title: 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.
authors.affiliation: UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, Villenave d'Ornon Cedex, France.
authors.forename: Patricia
authors.initials: P
authors.lastname: Carle
authors.forename: Colette
authors.initials: C
authors.lastname: Saillard
authors.forename: Nathalie
authors.initials: N
authors.lastname: Carrère
authors.forename: Sébastien
authors.initials: S
authors.lastname: Carrère
authors.forename: Sybille
authors.initials: S
authors.lastname: Duret
authors.forename: Sandrine
authors.initials: S
authors.lastname: Eveillard
authors.forename: Patrice
authors.initials: P
authors.lastname: Gaurivaud
authors.forename: Géraldine
authors.initials: G
authors.lastname: Gourgues
authors.forename: Jérome
authors.initials: J
authors.lastname: Gouzy
authors.forename: Pascal
authors.initials: P
authors.lastname: Salar
authors.forename: Eric
authors.initials: E
authors.lastname: Verdin
authors.forename: Marc
authors.initials: M
authors.lastname: Breton
authors.forename: Alain
authors.initials: A
authors.lastname: Blanchard
authors.forename: Frédéric
authors.initials: F
authors.lastname: Laigret
authors.forename: Joseph-Marie
authors.initials: JM
authors.lastname: Bové
authors.forename: Joel
authors.initials: J
authors.lastname: Renaudin
authors.forename: Xavier
authors.initials: X
authors.lastname: Foissac
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D001435:Bacteriophages / Q000235:genetics*; D002876:Chromosomes, Bacterial / Q000235:genetics* / Q000821:virology*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D020071:Interspersed Repetitive Sequences; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion; D045642:Spiroplasma citri / Q000235:genetics* / Q000821:virology*; D019895:Transposases / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D019895:Transposases