ArticleGenetics2010
Inferring bacterial genome flux while considering truncated genes.
Article in Genetics, 2010. 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.
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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, 12 citations in OpenAlex.
- Comparative Genome Analysis of 19Antibiotics (Basel, Switzerland) · 2022Article
- Differences in genetic flux in invasiveHeliyon · 2022Article
- Origin and Spread of Spliceosomal Introns: Insights from the Fungal Clade Zymoseptoria.Genome biology and evolution · 2017Article
- The Divided Bacterial Genome: Structure, Function, and Evolution.Microbiology and molecular biology reviews : MMBR · 2017Review
- Complete Genome Analysis ofFrontiers in microbiology · 2017Article
- Inferring horizontal gene transfer.PLoS computational biology · 2015Article
- DiscML: an R package for estimating evolutionary rates of discrete characters using maximum likelihood.BMC bioinformatics · 2014Article
- Horizontal transfer and gene conversion as an important driving force in shaping the landscape of mitochondrial introns.G3 (Bethesda, Md.) · 2014Article
- Homologous recombination drives both sequence diversity and gene content variation in Neisseria meningitidis.Genome biology and evolution · 2013Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacterial gene content variation during the course of evolution has been widely acknowledged and its pattern has been actively modeled in recent years. Gene truncation or gene pseudogenization also plays an important role in shaping bacterial genome content. Truncated genes could also arise from small-scale lateral gene transfer events. Unfortunately, the information of truncated genes has not been considered in any existing mathematical models on gene content variation. In this study, we developed a model to incorporate truncated genes. Maximum-likelihood estimates (MLEs) of the new model reveal fast rates of gene insertions/deletions on recent branches, suggesting a fast turnover of many recently transferred genes. The estimates also suggest that many truncated genes are in the process of being eliminated from the genome. Furthermore, we demonstrate that the ignorance of truncated genes in the estimation does not lead to a systematic bias but rather has a more complicated effect. Analysis using the new model not only provides more accurate estimates on gene gains/losses (or insertions/deletions), but also reduces any concern of a systematic bias from applying simplified models to bacterial genome evolution. Although not a primary purpose, the model incorporating truncated genes could be potentially used for phylogeny reconstruction using gene family content.
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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.