-MY3
6 · The paper itself

Abstract

backgroundThe 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.

conclusionsOrchidBase 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/.

Indexed as

Databases, GeneticGenome, PlantOrchidaceaeApostasia shenzhenicaDatabaseDendrobium catenatumOrchidPhalaenopsis equestrisWhole-genome sequences

Identifiers

PMID34384382
PMCPMC8359044
OpenAlexW3191431205

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.