ArticlePLoS computational biology2011
A semi-quantitative, synteny-based method to improve functional predictions for hypothetical and poorly annotated bacterial and archaeal genes.
Article in PLoS computational biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 48 citations in OpenAlex.
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- OrthoRefine: automated enhancement of prior ortholog identification via synteny.BMC bioinformatics · 2024Article
- Genomic language model predicts protein co-regulation and function.Nature communications · 2024Article
- Genetic and Structural Diversity of Prokaryotic Ice-Binding Proteins from the Central Arctic Ocean.Genes · 2023Article
- A novel gene from the acidophilic bacterium Leptospirillum sp. CF-1 and its role in oxidative stress and chromate tolerance.Biological research · 2022Article
- Genomic Characterization Provides an Insight into the Pathogenicity of the Poplar Canker BacteriumGenes · 2021Article
- Comparative Genomics of the GenusFrontiers in microbiology · 2019Article
- Trajectories and Drivers of Genome Evolution in Surface-Associated Marine Phaeobacter.Genome biology and evolution · 2017Article
- Assessment of genome annotation using gene function similarity within the gene neighborhood.BMC bioinformatics · 2017Article
- Unexpected Dominance of Elusive Acidobacteria in Early Industrial Soft Coal Slags.Frontiers in microbiology · 2017Article
- Global genetic capacity for mixotrophy in marine picocyanobacteria.The ISME journal · 2016Article
- Clustering analysis of proteins from microbial genomes at multiple levels of resolution.BMC bioinformatics · 2016Article
- Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines.The ISME journal · 2016Article
- PanFP: pangenome-based functional profiles for microbial communities.BMC research notes · 2015Article
- Accurate, multi-kb reads resolve complex populations and detect rare microorganisms.Genome research · 2015Article
- Microbial diversity and metabolic networks in acid mine drainage habitats.Frontiers in microbiology · 2015Review
- Insyght: navigating amongst abundant homologues, syntenies and gene functional annotations in bacteria, it's that symbol!Nucleic acids research · 2014Article
- Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype.The ISME journal · 2014Article
- Interactions in the microbiome: communities of organisms and communities of genes.FEMS microbiology reviews · 2014Review
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
During microbial evolution, genome rearrangement increases with increasing sequence divergence. If the relationship between synteny and sequence divergence can be modeled, gene clusters in genomes of distantly related organisms exhibiting anomalous synteny can be identified and used to infer functional conservation. We applied the phylogenetic pairwise comparison method to establish and model a strong correlation between synteny and sequence divergence in all 634 available Archaeal and Bacterial genomes from the NCBI database and four newly assembled genomes of uncultivated Archaea from an acid mine drainage (AMD) community. In parallel, we established and modeled the trend between synteny and functional relatedness in the 118 genomes available in the STRING database. By combining these models, we developed a gene functional annotation method that weights evolutionary distance to estimate the probability of functional associations of syntenous proteins between genome pairs. The method was applied to the hypothetical proteins and poorly annotated genes in newly assembled acid mine drainage Archaeal genomes to add or improve gene annotations. This is the first method to assign possible functions to poorly annotated genes through quantification of the probability of gene functional relationships based on synteny at a significant evolutionary distance, and has the potential for broad application.
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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.