Genetic Variation and Preliminary Indications of Divergent Niche Adaptation in Cryptic Clade II of Escherichia
| Autor: | Stanley C.K. Lau, Zhi Yong Shen, Xiu Pei Koh, Yan Ping Yu |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
Microbiology (medical)
Escherichia Population ecotype Biology Microbiology Genome Article 03 medical and health sciences Virology Genetic variation education Clade lcsh:QH301-705.5 030304 developmental biology 0303 health sciences education.field_of_study cryptic clades 030306 microbiology fungi bitscore biology.organism_classification lcsh:Biology (General) Evolutionary biology genetic variation Adaptation Niche adaptation Functional divergence |
| Zdroj: | Microorganisms Microorganisms, Vol 8, Iss 1713, p 1713 (2020) Volume 8 Issue 11 |
| ISSN: | 2076-2607 |
| Popis: | The evolution, habitat, and lifestyle of the cryptic clade II of Escherichia, which were first recovered at low frequency from non-human hosts and later from external environments, were poorly understood. Here, the genomes of selected strains were analyzed for preliminary indications of ecological differentiation within their population. We adopted the delta bitscore metrics to detect functional divergence of their orthologous genes and trained a random forest classifier to differentiate the genomes according to habitats (gastrointestinal vs external environment). Model was built with inclusion of other Escherichia genomes previously demonstrated to have exhibited genomic traits of adaptation to one of the habitats. Overall, gene degradation was more prominent in the gastrointestinal strains. The trained model correctly classified the genomes, identifying a set of predictor genes that were informative of habitat association. Functional divergence in many of these genes were reflective of ecological divergence. Accuracy of the trained model was confirmed by its correct prediction of the habitats of an independent set of strains with known habitat association. In summary, the cryptic clade II of Escherichia displayed genomic signatures that are consistent with divergent adaptation to gastrointestinal and external environments. |
| Databáze: | OpenAIRE |
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