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

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.

Whole-genome re-sequencing of non-model organisms: lessons from unmapped reads

“…Although at the nucleotide level, these contigs showed weak similarity to available Spiroplasma genomes, at the protein level their relationship with Mollicute (and mainly Spiroplasma) proteins was confirmed for 546 annotated genes (on contigs summing to 780 kb). Moreover, the assembly size, low GC content (24%) and the fragmented assembly were consistent with known Spiroplasma genome features: the genome size varies from 1.4 to 1.9 Mb, GC content is around 26%, and the genomes contain lots of repeated sequences and viral elements that make the assembly task harder (Carle et al, 2010;Lo et al, 2013). Additionally, a phylogenetic analysis of its 16S RNA gene confirmed its membership to the Spiroplasma genus and the absence of any close relative with a complete genome available in the databases (Supplementary Figure S2 in Supplementary Material).…”

Winding paths to simplicity: genome evolution in facultative insect symbionts

“…2003), the procedure of data analysis is based on that described in Lo et al. (2013a). Not all genomes listed in Table 1 are included for the following reasons: for closely related Spiroplasma species with nearly identical patterns, only few representatives are selected; for other genera, several draft genomes are omitted because the sequence records obtained from GenBank lack annotation of genes.…”

“…melliferum have a genome-wide nucleotide sequence identity of 99%, yet extensive rearrangements were found in their genome alignment (Lo et al. 2013a). Moreover, general genomic characteristics such as chromosome size, GC content, coding density and gene number all varied considerable among these closely related species (Table 1).…”

“…2013), and may have promoted their ecological diversification (Lo et al. 2013a; Paredes et al. 2015).…”

“…2010; Lo et al. 2013a). In addition to the 1504 full-length CDSs annotated, there are 401 putative pseudogenes annotated as truncated CDSs.…”