ArticleBMC bioinformatics2010
Gene-centric association analysis for the correlation between the guanine-cytosine content levels and temperature range conditions of prokaryotic species.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
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- Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets.Communications biology · 2025Article
- Hot spring distribution and survival mechanisms of thermophilic comammox Nitrospira.The ISME journal · 2023Article
- Comparative genomics reveals intraspecific divergence ofMicrobial genomics · 2023Article
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- Genomes of NovelApplied and environmental microbiology · 2021Article
- Genomic adaptations enabling Acidithiobacillus distribution across wide-ranging hot spring temperatures and pHs.Microbiome · 2021Article
- Design and assembly of DNA molecules using multi-objective optimization.Synthetic biology (Oxford, England) · 2021Article
- Vestiges of Adaptation to the Mesophilic Environment in the Genome of Tepiditoga spiralis gen. nov., sp. nov.Microbes and environments · 2020Article
- Predicting the optimal growth temperatures of prokaryotes using only genome derived features.Bioinformatics (Oxford, England) · 2019Article
- The nucleotide composition of microbial genomes indicates differential patterns of selection on core and accessory genomes.BMC genomics · 2017Article
- Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes.Computational and structural biotechnology journal · 2017Article
- Rapid Bioinformatic Identification of Thermostabilizing Mutations.Biophysical journal · 2015Article
- Variation, evolution, and correlation analysis of C+G content and genome or chromosome size in different kingdoms and phyla.PloS one · 2014Article
- Identification and analysis of putative promoter motifs in bovine herpes virus.Bioinformation · 2012Article
- Bayesian prediction of bacterial growth temperature range based on genome sequences.BMC genomics · 2012Article
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2 authors.
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Abstract
backgroundThe environment has been playing an instrumental role in shaping and maintaining the morphological, physiological and biochemical diversities of prokaryotes. It has been debatable whether the whole-genome Guanine-Cytosine (GC) content levels of prokaryotic organisms are correlated with their optimal growth temperatures. Since the GC content is variable within a genome, we here focus on the correlation between the genic GC content levels and the temperature range conditions of prokaryotic organisms.
resultsThe GC content levels in the coding regions of four genes were consistently identified as correlated with the temperature range condition when the association analysis was applied to (i) the 722 mesophilic and 93 thermophilic/hyperthermophilic organisms regardless of their phylogeny, oxygen requirement, salinity, or habitat conditions, and (ii) partial lists of organisms when organisms with certain phylogeny, oxygen requirement, salinity or habitat conditions were excluded. These four genes are K01251 (adenosylhomocysteinase), K03724 (DNA repair and recombination proteins), K07588 (LAO/AO transport system kinase), and K09122 (hypothetical protein).To further validate the identified correlation relationships, we examined to what extent the temperature range condition of an organism can be predicted based on the GC content levels in the coding regions of the selected genes. The 84.52% accuracy for the complete genomes, the 84.09% accuracy for the in-progress genomes, and 82.70% accuracy for the metagenomes, especially when being compared to the 50% accuracy rendered by random guessing, suggested that the temperature range condition of a prokaryotic organism can generally be predicted based on the GC content levels of the selected genomic regions.
conclusionsThe results rendered by various statistical tests and prediction tests indicated that the GC content levels of the coding/non-coding regions of certain genes are highly likely to be correlated with the temperature range conditions of prokaryotic organisms. Therefore, it is promising to carry out "reverse ecology" and to complete the ecological characterizations of prokaryotic organisms, i.e., to infer their temperature range conditions based on the GC content levels of certain genomic regions.
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