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Genome sequence of Diplorickettsia massiliensis, an emerging Ixodes ricinus-associated human pathogen.

ABSTRACT: Diplorickettsia massiliensis is a gammaproteobacterium in the order Legionellales and an agent of tick-borne infection. We sequenced the genome from strain 20B, isolated from an Ixodes ricinus tick. The genome consists of a 1,727,973-bp chromosome but no plasmid and includes 2,269 protein-coding genes and 42 RNA genes, including 3 rRNA genes.

SUBMITTER: Mathew MJ

PROVIDER: S-EPMC3370879 | biostudies-literature | 2012 Jun

REPOSITORIES: biostudies-literature

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Genome sequence of Diplorickettsia massiliensis, an emerging Ixodes ricinus-associated human pathogen.

Mathew Mano J MJ Subramanian Geetha G Nguyen Thi-Tien TT Robert Catherine C Mediannikov Oleg O Fournier Pierre-Edouard PE Raoult Didier D

Journal of bacteriology 20120601 12

Diplorickettsia massiliensis is a gammaproteobacterium in the order Legionellales and an agent of tick-borne infection. We sequenced the genome from strain 20B, isolated from an Ixodes ricinus tick. The genome consists of a 1,727,973-bp chromosome but no plasmid and includes 2,269 protein-coding genes and 42 RNA genes, including 3 rRNA genes. ...[more]

PMID: 22628513

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Project description:BACKGROUNDGlobal warming and other ecological changes have facilitated the expansion of Ixodes ricinus tick populations. Ixodes ricinus is the most important carrier of vector-borne pathogens in Europe, transmitting viruses, protozoa and bacteria, in particular Borrelia burgdorferi (sensu lato), the causative agent of Lyme borreliosis, the most prevalent vector-borne disease in humans in the Northern hemisphere. To faster control this disease vector, a better understanding of the I. ricinus tick is necessary. To facilitate such studies, we recently published the first reference genome of this highly prevalent pathogen vector. Here, we further extend these studies by scaffolding and annotating the first reference genome by using ultra-long sequencing reads from third generation single molecule sequencing. In addition, we present the first genome size estimation for I. ricinus ticks and the embryo-derived cell line IRE/CTVM19.RESULTS235,953 contigs were integrated into 204,904 scaffolds, extending the currently known genome lengths by more than 30% from 393 to 516 Mb and the N50 contig value by 87% from 1643 bp to a N50 scaffold value of 3067 bp. In addition, 25,263 sequences were annotated by comparison to the tick's North American relative Ixodes scapularis. After (conserved) hypothetical proteins, zinc finger proteins, secreted proteins and P450 coding proteins were the most prevalent protein categories annotated. Interestingly, more than 50% of the amino acid sequences matching the homology threshold had 95-100% identity to the corresponding I. scapularis gene models. The sequence information was complemented by the first genome size estimation for this species. Flow cytometry-based genome size analysis revealed a haploid genome size of 2.65Gb for I. ricinus ticks and 3.80 Gb for the cell line.CONCLUSIONSWe present a first draft sequence map of the I. ricinus genome based on a PacBio-Illumina assembly. The I. ricinus genome was shown to be 26% (500 Mb) larger than the genome of its American relative I. scapularis. Based on the genome size of 2.65 Gb we estimated that we covered about 67% of the non-repetitive sequences. Genome annotation will facilitate screening for specific molecular pathways in I. ricinus cells and provides an overview of characteristics and functions.

Project description:BackgroundUsing a combination of pyrosequencing and conventional Sanger sequencing, the complete genome sequence of the recently described novel Brucella species, Brucella microti, was determined. B. microti is a member of the genus Brucella within the Alphaproteobacteria, which consists of medically important highly pathogenic facultative intracellular bacteria. In contrast to all other Brucella species, B. microti is a fast growing and biochemically very active microorganism with a phenotype more similar to that of Ochrobactrum, a facultative human pathogen. The atypical phenotype of B. microti prompted us to look for genomic differences compared to other Brucella species and to look for similarities with Ochrobactrum.ResultsThe genome is composed of two circular chromosomes of 2,117,050 and 1,220,319 base pairs. Unexpectedly, we found that the genome sequence of B. microti is almost identical to that of Brucella suis 1330 with an overall sequence identity of 99.84% in aligned regions. The most significant structural difference between the two genomes is a bacteriophage-related 11,742 base pairs insert only present in B. microti. However, this insert is unlikely to have any phenotypical consequence. Only four protein coding genes are shared between B. microti and Ochrobactrum anthropi but impaired in other sequenced Brucella. The most noticeable difference between B. microti and other Brucella species was found in the sequence of the 23S ribosomal RNA gene. This unusual variation could have pleiotropic effects and explain the fast growth of B. microti.ConclusionContrary to expectations from the phenotypic analysis, the genome sequence of B. microti is highly similar to that of known Brucella species, and is remotely related to the one of O. anthropi. How the few differences in gene content between B. microti and B. suis 1330 could result in vastly different phenotypes remains to be elucidated. This unexpected finding will complicate the task of identifying virulence determinants in the Brucella genus. The genome sequence of B. microti will serve as a model for differential expression analysis and complementation studies. Our results also raise some concerns about the importance given to phenotypical traits in the definition of bacterial species.

Dataset Information

Genome sequence of Diplorickettsia massiliensis, an emerging Ixodes ricinus-associated human pathogen.

Publications

Genome sequence of Diplorickettsia massiliensis, an emerging Ixodes ricinus-associated human pathogen.

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