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

Le, Phuong Thi; Ramulu, Hemalatha Golaconda; Guijarro, Laurent; Paganini, Julien; Gouret, Philippe; Chabrol, Olivier; Raoult, Didier; Pontarotti, Pierre

doi:10.1186/1471-2148-12-243

Cited by 13 publications

(27 citation statements)

References 90 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We compared the gene content of Jidaibacter with other Alphaproteobacteria (http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12881/suppinfo); in total, 330 clusters of orthologous groups (COGs) are shared between all members of the order Rickettsiales , which is similar to what was found previously (Fig. ; Le et al ., ). However, the Jidaibacter genome is markedly distinct from other Rickettsiales because (i) it contains the highest number of COGs shared with bacteria outside the order or unique to Jidaibacter ( n = 341), (ii) it encodes the highest number of singletons ( n = 451), i.e.…”

Section: Resultsmentioning

confidence: 97%

A Rickettsiales symbiont of amoebae with ancient features

Schulz

Martijn

Wascher

et al. 2015

Environmental Microbiology

View full text Add to dashboard Cite

The Rickettsiae comprise intracellular bacterial symbionts and pathogens infecting diverse eukaryotes. Here, we provide a detailed characterization of 'Candidatus Jidaibacter acanthamoeba', a rickettsial symbiont of Acanthamoeba. The bacterium establishes the infection in its amoeba host within 2 h where it replicates within vacuoles. Higher bacterial loads and accelerated spread of infection at elevated temperatures were observed. The infection had a negative impact on host growth rate, although no increased levels of host cell lysis were seen. Phylogenomic analysis identified this bacterium as member of the Midichloriaceae. Its 2.4 Mb genome represents the largest among Rickettsiales and is characterized by a moderate degree of pseudogenization and a high coding density. We found an unusually large number of genes encoding proteins with eukaryotic-like domains such as ankyrins, leucine-rich repeats and tetratricopeptide repeats, which likely function in host interaction. There are a total of three divergent, independently acquired type IV secretion systems, and 35 flagellar genes representing the most complete set found in an obligate intracellular Alphaproteobacterium. The deeply branching phylogenetic position of 'Candidatus Jidaibacter acanthamoeba' together with its ancient features place it closely to the rickettsial ancestor and helps to better understand the transition from a free-living to an intracellular lifestyle.

show abstract

Section: Resultsmentioning

confidence: 97%

A Rickettsiales symbiont of amoebae with ancient features

Schulz

Martijn

Wascher

et al. 2015

Environmental Microbiology

View full text Add to dashboard Cite

show abstract

“…The most in depth analysis was conducted on the Rickettsia dataset, because it affords comparisons to previous results obtained with a variety of methods [29, 36, 37, 39, 65, 66]. …”

Section: Methodsmentioning

confidence: 99%

“…The method was also tested on real genomic datasets from multiple organismal groups, as exemplified by Rickettsia , whose HGT patterns have been previously studied [36–41]. The consistency of these results was compared to those obtained by other methods, including sequence composition and phylogenetic approaches.…”

Section: Introductionmentioning

confidence: 99%

HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers

2014

View full text Add to dashboard Cite

BackgroundFirst pass methods based on BLAST match are commonly used as an initial step to separate the different phylogenetic histories of genes in microbial genomes, and target putative horizontal gene transfer (HGT) events. This will continue to be necessary given the rapid growth of genomic data and the technical difficulties in conducting large-scale explicit phylogenetic analyses. However, these methods often produce misleading results due to their inability to resolve indirect phylogenetic links and their vulnerability to stochastic events.ResultsA new computational method of rapid, exhaustive and genome-wide detection of HGT was developed, featuring the systematic analysis of BLAST hit distribution patterns in the context of a priori defined hierarchical evolutionary categories. Genes that fall beyond a series of statistically determined thresholds are identified as not adhering to the typical vertical history of the organisms in question, but instead having a putative horizontal origin. Tests on simulated genomic data suggest that this approach effectively targets atypically distributed genes that are highly likely to be HGT-derived, and exhibits robust performance compared to conventional BLAST-based approaches. This method was further tested on real genomic datasets, including Rickettsia genomes, and was compared to previous studies. Results show consistency with currently employed categories of HGT prediction methods. In-depth analysis of both simulated and real genomic data suggests that the method is notably insensitive to stochastic events such as gene loss, rate variation and database error, which are common challenges to the current methodology. An automated pipeline was created to implement this approach and was made publicly available at: https://github.com/DittmarLab/HGTector. The program is versatile, easily deployed, has a low requirement for computational resources.ConclusionsHGTector is an effective tool for initial or standalone large-scale discovery of candidate HGT-derived genes.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-717) contains supplementary material, which is available to authorized users.

show abstract

“…The M. abscessus tree was used as a reference to infer topologies in order to detect gene gain and lost as previously described [35]. The results were submitted to FIGENIX [36] for phylogenetic reconstruction within the DAGOBAH framework as previously described [35].…”

Section: Methodsmentioning

confidence: 99%

Mycobacteriophage-drived diversification of Mycobacterium abscessus

et al. 2014

Self Cite

View full text Add to dashboard Cite

BackgroundMycobacterium abscessus is an emerging opportunistic pathogen which diversity was acknowledged by the recent description of two subspecies accommodating M. abscessus, Mycobacterium bolletii and Mycobacterium massiliense isolates.ResultsHere, genome analysis found 1–8 prophage regions in 47/48 M. abscessus genomes ranging from small prophage-like elements to complete prophages. A total of 20,304 viral and phage proteins clustered into 853 orthologous groups. Phylogenomic and phylogenetic analyses based on prophage region homology found three main clusters corresponding to M. abscessus, M. bolletii and M. massiliense. Analysing 135 annotated Tape Measure Proteins found thirteen clusters and four singletons, suggesting that at least 17 mycobacteriophages had infected M. abscessus during its evolution. The evolutionary history of phages differed from that of their mycobacterial hosts. In particular, 33 phage-related proteins have been horizontally transferred within M. abscessus genomes. They comprise of an integrase, specific mycobacteriophage proteins, hypothetical proteins and DNA replication and metabolism proteins. Gene exchanges, loss and gains which occurred in M. abscessus genomes have been driven by several mycobacteriophages.ConclusionsThis analysis of phage-mycobacterium co-evolution suggests that mycobacteriophages are playing a key-role in the on-going diversification of M. abscessus.ReviewersThis article was reviewed by Eric Bapteste, Patrick Forterre and Eugene Koonin.

show abstract

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

Cited by 13 publications

References 90 publications

A Rickettsiales symbiont of amoebae with ancient features

A Rickettsiales symbiont of amoebae with ancient features

HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers

Mycobacteriophage-drived diversification of Mycobacterium abscessus

Contact Info

Product

Resources

About