An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales

BMC Evolutionary Biology
Phuong Thi LePierre Pontarotti

Abstract

Horizontal 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. We 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...Continue Reading

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Citations

Mar 20, 2014·PloS One·Ana M S GuimaraesJoanne B Messick
Sep 17, 2014·Biology Direct·Mohamed SassiMichel Drancourt
Jan 28, 2014·Trends in Microbiology·Phuong Thi LeDidier Raoult
Apr 25, 2015·Environmental Microbiology·Frederik SchulzMatthias Horn
Jul 24, 2014·Environmental Microbiology·Mathieu SicardChristine Braquart-Varnier
Mar 10, 2017·BMC Evolutionary Biology·Sandrine PinosVicky Merhej

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Methods Mentioned

BETA
gene exchange

Software Mentioned

FigTree
FIGENIX
Blast filter
- PUZZLE
PhyloPattern
PAUP
TREE
MUSCLE
stringenet FIGENIX
Phylobayes

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