ArticleNucleic acids research2021
GreenPhylDB v5: a comparative pangenomic database for plant genomes.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 21 papers, 1 of them a synthesis that pooled 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.
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.
Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Multi-omics revolution to promote plant breeding efficiency.Frontiers in plant science · 2022Pooled it
- Revolutionizing drug discovery from natural products: The roles of artificial intelligence and multi-omics in accelerating innovation.Acta pharmaceutica Sinica. B · 2026Article
- BAT: an integrated pipeline for gene tree construction, annotation, and functional inference.bioRxiv : the preprint server for biology · 2026Article
- AgroLD: a knowledge graph for the plant sciences.BMC genomic data · 2025Article
- Deciphering metabolic regulation in overripe grapes through multi-omics analysis of non-targeted metabolome, proteome, and transcriptome.BMC plant biology · 2025Article
- Evidence-based unification of potato gene models with the UniTato collaborative genome browser.Frontiers in plant science · 2024Article
- Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes.Biomolecules · 2023Review
- The Progression in Developing Genomic Resources for Crop Improvement.Life (Basel, Switzerland) · 2023Review
- From single- to multi-omics: future research trends in medicinal plants.Briefings in bioinformatics · 2023Article
- The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B5.Nature communications · 2022Article
- Genome-Wide Classification and Phylogenetic Analyses of the GDSL-Type Esterase/Lipase (GELP) Family in Flowering Plants.International journal of molecular sciences · 2022Review
- PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants.Nucleic acids research · 2022Article
- Research Advances and Prospects of Orphan Genes in Plants.Frontiers in plant science · 2022Review
- The banana genome hub: a community database for genomics in the Musaceae.Horticulture research · 2022Article
- PlantTribes2: Tools for comparative gene family analysis in plant genomics.Frontiers in plant science · 2022Article
- RapGreen, an interactive software and web package to explore and analyze phylogenetic trees.NAR genomics and bioinformatics · 2021Article
- SorGSD: updating and expanding the sorghum genome science database with new contents and tools.Biotechnology for biofuels · 2021Article
- Sorghum's Whole-Plant Transcriptome and Proteome Responses to Drought Stress: A Review.Life (Basel, Switzerland) · 2021Review
- Correction to 'GreenPhylDB v5: a comparative pangenomic database for plant genomes'.Nucleic acids research · 2021Article
- The 2021 Nucleic Acids Research database issue and the online molecular biology database collection.Nucleic acids research · 2021Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Comparative genomics is the analysis of genomic relationships among different species and serves as a significant base for evolutionary and functional genomic studies. GreenPhylDB (https://www.greenphyl.org) is a database designed to facilitate the exploration of gene families and homologous relationships among plant genomes, including staple crops critically important for global food security. GreenPhylDB is available since 2007, after the release of the Arabidopsis thaliana and Oryza sativa genomes and has undergone multiple releases. With the number of plant genomes currently available, it becomes challenging to select a single reference for comparative genomics studies but there is still a lack of databases taking advantage several genomes by species for orthology detection. GreenPhylDBv5 introduces the concept of comparative pangenomics by harnessing multiple genome sequences by species. We created 19 pangenes and processed them with other species still relying on one genome. In total, 46 plant species were considered to build gene families and predict their homologous relationships through phylogenetic-based analyses. In addition, since the previous publication, we rejuvenated the website and included a new set of original tools including protein-domain combination, tree topologies searches and a section for users to store their own results in order to support community curation efforts.
Indexed as
Identifiers
What OpenQuestion holds
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.