ArticleBMC plant biology2023
Plant GARDEN: a portal website for cross-searching between different types of genomic and genetic resources in a wide variety of plant species.
Article in BMC plant biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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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.
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.
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Who cites it
9 citing papers in PubMed.
- PlantGATA: a comprehensive database for plant GATA transcription factors.Functional & integrative genomics · 2026Article
- Current status and future perspective of genomics-assisted breeding in wheat (Breeding science · 2026Article
- A systems biology framework integrating cross-species transcriptomics and PPI networks for Xylella fastidiosa resistance gene identification.BMC plant biology · 2025Article
- Reference-based chromosome-scale assembly of Japanese barley (Hordeum vulgare ssp. vulgare) cultivar Hayakiso 2.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Development and interlaboratory validation of a cultivar-specific identification method for the table grape 'Shine Muscat' using loop-mediated isothermal amplification (LAMP).Breeding science · 2025Article
- Near-complete genome assembly of tomato (Plant biotechnology (Tokyo, Japan) · 2024Article
- Chromosome-scale genome assembly of acerola (Malpighia emarginata DC.).DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Genomic variation across distribution of Micro-Tom, a model cultivar of tomato (Solanum lycopersicum).DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Evolutionary origin and gradual accumulation with plant evolution of the LACS family.BMC plant biology · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
18 authors.
Funding
Abstract
backgroundPlant genome information is fundamental to plant research and development. Along with the increase in the number of published plant genomes, there is a need for an efficient system to retrieve various kinds of genome-related information from many plant species across plant kingdoms. Various plant databases have been developed, but no public database covers both genomic and genetic resources over a wide range of plant species. MAIN BODY: We have developed a plant genome portal site, Plant GARDEN (Genome And Resource Database Entry: https://plantgarden.jp/en/index ), to provide diverse information related to plant genomics and genetics in divergent plant species. Elasticsearch is used as a search engine, and cross-keyword search across species is available. Web-based user interfaces (WUI) for PCs and tablet computers were independently developed to make data searches more convenient. Several types of data are stored in Plant GARDEN: reference genomes, gene sequences, PCR-based DNA markers, trait-linked DNA markers identified in genetic studies, SNPs, and in/dels on publicly available sequence read archives (SRAs). The data registered in Plant GARDEN as of March 2023 included 304 assembled genome sequences, 11,331,614 gene sequences, 419,132 DNA markers, 8,225 QTLs, and 5,934 SNP lists (gvcf files). In addition, we have re-annotated all the genes registered in Plant GARDEN by using a functional annotation tool, Hayai-Annotation, to compare the orthologous relationships among genes.
conclusionThe aim of Plant GARDEN is to provide plant genome information for use in the fields of plant science as well as for plant-based industries, education, and other relevant areas. Therefore, we have designed a WUI that allows a diverse range of users to access such information in an easy-to-understand manner. Plant GARDEN will eventually include a wide range of plant species for which genome sequences are assembled, and thus the number of plant species in the database will continue to expand. We anticipate that Plant GARDEN will promote the understanding of genomes and gene diversity by facilitating comparisons of the registered sequences.
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Registered trials
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.