Comparative Genomic and Phylogenetic Approaches to Characterize the Role of Genetic Recombination in Mycobacterial Evolution

Abstract

The genus Mycobacterium encompasses over one hundred named species of environmental and pathogenic organisms, including the causative agents of devastating human diseases such as tuberculosis and leprosy. The success of these human pathogens is due in part to their ability to rapidly adapt to their changing environment and host. Recombination is the fastest way for bacterial genomes to acquire genetic material, but conflicting results about the extent of recombination in the genus Mycobacterium have been reported. We examined a data set comprising 18 distinct strains from 13 named species for evidence of recombination. Genomic regions common to all strains (accounting for 10% to 22% of the full genomes of all examined species) were aligned and concatenated in the chromosomal order of one mycobacterial reference species. The concatenated sequence was screened for evidence of recombination using a variety of statistical methods, with each proposed event evaluated by comparing maximum-likelihood phylogenies of the recombinant section with the non-recombinant portion of the dataset. Incongruent phylogenies were identified by comparing the site-wise log-likelihoods of each tree using multiple tests. We also used a phylogenomic approach to identify genes that may have been acquired through horizontal transfer from non-mycobacterial sources. The most frequent associated lineages (and potential gene transfer partners) in the Mycobacterium lineage-restricted gene trees are other members of suborder Corynebacterinae, but more-distant partners were identified as well. In two examined cases of potentially frequent and habitat-directed transfer (M. abscessus to Segniliparus and M. smegmatis to Streptomyces), observed sequence distances were small and consistent with a hypothesis of transfer, while in a third case (M. vanbaalenii to Streptomyces) distances were larger. The analyses described here indicate that whereas evidence of recombination in core regions within the genus is relatively sparse, the acquisition of genes from non-mycobacterial lineages is a significant feature of mycobacterial evolution.

Genomic characterization of Nontuberculous Mycobacteria

“…Additionally, between-NTM recombination analysis of the core genes revealed no large (>1 kb) events, which is also indicative of no other large recombinations as these genes are spread through the genomes of each species. These results suggest that LGT has very little impact on mycobacterial genomes, perhaps even lower than has been previously reported42. The potential donors of these LGT-derived genes were found to derive from over 130 genera, primarily from the Actinobacteria and a small number of Beta-proteobacteria.…”

Genome sequencing and analysis of a novel recombinant porcine epidemic diarrhea virus strain from Henan, China

“…However, the CV777-based vaccine is not effective against the new PEDV variants circulated in China since 2011 [21]. Genetic recombination plays a critical role in virus evolution and presents one of the greatest challenges to prevent PEDV infection and combating PED because it introduces genetic variation that complicates vaccine development [22]. Divergence of PEDV is driven by genetic recombination, as in other coronaviruses.…”

“…2 Detection of potential recombination events in CH/HNQX-3/ 14 by RDP4. a Four major recombination breakpoints were located, respectively, at the ORF1a (nt 2769), S (nt 20,691 and nt 22,176), and N (nt 27,252) genes. The analysis was performed with an F84 distance model, a window size of 1000 base pairs and a step size of 200 base pairs.…”

“…Filled triangle indicates the CH/ HNQX-3/14 strain from this study (BJ-2011-1 and CH/JX-2/2013), cluster 2 (AH2012), cluster 3 (CH/ZMDZY/11), cluster 5 (LC), and cluster 7 (CV777 and DR13). The results showed that four putatively major recombinant breakpoints in the CH/HNQX-3/ 14 genome with a high degree of reliability were detected, which were located, respectively, at the ORF1a (nt 2, 769), S (nt 20, 691 and nt 22,176), and N (nt 27, 252) genes ( Fig. 2a; Table 2).…”

Detection of Horizontal Transfer of Housekeeping and Hydrocarbons Catabolism Genes in Bacterial Genus with Potential to Application in Bioremediation Process

“…The topologies are different among both tree and these with 16S gene tree. Gordonia, Nocardia and Rhodococcus are very near genus, however, appear no so much near on the rpoD tree, these genus appear in over half of the disrupted mycobacterial clans, suggesting relatively short-distance transfers of genetic material either into or out mycobacterial species [30]. The genus Gordonia and Nocardia are distinct only by ability of Gordonia representants may reduce nitrate, which not occur with Nocardia [31] [32].…”