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Genome Project Reveals a Putative Rickettsial Endosymbiont

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Genome Project Reveals a Putative Rickettsial Endosymbiont GBE Bacterial DNA Sifted from the Trichoplax adhaerens (Animalia: Placozoa) Genome Project Reveals a Putative Rickettsial Endosymbiont Timothy Driscoll1,y, Joseph J. Gillespie1,2,*,y, Eric K. Nordberg1,AbduF.Azad2, and Bruno W. Sobral1,3 1Virginia Bioinformatics Institute at Virginia Polytechnic Institute and State University 2Department of Microbiology and Immunology, University of Maryland School of Medicine 3Present address: Nestle´ Institute of Health Sciences SA, Campus EPFL, Quartier de L’innovation, Lausanne, Switzerland *Corresponding author: E-mail: [email protected]. yThese authors contributed equally to this work. Accepted: March 1, 2013 Abstract Eukaryotic genome sequencing projects often yield bacterial DNA sequences, data typically considered as microbial contamination. However, these sequences may also indicate either symbiont genes or lateral gene transfer (LGT) to host genomes. These bacterial sequences can provide clues about eukaryote–microbe interactions. Here, we used the genome of the primitive animal Trichoplax adhaerens (Metazoa: Placozoa), which is known to harbor an uncharacterized Gram-negative endosymbiont, to search for the presence of bacterial DNA sequences. Bioinformatic and phylogenomic analyses of extracted data from the genome assembly (181 bacterial coding sequences [CDS]) and trace read archive (16S rDNA) revealed a dominant proteobacterial profile strongly skewed to Rickettsiales (Alphaproteobacteria) genomes. By way of phylogenetic analysis of 16S rDNA and 113 proteins conserved across proteobacterial genomes, as well as identification of 27 rickettsial signature genes, we propose a Rickettsiales endosymbiont of T. adhaerens (RETA). The majority (93%) of the identified bacterial CDS belongs to small scaffolds containing prokaryotic-like genes; however, 12 CDS were identified on large scaffolds comprised of eukaryotic-like genes, suggesting that T. adhaerens might have recently acquired bacterial genes. These putative LGTs may coincide with the placozoan’s aquatic niche and symbiosis with RETA. This work underscores the rich, and relatively untapped, resource of eukaryotic genome projects for harboring data pertinent to host–microbial interactions. The nature of unknown (or poorly characterized) bacterial species may only emerge via analysis of host genome sequencing projects, particularly if these species are resistant to cell culturing, as are many obligate intracellular microbes. Our work provides methodological insight for such an approach. Key word: endosymbiont, genome-mining, host–microbe interactions, intracellular bacteria, Rickettsiales, symbiosis. Introduction bacterial sequences to the genome of the eukaryote]. Aside Bacterial DNA sequences may be generated as a byproduct of from contamination, the remaining sources of bacterial DNA eukaryotic genome sequencing. The source of this bacterial sequences generated by eukaryotic genome projects provide DNA can be 1) contamination (failure to separate incidental clues about the biological relationships between eukaryotes bacterial species from eukaryotic cell preparation, or even fail- and their associated bacterial species. Thus, the creation of ure to completely eliminate sequencing adapters or cloning methods for the detection, extraction, and characterization vector sequences); 2) environmental (extracellular bacteria of microbial sequences generated by eukaryotic genome sequenced as a consequence of occupying the same niche sequencing studies are of critical importance, particularly for as the eukaryote); 3) symbiotic (extracellular or facultative/ gaining insight on poorly characterized bacterial species, some obligate intracellular bacterial species directly associated with of which may be recalcitrant to cultivation. Furthermore, the eukaryotic host); or 4) LGT [lateral gene transfer of annotation of such bacterial reads or genomes and deposition ß The Author(s) 2013. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Genome Biol. Evol. 5(4):621–645. doi:10.1093/gbe/evt036 Advance Access publication March 7, 2013 621 Driscoll et al. GBE into appropriate public databases is paramount for facilitating (Gammaproteobacteria: Enterobacteriales), potentially rele- this approach. gating the symbiont to aphid bacteriocytes (Nikoh and Studies identifying endosymbiotic bacterial genomes within Nakabachi 2009; Nikoh et al. 2010). These studies of bacterial the data generated from eukaryotic sequencing projects are gene incorporation into eukaryotic genomes illustrate the growing. Inspection by Salzberg et al. (2005a, 2005b)of need to develop tools to distinguish congener bacterial disparate fruit fly (Arthropoda: Diptera: Drosophila ananassae, genes serendipitously captured in eukaryotic sequencing proj- D. simulans,andD. willistoni) genome trace file archives re- ects from true LGT events. sulted in the identification of three novel species of Wolbachia In this study, we analyzed the genome project (reads and (Alphaproteobacteria: Rickettsiales: Anaplasmataceae). The assembly) of the primitive metazoan Trichoplax adhaerens genome sequence of another Wolbachia strain was discov- (Animalia: Placozoa) for the presence of bacterial DNA ered within the whole-genome sequencing data for the mos- sequences. Published in 2008, the T. adhaerens genome re- quito Culex quinquefasciatus strain JHB (Salzberg et al. 2009). vealed “cryptic complexity,” as most genes encoding tran- Sequencing of the Hydra magnipapillata (Cnidaria: Hydrozoa) scription factors and signaling pathways underpinning genome revealed the presence of an endosymbiont most clo- eumetazoan cellular differentiation and development are pre- sely related to species of Curvibacter (Betaproteobacteria: sent in this simple animal (Srivastava et al. 2008). Trichoplax Burkholderiales: Comamonadaceae) (Chapman et al. 2010). adhaerens lacks nerves, sensory cells, and muscle cells, with Most recently, the genome of a Rickettsiales endosymbiont of only four cell types previously described (Grell 1971; Ixodes scapularis (Rickettsiales: Rickettsiaceae: REIS) was Schierwater 2005). Morphologically, the animal resembles a assembled from mining the initial data generated from the flat disc of cells with two epithelial layers sandwiching a region deer tick sequencing effort (Gillespie et al. 2012). All of of multinucleate fiber cells (Grell and Ruthmann 1991; Guidi these studies have revealed genomic data essential for further- et al. 2011). Trichoplax adhaerens is known to harbor a Gram- ing the knowledge of bacterial endosymbioses within animal negative endosymbiont within fiber cells (Grell 1972; Grell and species. In the case of REIS, important characteristics of a Benwitz 1974), with bacteria passed to developing oocytes via nonpathogen came to light when compared with the fiber cell extensions (Eitel et al. 2011). Our motivation for an- genomes of closely related pathogenic-spotted fever group alyzing the T. adhaerens genomic data for sequences belong- rickettsiae (Gillespie et al. 2012). ing to this symbiont was generated by previous studies that Genomic analyses of several eukaryotes, such as the rotifers included bacterial-like genes from T. adhaerens in phylogeny Adineta vaga and A. ricciae (Rotifera; Bdelloidea) estimations (Felsheim et al. 2009; Baldridge et al. 2010; (Gladyshev et al. 2008; Boschetti et al. 2012), H. magnipapil- Gillespie et al. 2010; Nikoh et al. 2010). As two of lata (Chapman et al. 2010), the silkmoth Bombyx mori these genes are rickettsial signatures (virD4 and plasmid-like (Arthropoda: Lepidoptera) (Li et al. 2011), and the spider parA), we considered it likely that the T. adhaerens fiber cell mite Tetranychus uriticae (Arthropoda: Acari) (Grbic et al. symbiont is a member of the obligate intracellular 2011), have revealed the presence of many genes originating from diverse bacterial species, illustrating the role of LGT in the Rickettsiales. diversification of eukaryotic genomes. For instance, a bacterial We report an in-depth analysis of the T. adhaerens genome mannanase gene from Bacillus spp. (Firmicutes: Bacilliales) was assembly and trace read archive, which divulged bacterial 16S recently reported in the genome of the coffee berry borer rDNA sequences, 181 bacterial-like coding sequences (CDS) beetle, Hypothenemus hampei (Arthropoda: Coleoptera), and many additional partial gene fragments of probable and demonstrated to metabolize galactomannan, the major bacterial nature. Robust phylogenomic analyses grouped the storage polysaccharide of coffee (Acuna et al. 2012). Large T. adhaerens bacterium with the mitochondria invader portions of Wolbachia genomes have been identified in sev- “Candidatus Midichloria mitochondrii” (Alphaproteobacteria: eral arthropod host genomes, including the bean beetle Rickettsiales), albeit with only 53% conservation across the Callosobruchus chinensis (Kondo et al. 2002; Nikoh et al. core proteins of these two species. Using this substantial 2008), the longicorn beetle Monochamus alternatus molecular evidence, we name a Rickettsiales endosymbiont (Aikawa et al. 2009), D. ananassae,(Dunning Hotopp et al. of T. adhaerens (RETA) and provide adjusted annotation 2007), the parasitoid wasp Nasonia
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