ArticleBMC evolutionary biology2012
An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales.
Article in BMC evolutionary biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Conceptual risk assessment of mosquito population modification gene-drive systems to control malaria transmission: preliminary hazards list workshops.Frontiers in bioengineering and biotechnology · 2023Article
- Horizontal gene transfer contributes to virulence and antibiotic resistance of Vibrio harveyi 345 based on complete genome sequence analysis.BMC genomics · 2019Article
- Identification of constraints influencing the bacterial genomes evolution in the PVC super-phylum.BMC evolutionary biology · 2017Article
- The Phylogeny of Rickettsia Using Different Evolutionary Signatures: How Tree-Like is Bacterial Evolution?Systematic biology · 2016Article
- Mycobacteriophage-drived diversification of Mycobacterium abscessus.Biology direct · 2014Article
- Phylogenomic study indicates widespread lateral gene transfer in Entamoeba and suggests a past intimate relationship with parabasalids.Genome biology and evolution · 2014Article
- HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers.BMC genomics · 2014Article
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8 authors.
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Abstract
backgroundHorizontal gene transfer (HGT) is considered to be a major force driving the evolutionary history of prokaryotes. HGT is widespread in prokaryotes, contributing to the genomic repertoire of prokaryotic organisms, and is particularly apparent in Rickettsiales genomes. Gene gains from both distantly and closely related organisms play crucial roles in the evolution of bacterial genomes. In this work, we focus on genes transferred from distantly related species into Rickettsiales species.
resultsWe developed an automated approach for the detection of HGT from other organisms (excluding alphaproteobacteria) into Rickettsiales genomes. Our systematic approach consisted of several specialized features including the application of a parsimony method for inferring phyletic patterns followed by blast filter, automated phylogenetic reconstruction and the application of patterns for HGT detection. We identified 42 instances of HGT in 31 complete Rickettsiales genomes, of which 38 were previously unidentified instances of HGT from Anaplasma, Wolbachia, Candidatus Pelagibacter ubique and Rickettsia genomes. Additionally, putative cases with no phylogenetic support were assigned gene ontology terms. Overall, these transfers could be characterized as "rhizome-like".
conclusionsOur analysis provides a comprehensive, systematic approach for the automated detection of HGTs from several complete proteome sequences that can be applied to detect instances of HGT within other genomes of interest.
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