Horizontal Gene Acquisitions Contributed to Genome Expansion in Insect-Symbiotic Spiroplasma clarkii

Tsai, Yi-Ming; Chang, An; Kuo, Chih-Horng

doi:10.1093/gbe/evy113

Cited by 23 publications

(20 citation statements)

References 40 publications

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“…Such extensive HGT for re-shaping the gene content has been reported previously for Spiroplasma ( Lo et al. 2015 ), and the shared ecological niches as insect symbionts may have promoted the HGT between Spiroplasma and Entomoplasma / Mesoplasma ( Lo and Kuo 2017 ; Tsai et al. 2018 ).…”

Section: Discussionsupporting

confidence: 62%

Convergent Evolution among Ruminant-Pathogenic Mycoplasma Involved Extensive Gene Content Changes

Gasparich

Kuo

2018

Genome Biology and Evolution

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Convergent evolution, a process by which organisms evolved independently to have similar traits, provides opportunities to understand adaptation. The bacterial genus Mycoplasma contains multiple species that evolved independently to become ruminant pathogens, which represents an interesting study system for investigating the process. In this work, we determined the genome sequences of 11 Entomoplasma/Mesoplasma species. This new data set, together with the other available Mollicutes genomes, provided comprehensive taxon sampling for inferring the gene content evolution that led to the emergence of Mycoplasma Mycoides cluster. Our results indicated that the most recent common ancestor (MRCA) of the Mycoides-Entomoplasmataceae clade lost ∼15% of the core genes when it diverged from the Spiroplasma Apis clade. After this initial wave of genome reduction, relatively few gene gains or losses were inferred until the emergence of the Mycoides cluster. Compared with those Entomoplasmataceae lineages that maintained the association with insects, the MRCA of the Mycoides cluster experienced a second wave of gene losses, as well as acquiring >100 novel genes through horizontal gene transfer. These gene acquisitions involved many with the Mycoplasma Hominis/Pneumoniae lineages as the putative donors, suggesting that gene exchanges among these vertebrate symbionts with distinct phylogenetic affiliations may be important in the emergence of the Mycoides cluster. These findings demonstrated that the gene content of bacterial genomes could be exceedingly dynamic, even for those symbionts with highly reduced genomes. Moreover, the emergence of novel pathogens may involve extensive remodeling of gene content, rather than acquisition of few virulence genes.

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Section: Discussionsupporting

confidence: 62%

Convergent Evolution among Ruminant-Pathogenic Mycoplasma Involved Extensive Gene Content Changes

Gasparich

Kuo

2018

Genome Biology and Evolution

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“…Dynamic gains and losses via horizontal gene transfer through plasmids, phage, and other mobile genetic elements, appear to be very common in Spiroplasma (Lo and Kuo 2017; Tsai et al. 2018) and in defensive symbionts in general.…”

Section: Discussionmentioning

confidence: 99%

Toxin and Genome Evolution in aDrosophilaDefensive Symbiosis

Ballinger

Gawryluk

Perlman

2018

Genome Biology and Evolution

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Defenses conferred by microbial symbionts play a vital role in the health and fitness of their animal hosts. An important outstanding question in the study of defensive symbiosis is what determines long term stability and effectiveness against diverse natural enemies. In this study, we combine genome and transcriptome sequencing, symbiont transfection and parasite protection experiments, and toxin activity assays to examine the evolution of the defensive symbiosis between Drosophila flies and their vertically transmitted Spiroplasma bacterial symbionts, focusing in particular on ribosome-inactivating proteins (RIPs), symbiont-encoded toxins that have been implicated in protection against both parasitic wasps and nematodes. Although many strains of Spiroplasma, including the male-killing symbiont (sMel) of Drosophila melanogaster, protect against parasitic wasps, only the strain (sNeo) that infects the mycophagous fly Drosophila neotestacea appears to protect against parasitic nematodes. We find that RIP repertoire is a major differentiating factor between strains that do and do not offer nematode protection, and that sMel RIPs do not show activity against nematode ribosomes in vivo. We also discovered a strain of Spiroplasma infecting a mycophagous phorid fly, Megaselia nigra. Although both the host and its Spiroplasma are distantly related to D. neotestacea and its symbiont, genome sequencing revealed that the M. nigra symbiont encodes abundant and diverse RIPs, including plasmid-encoded toxins that are closely related to the RIPs in sNeo. Our results suggest that distantly related Spiroplasma RIP toxins may perform specialized functions with regard to parasite specificity and suggest an important role for horizontal gene transfer in the emergence of novel defensive phenotypes.

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“…The procedures for genome analysis were based on those described in our previous work Lo et al, 2013;Tsai et al, 2018). Briefly, the genome map was prepared by using Circos v0.69-6 (Krzywinski et al, 2009).…”

Section: Genome Analysismentioning

confidence: 99%

Comparative Genomic Analysis of a Novel Strain of Taiwan Hot-Spring Cyanobacterium Thermosynechococcus sp. CL-1

et al. 2020

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Thermosynechococcus is a genus of thermophilic unicellular cyanobacteria that are dominant in microbial mats at about 50-65 • C in alkaline hot springs of eastern Asia. We used PacBio SMRT Sequencing to sequence the complete genome of a novel strain of thermophilic cyanobacterium, Thermosynechococcus sp. CL-1, isolated from the Chin-Lun hot spring (pH 9.3, 62 • C) in Taiwan. Genome-scale phylogenetic analysis and average nucleotide identity (ANI) results suggested that CL-1 is a new species in the genus Thermosynechococcus. Comparative genome analysis revealed divergent genome structures of Thermosynechococcus strains. In addition, the distinct genetic differences between CL-1 and the other Thermosynechococcus strains are related to photosynthesis, transporters, signal transduction, the chaperone/usher system, nitric oxide protection, antibiotic resistance, prokaryotic immunity systems, and other physiological processes. This study suggests that Thermosynechococcus strains have actively acquired many putative horizontally transferred genes from other bacteria that enabled them to adapt to different ecological niches and stressful conditions in hot springs.

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Horizontal Gene Acquisitions Contributed to Genome Expansion in Insect-Symbiotic Spiroplasma clarkii

Cited by 23 publications

References 40 publications

Convergent Evolution among Ruminant-Pathogenic Mycoplasma Involved Extensive Gene Content Changes

Convergent Evolution among Ruminant-Pathogenic Mycoplasma Involved Extensive Gene Content Changes

Toxin and Genome Evolution in aDrosophilaDefensive Symbiosis

Comparative Genomic Analysis of a Novel Strain of Taiwan Hot-Spring Cyanobacterium Thermosynechococcus sp. CL-1

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