Partial Chromosome Sequence of Spiroplasma citri Reveals Extensive Viral Invasion and Important Gene Decay

Abstract

The assembly of 20,000 sequencing reads obtained from shotgun and chromosome-specific libraries of the Spiroplasma citri genome yielded 77 chromosomal contigs totaling 1,674 kbp (92%) of the 1,820-kbp chromosome. The largest chromosomal contigs were positioned on the physical and genetic maps constructed from pulsed-field gel electrophoresis and Southern blot hybridizations. Thirty-eight contigs were annotated, resulting in 1,908 predicted coding sequences (CDS) representing an overall coding density of only 74%. Cellular processes, cell metabolism, and structural-element CDS account for 29% of the coding capacity, CDS of external origin such as viruses and mobile elements account for 24% of the coding capacity, and CDS of unknown function account for 47% of the coding capacity. Among these, 21% of the CDS group into 63 paralog families. The organization of these paralogs into conserved blocks suggests that they represent potential mobile units. Phage-related sequences were particularly abundant and include plectrovirus SpV1 and SVGII3 and lambda-like SpV2 sequences. Sixty-nine copies of transposases belonging to four insertion sequence (IS) families (IS30, IS481, IS3, and ISNCY) were detected. Similarity analyses showed that 21% of chromosomal CDS were truncated compared to their bacterial orthologs. Transmembrane domains, including signal peptides, were predicted for 599 CDS, of which 58 were putative lipoproteins. S. citri has a Sec-dependent protein export pathway. Eighty-four CDS were assigned to transport, such as phosphoenolpyruvate phosphotransferase systems (PTS), the ATP binding cassette (ABC), and other transporters. Besides glycolytic and ATP synthesis pathways, it is noteworthy that S. citri possesses a nearly complete pathway for the biosynthesis of a terpenoid.

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

“…Based on the results reported in the literature (Carle et al. 2010; Thiaucourt et al. 2011; Alexeev et al.…”

Minimal genomes of mycoplasma-related endobacteria are plastic and contain host-derived genes for sustained life within Glomeromycota

“…The unusually high copy number of the XerC/D genes, combined with the AT richness of MRE genomes, increases the likelihood of Xer recombinase target sites and suggests that Xer recombinase is important for the chromosome structure and plasticity of MRE genomes. In addition to mobile elements and recombination events as factors responsible for genome plasticity (SI Appendix, Table S2), the genomes of MRE-CE and MRE-RV display evidence of a historical invasion by plectrovirus, a phage known to infect Spiroplasma species (17). Although the MRE genomes harbor only partial plectroviral genes, some genomic rearrangements may be a result of past phage activity, as seen in the Spiroplasma genomes.…”