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

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.Spiroplasmas are arthropod-associated bacteria belonging to the class Mollicutes, a group of wall-less microorganisms phylogenetically related to low-G+C-content, Gram-positive bacteria (51). Spiroplasma citri is a helical plant-pathogenic mollicute responsible for the “stubborn” disease of citrus (39). It inhabits the phloem sap of infected plants to which it is transmitted by sap-sucking hemipteran insect in a circulative and propagative manner (31, 32). S. citri can infect a wide range of plant species, including crop and wild plants, as it is transmitted by polyphagous leafhoppers (13). Spiroplasmas are available in pure culture, and their study has therefore benefited from the use of molecular genetics. In particular, the relationships of spiroplasmas with their two hosts, the plant and the leafhopper vector, have been extensively studied (11, 22). In S. citri, the inactivation of genes and functional complementation of mutants have shown that (i) fructose consumption by the spiroplasma is a major cause for symptom production in plants, (ii) the solute binding protein of a putative ABC-type transporter is involved in the insect transmission process, and (iii) spiralin, the major membrane protein, is not essential for helicity, motility, and pathogenicity but is required for efficient transmission by the leafhopper vector (10, 19, 23, 24, 28). To characterize other spiroplasma genes potentially involved in insect transmission and pathogenicity, the genome of S. citri strain GII3-3X is currently being deciphered.The S. citri genome is characterized by an abundance of extrachromosomal elements, including seven plasmids, pSciA and pSci1 to pSci6, present as 10 to 14 copies per cell. These plasmids are vertically inherited, but some of them could also be horizontally transferred, as they encode proteins involved in partitioning and the cell-to-cell transfer of DNA molecules (12, 40). Plasmids pSci1 to pSci5 encode surface proteins of the S. citri adhesion-related protein (ScARP) family, and pSci6 was previously shown to confer insect transmissibility (9). Therefore, it is likely that the abundance and diversity of plasmids could provide S. citri strain GII3-3X with the ability to quickly adapt to various vector insects and, hence, to be transmitted to diverse host plants. However, chromosome-encoded determinants are also expected to play a role in spiroplasma biology. In S. citri, the chromosome sizes vary from 1.6 to 1.9 Mbp among strains (53, 54), and part of the size variation is thought to result from different amounts of prophage sequences (35). Many S. citri strains are infected by single-stranded DNA-containing filamentous phages (Plectrovirus), whose sequences also occur as partial or full-length prophages integrated into the spiroplasma chromosome (7, 35, 38). Here we report the partial chromosome sequence of S. citri strain GII3-3X and the functional assignment of the predicted coding sequences.