Comparative genome analysis of Spiroplasma melliferumIPMB4A, a honeybee-associated bacterium

Ling-Ling Chen,Wan-Chia Chung,Wen-Sui Lo,Gail E Gasparich,Chih-Horng Kuo

doi:10.1186/1471-2164-14-22

Abstract

BackgroundThe genus Spiroplasma contains a group of helical, motile, and wall-less bacteria in the class Mollicutes. Similar to other members of this class, such as the animal-pathogenic Mycoplasma and the plant-pathogenic ‘Candidatus Phytoplasma’, all characterized Spiroplasma species were found to be associated with eukaryotic hosts. While most of the Spiroplasma species appeared to be harmless commensals of insects, a small number of species have evolved pathogenicity toward various arthropods and plants. In this study, we isolated a novel strain of honeybee-associated S. melliferum and investigated its genetic composition and evolutionary history by whole-genome shotgun sequencing and comparative analysis with other Mollicutes genomes.ResultsThe whole-genome shotgun sequencing of S. melliferum IPMB4A produced a draft assembly that was ~1.1 Mb in size and covered ~80% of the chromosome. Similar to other Spiroplasma genomes that have been studied to date, we found that this genome contains abundant repetitive sequences that originated from plectrovirus insertions. These phage fragments represented a major obstacle in obtaining a complete genome sequence of Spiroplasma with the current sequencing technology. Comparative analysis of S. melliferum IPMB4A with other Spiroplasma genomes revealed that these phages may have facilitated extensive genome rearrangements in these bacteria and contributed to horizontal gene transfers that led to species-specific adaptation to different eukaryotic hosts. In addition, comparison of gene content with other Mollicutes suggested that the common ancestor of the SEM (Spiroplasma, Entomoplasma, and Mycoplasma) clade may have had a relatively large genome and flexible metabolic capacity; the extremely reduced genomes of present day Mycoplasma and ‘Candidatus Phytoplasma’ species are likely to be the result of independent gene losses in these lineages.ConclusionsThe findings in this study highlighted the significance of phage insertions and horizontal gene transfer in the evolution of bacterial genomes and acquisition of pathogenicity. Furthermore, the inclusion of Spiroplasma in comparative analysis has improved our understanding of genome evolution in Mollicutes. Future improvements in the taxon sampling of available genome sequences in this group are required to provide further insights into the evolution of these important pathogens of humans, animals, and plants.

Highlights

The genus Spiroplasma contains a group of helical, motile, and wall-less bacteria in the class Mollicutes
Serological tests were confirmatory for the molecular phylogeny and supported the close association of S. melliferum IPMB4A with other S. melliferum strains
Inspection of the gene lists suggested that this comparison of gene content provided results that were consistent with our expectations. We found that both S. melliferum KC3 and S. citri GII3-3X contained large numbers of genomespecific genes and shared 85 homologous gene clusters that were absent in S. melliferum IPMB4A

Summary

Introduction

The genus Spiroplasma contains a group of helical, motile, and wall-less bacteria in the class Mollicutes. Similar to other members of this class, such as the animal-pathogenic Mycoplasma and the plant-pathogenic ‘Candidatus Phytoplasma’, all characterized Spiroplasma species were found to be associated with eukaryotic hosts. Spiroplasma are more similar to ‘Candidatus Phytoplasma’ in terms of the ecological niches occupied, because both groups have complex life cycles that involve insect and plant hosts [4]. For this reason, comparative analysis of gene content among these three groups of Mollicutes can provide insights into host adaptation in these parasites [8]. Most of the pathogenic Spiroplasma species belong to the Citri-Chrysopicola-Mirum clade [3], notable examples include S. citri that causes the Citrus Stubborn Disease [9], S. kunkelii that causes the Corn Stunt Disease [10], S. phoeniceum that infects periwinkle [11], S. penaei that infects Pacific white shrimp [12,13], S. eriocheiris that infects Chinese mitten crab [14], and S. melliferum that infects honeybee [15]

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