ArticleCurrent microbiology2012
Codon usage methods for horizontal gene transfer detection generate an abundance of false positive and false negative results.
Article in Current microbiology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Comparative transcriptomics and scarless genome editing uncover a periplasmicApplied and environmental microbiology · 2026Article
- Natural Selection Drives AT-Biased Codon Usage in Mitochondrial Genomes of Early-DivergingJournal of fungi (Basel, Switzerland) · 2026Article
- Mechanisms, detection, and impact of horizontal gene transfer in plant functional evolution.The Plant cell · 2025Review
- Current state and future prospects of Horizontal Gene Transfer detection.NAR genomics and bioinformatics · 2025Review
- Machine learning classifiers predict key genomic and evolutionary traits across the kingdoms of life.Scientific reports · 2023Article
- Current Methods for Recombination Detection in Bacteria.International journal of molecular sciences · 2022Review
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- Recombination and gene loss occur simultaneously during bacterial horizontal gene transfer.PloS one · 2020Article
- The genome of a subterrestrial nematode reveals adaptations to heat.Nature communications · 2019Article
- Genome Comparisons of Wild Isolates of Caulobacter crescentus Reveal Rates of Inversion and Horizontal Gene Transfer.Current microbiology · 2019Article
- Origin of microbial biomineralization and magnetotaxis during the Archean.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- AS3MT-mediated tolerance to arsenic evolved by multiple independent horizontal gene transfers from bacteria to eukaryotes.PloS one · 2017Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacteria acquire new DNA in a process known as horizontal gene transfer (HGT). To investigate the evolutionary impact of this transfer of DNA, various methods have been developed to detect past HGT events. For example, codon usage-based methods detect the presence of transferred genes by identifying atypical patterns of codon usage. However, some inherited genes exhibit atypical codon usage and some transferred genes have codon usage patterns similar to those of the inherited genes. In this study, we used a comparative phylogenetic approach with Methylobacterium and Caulobacter species to demonstrate that even well-designed codon usage methods fail to detect many HGT events and generate a high rate of false positives (60-75 %) and false negatives (23-61 %). Therefore, we recommend caution when employing codon usage methods to identify transferred genes and suggest that the rapidly increasing availability of bacterial genome sequences makes the phylogenetic approach the method of choice.
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