Analysis of gene gain and loss in the evolution of predatory bacteria

Li, Nan; Wang, Kai; Williams, Henry N.; Sun, Jun; Ding, Chan; Leng, Xiaoyun

doi:10.1016/j.gene.2016.10.039

Cited by 23 publications

(25 citation statements)

References 49 publications

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“…The trend toward massive gene loss suggested that gene loss might play an important role in the adaptive evolution of P. shigelloides . Gene gain and loss are also associated with functional change ( 29 ). The contracted families were enriched in “K: transcription” (104, 7.1%), “M: cell wall/membrane/envelope biogenesis” (102, 7.0%), “N: cell motility” (97, 6.6%), and “E: amino acid transport and metabolism” (94, 6.4%).…”

Section: Resultsmentioning

confidence: 99%

Horizontal Gene Transfer Clarifies Taxonomic Confusion and Promotes the Genetic Diversity and Pathogenicity of Plesiomonas shigelloides

Yin

Zhang

et al. 2020

mSystems

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Plesiomonas shigelloides is an emerging pathogen that has been shown to be involved in gastrointestinal diseases and extraintestinal infections in humans. However, the taxonomic position, evolutionary dynamics, and pathogenesis of P. shigelloides remain unclear. We reported the draft genome sequences of 12 P. shigelloides strains representing different serogroups. We were able to determine a clear distinction between P. shigelloides and other members of Enterobacterales via core genome phylogeny, Neighbor-Net network, and average genome identity analysis. The pan-genome analysis of P. shigelloides revealed extensive genetic diversity and presented large flexible gene repertoires, while the core genome phylogeny exhibited a low level of clonality. The discordance between the core genome phylogeny and the pan-genome phylogeny indicated that flexible accessory genomes account for an important proportion of the evolution of P. shigelloides, which was subsequently characterized by determinations of hundreds of horizontally transferred genes (horizontal genes), massive gene expansions and contractions, and diverse mobile genetic elements (MGEs). The apparently high levels of horizontal gene transfer (HGT) in P. shigelloides were conferred from bacteria with novel properties from other taxa (mainly Vibrionaceae and Aeromonadaceae), which caused the historical taxonomic confusion and shaped the virulence gene pools. Furthermore, P. shigelloides genomes contain many macromolecular secretion system genes, virulence factor genes, and resistance genes, indicating its potential to cause intestinal and invasive infections. Collectively, our work provides insights into the phylogenetic position, evolutionary dynamic, and pathogenesis of P. shigelloides at the genomic level, which could facilitate the observation and research of this important pathogen. IMPORTANCE The taxonomic position of P. shigelloides has been the subject of debate for a long time, and until now, the evolutionary dynamics and pathogenesis of P. shigelloides were unclear. In this study, pan-genome analysis indicated extensive genetic diversity and the presence of large and variable gene repertoires. Our results revealed that horizontal gene transfer was the focal driving force for the genetic diversity of the P. shigelloides pan-genome and might have contributed to the emergence of novel properties. Vibrionaceae and Aeromonadaceae were found to be the predominant donor taxa for horizontal genes, which might have caused the taxonomic confusion historically. Comparative genomic analysis revealed the potential of P. shigelloides to cause intestinal and invasive diseases. Our results could advance the understanding of the evolution and pathogenesis of P. shigelloides, particularly in elucidating the role of horizontal gene transfer and investigating virulence-related elements.

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Section: Resultsmentioning

confidence: 99%

Horizontal Gene Transfer Clarifies Taxonomic Confusion and Promotes the Genetic Diversity and Pathogenicity of Plesiomonas shigelloides

Yin

Zhang

et al. 2020

mSystems

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“…The fact that gene contraction remained greater than expansion suggests that loss of function has an important role in functional evolution and reflects probable vertical descent in most known genomes. Previous studies have reported that gene gain and loss are two contributors to functional change (42). Importantly, the expanded gene families by external branches were enriched in “cell wall/membrane/envelope biogenesis” (Fisher’s exact test P value = 0.03) and “cell motility” (Fisher’s exact test P value < 0.001), functions related to cellular processes and signaling (Fig.…”

Section: Resultsmentioning

confidence: 99%

Comprehensive Analysis Reveals the Evolution and Pathogenicity of Aeromonas , Viewed from Both Single Isolated Species and Microbial Communities

et al. 2019

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Aeromonas has long been known as a gastrointestinal pathogen, yet it has many species whose evolutionary dynamics and genetic diversity had been unclear until now. We have conducted pan-genome analysis for 29 Aeromonas species and revealed a high level of genome plasticity exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. These species also contained many virulence factors both identified from single isolated species and microbial community. This pan-genome study could elevate the level for detection and prevention of Aeromonas infections.

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“…For instance, changes in the environment can result in gene loss [66] due to the relaxation of purifying selection, and can also reduce fitness costs [67]. Likewise, gene gain has been associated with environmental adaptation [68]. The patterns observed in freeliving bacteria are likely also present in pathogens such as X. fastidiosa, where environmental changes are analogue to host switch events.…”

Section: Discussionmentioning

confidence: 99%

Impacts of local population history and ecology on the evolution of a globally dispersed pathogen

et al. 2020

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Background: Pathogens with a global distribution face diverse biotic and abiotic conditions across populations. Moreover, the ecological and evolutionary history of each population is unique. Xylella fastidiosa is a xylem-dwelling bacterium infecting multiple plant hosts, often with detrimental effects. As a group, X. fastidiosa is divided into distinct subspecies with allopatric historical distributions and patterns of multiple introductions from numerous source populations. The capacity of X. fastidiosa to successfully colonize and cause disease in naïve plant hosts varies among subspecies, and potentially, among populations. Within Central America (i.e. Costa Rica) two X. fastidiosa subspecies coexist: the native subsp. fastidiosa and the introduced subsp. pauca. Using whole genome sequences, the patterns of gene gain/loss, genomic introgression, and genetic diversity were characterized within Costa Rica and contrasted to other X. fastidiosa populations. Results: Within Costa Rica, accessory and core genome analyses showed a highly malleable genome with numerous intra-and inter-subspecific gain/loss events. Likewise, variable levels of inter-subspecific introgression were found within and between both coexisting subspecies; nonetheless, the direction of donor/recipient subspecies to the recombinant segments varied. Some strains appeared to recombine more frequently than others; however, no group of genes or gene functions were overrepresented within recombinant segments. Finally, the patterns of genetic diversity of subsp. fastidiosa in Costa Rica were consistent with those of other native populations (i.e. subsp. pauca in Brazil). Conclusions: Overall, this study shows the importance of characterizing local evolutionary and ecological history in the context of worldwide pathogen distribution.

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Analysis of gene gain and loss in the evolution of predatory bacteria

Cited by 23 publications

References 49 publications

Horizontal Gene Transfer Clarifies Taxonomic Confusion and Promotes the Genetic Diversity and Pathogenicity of Plesiomonas shigelloides

Horizontal Gene Transfer Clarifies Taxonomic Confusion and Promotes the Genetic Diversity and Pathogenicity of Plesiomonas shigelloides

Comprehensive Analysis Reveals the Evolution and Pathogenicity of Aeromonas , Viewed from Both Single Isolated Species and Microbial Communities

Impacts of local population history and ecology on the evolution of a globally dispersed pathogen

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