Members of our Pathosystems Resource Integration Center have aided in sequencing the genome of the deer tick and its rickettsial symbiont.
Several members of the Pathosystems Resource Integration Center have participated in the community project for the genome sequencing of the deer tick (Ixodes scapularis), an impor tant ar thropod vector of many pathogenic microbial species. Our collaboration with the J. Craig Venter Institute and other members of the community involved an in-depth analysis of a rickettsial species (Alphaproteobacteria: Rickettsiales: Rickettsiaceae) that was serendipitously sequenced along with the tick genome. Importantly, this genome from the Rickettsia endosymbiont of Ixodes scapularis (REIS) is the ﬁrst genome from Rickettsia spp. to be assembled entirely from a eukaryotic sequencing project, as the bacterial reads were separated from the I. scapularis whole genome shotgun sequencing data. Aside from this novelty, the characteristics of this rickettsial genome were extraordinary in comparison to other sequenced Rickettsia genomes, and most importantly, highlighted a hereto undescribed look into a dynamic rickettsial mobilome that carries many important genes for obligate intracellular survival, and mechanisms of pathogenicity by comparing this symbiont genome to genomes of closely related human pathogens.
Genome-based phylogeny estimation suggests that REIS is the most basal member of the spotted fever group (SFG), sharing attributes with both pathogenic and non-pathogenic rickettsiae (Fig. 5A). REIS is the largest Rickettsia genome sequenced to date (>2Mb), with a chromosome size >1.8Mb that contains 2059 predicted open reading frames (ORFs) (Fig. 5B). The accessory genome alone encodes almost twice as many genes as the entire R. prowazekii genome. Plasmids pREIS1-4 are novel to Rickettsia species, and contain 59, 83, 43, and 65 predicted ORFs, respectively. Many of these ORFs have homologs in other species of diverse obligate intracellular bacteria. Perhaps the most outstanding ﬁnding within the REIS genome is the extraordinary proliferation of mobile genetic elements (MGEs), which contributes to a limited synteny with other Rickettsia genomes and places REIS among the most repetitive bacterial genomes. In particular, a Rickettsiales ampliﬁed genetic element (RAGE), previously identiﬁed as a "proliferated-yet-decayed" element in scrub typhus rickettsiae (Orientia tsutsugamushi) genomes, is present on both the REIS chromosome and plasmids (pREIS1 and pREIS3). However, unlike O. tsutsugamushi, nine complete (or nearly complete) RAGEs exist within the REIS genome and encode entire F-like type IV secretion systems similar to the single copy tra cluster present in the genomes of R. bellii and R. massiliae. An unparalleled abundance of encoded transposases (>650) relative to genome size, together with the RAGEs and other MGEs, comprise >35% of the total genome, making REIS one of the most dynamic bacterial genomes sequenced to date.
Despite an extraordinarily plastic accessory genome, including several intriguing lateral gene transfers (e.g., a complete biotin biosynthesis operon, remnants of the WO-B prophage, a Gram- positive aminoglycoside antibiotic synthesis and
resistance cluster) from other diverse intracellular bacteria, comparative analysis with Rickettsiaceae genomes indicates that REIS does not differ in the mode and tempo of gene loss typical of rickettsial reductive genome evolution. As REIS is not known to invade ver tebrate cells and has no known pathogenic effects on I. scapularis, its genome sequence provides an invaluable tool for deciphering the mechanisms of arthropod and vertebrate pathogenicity via comparison with the genomes of virulent and avirulent Rickettsia species. Of signiﬁcance to Rickettsiaceae evolution, we present compelling evidence that many of the genes involved in obligate intracellular lifestyle were acquired via MGEs, especially the RAGE, through a continuum of genomic invasions by these integrative conjugative elements.
At the time of its publication, the REIS genome was the sixteenth Rickettsia genome sequenced to date, with its four distinct plasmids (pREIS1-4) bringing the total number of sequenced rickettsial plasmids to eleven. Remarkably, an explosion of sequenced rickettsial genomes has occurred over the last year, bringing the total number of Rickettsia genomes to almost ﬁfty. Our research team has analyzed most of these genomes in a contribution to the American Society of Microbiology book titled Intracellular Pathogens II: Rickettsiales. Despite these additional genomes, as well as comparison across 80 Rickettsiales genomes, our results for REIS still stand and accentuate the outstanding nature of this genome.
This success of our project highlights the great opportunity for further studying a variety of bacterial genomes that have never been cultured or isolated. We are currently pursuing the extraction and assembly of other par tial (or nearly complete) bacterial genomes from a variety of eukaryotic genomes. The goal is to incorporate this information into PATRIC, and to cross-reference (whenever possible) extracted data with their respective host genomes available at other BRCs. We have very recently completed work on a partial rickettsial genome extracted from an animal genome (the placozoan Trichoplax adhaerens).
June 06, 2014