ArticleGenome research2004
Psi-Phi: exploring the outer limits of bacterial pseudogenes.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 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.
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Who cites it
65 citing papers in PubMed, 99 citations in OpenAlex.
- Pseudogenes and host specialization in the emergent bacterial plant pathogenApplied and environmental microbiology · 2025Article
- Loss to gain: pseudogenes in microorganisms, focusing on eubacteria, and their biological significance.Applied microbiology and biotechnology · 2024Review
- The Genome ofInsects · 2024Article
- Ongoing diversification of the global fish pathogen Piscirickettsia salmonis through genetic isolation and transposition bursts.The ISME journal · 2023Article
- The rate and role of pseudogenes of theMicrobial genomics · 2022Article
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- Bacteriophage and Bacterial Susceptibility, Resistance, and Tolerance to Antibiotics.Pharmaceutics · 2022Review
- Article
- Approaches for characterizing and tracking hospital-associated multidrug-resistant bacteria.Cellular and molecular life sciences : CMLS · 2021Review
- Gene loss through pseudogenization contributes to the ecological diversification of a generalist Roseobacter lineage.The ISME journal · 2021Article
- Computational Methods for Pseudogene Annotation Based on Sequence Homology.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Microevolution of Streptococcus agalactiae ST-261 from Australia Indicates Dissemination via Imported Tilapia and Ongoing Adaptation to Marine Hosts or Environment.Applied and environmental microbiology · 2018Article
- Patterns of Nucleotide Deletion and Insertion Inferred from Bacterial Pseudogenes.Genome biology and evolution · 2018Article
- Partnering With a Pest: Genomes of Hemlock Woolly Adelgid Symbionts Reveal Atypical Nutritional Provisioning Patterns in Dual-Obligate Bacteria.Genome biology and evolution · 2018Article
- Elucidation of the anti-hyperammonemic mechanism of Lactobacillus amylovorus JBD401 by comparative genomic analysis.BMC genomics · 2018Article
- The Divided Bacterial Genome: Structure, Function, and Evolution.Microbiology and molecular biology reviews : MMBR · 2017Review
- Free-Living EnterobacteriumEvolutionary bioinformatics online · 2017Article
- Evidence of horizontal gene transfer between obligate leaf nodule symbionts.The ISME journal · 2016Article
- Realizing Microbial Evolution.Cold Spring Harbor perspectives in biology · 2016Review
- Relation between tetR and tetA expression in tetracycline resistant Escherichia coli.BMC microbiology · 2016Article
5 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Because bacterial chromosomes are tightly packed with genes and were traditionally viewed as being optimized for size and replication speed, it was not surprising that the early annotations of sequenced bacterial genomes reported few, if any, pseudogenes. But because pseudogenes are generally recognized by comparisons with their functional counterparts, as more genome sequences accumulated, many bacterial pathogens were found to harbor large numbers of truncated, inactivated, and degraded genes. Because the mutational events that inactivate genes occur continuously in all genomes, we investigated whether the rarity of pseudogenes in some bacteria was attributable to properties inherent to the organism or to the failure to recognize pseudogenes. By developing a program suite (called Psi-Phi, for Psi-gene Finder) that applies a comparative method to identify pseudogenes (attributable both to misannotation and to nonrecognition), we analyzed the pseudogene inventories in the sequenced members of the Escherichia coli/Shigella clade. This approach recovered hundreds of previously unrecognized pseudogenes and showed that pseudogenes are a regular feature of bacterial genomes, even in those whose original annotations registered no truncated or otherwise inactivated genes. In Shigella flexneri 2a, large proportions of pseudogenes are generated by nonsense mutations and IS element insertions, events that seldom produce the pseudogenes present in the other genomes examined. Almost all (>95%) pseudogenes are restricted to only one of the genomes and are of relatively recent origin, suggesting that these bacteria possess active mechanisms to eliminate nonfunctional genes.
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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.