ArticlePeerJ2016
Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria.
Article in PeerJ, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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
24 citing papers in PubMed.
- A comparison of short- and long-read whole-genome sequencing for microbial pathogen epidemiology.mSystems · 2025Article
- A comparison of short- and long-read whole genome sequencing for microbial pathogen epidemiology.bioRxiv : the preprint server for biology · 2025Article
- From cantaloupe to cattle:International journal of systematic and evolutionary microbiology · 2025Article
- Article
- Article
- Article
- Article
- Mistranslation of the genetic code by a new family of bacterial transfer RNAs.The Journal of biological chemistry · 2023Article
- Article
- Dual adhesive unipolar polysaccharides synthesized by overlapping biosynthetic pathways in Agrobacterium tumefaciens.Molecular microbiology · 2022Article
- Symbiotic bacteria of the gall-inducing mite Fragariocoptes setiger (Eriophyoidea) and phylogenomic resolution of the eriophyoid position among Acari.Scientific reports · 2022Article
- Diversification of plasmids in a genus of pathogenic and nitrogen-fixing bacteria.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
- Unexpected distribution of the 4-formylaminooxyvinylglycine (FVG) biosynthetic pathway in Pseudomonas and beyond.PloS one · 2021Article
- Genome Sequences ofBiology · 2020Article
- Generation of a Prophage-Free Variant of the Fast-Growing Bacterium Vibrio natriegens.Applied and environmental microbiology · 2019Article
- Riding the wave of genomics to investigate aquatic coliphage diversity and activity.Environmental microbiology · 2019Article
- Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia.Scientific reports · 2019Article
- Genomic and metabolic differences between Pseudomonas putida populations inhabiting sugarcane rhizosphere or bulk soil.PloS one · 2019Article
- The Identification and Conservation of Tunicaminyluracil-Related Biosynthetic Gene Clusters in SeveralFrontiers in microbiology · 2019Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding the population structure and genetic diversity of plant pathogens, as well as the effect of agricultural practices on pathogen evolution, is important for disease management. Developments in molecular methods have contributed to increase the resolution for accurate pathogen identification, but those based on analysis of DNA sequences can be less straightforward to use. To address this, we developed Gall-ID, a web-based platform that uses DNA sequence information from 16S rDNA, multilocus sequence analysis and whole genome sequences to group disease-associated bacteria to their taxonomic units. Gall-ID was developed with a particular focus on gall-forming bacteria belonging to Agrobacterium, Pseudomonas savastanoi, Pantoea agglomerans, and Rhodococcus. Members of these groups of bacteria cause growth deformation of plants, and some are capable of infecting many species of field, orchard, and nursery crops. Gall-ID also enables the use of high-throughput sequencing reads to search for evidence for homologs of characterized virulence genes, and provides downloadable software pipelines for automating multilocus sequence analysis, analyzing genome sequences for average nucleotide identity, and constructing core genome phylogenies. Lastly, additional databases were included in Gall-ID to help determine the identity of other plant pathogenic bacteria that may be in microbial communities associated with galls or causative agents in other diseased tissues of plants. The URL for Gall-ID is http://gall-id.cgrb.oregonstate.edu/.
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.