Predatory bacteria remain molecularly enigmatic, despite their presence in many microbial communities. Here we report the complete genome of Bdellovibrio bacteriovorus HD100, a predatory Gram-negative bacterium that invades and consumes other Gram-negative bacteria. Its surprisingly large genome shows no evidence of recent gene transfer from its prey. A plethora of paralogous gene families coding for enzymes, such as hydrolases and transporters, are used throughout the life cycle of B. bacteriovorus for prey entry, prey killing, and the uptake of complex molecules.
Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum 1 . Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance 2 . Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm.Crosses between distantly related plants can lead to substantial improvements in performance. Notably, S. pennellii × S. lycopersicum ILs have been used to define numerous quantitative trait loci (QTLs) for superior yield, chemical composition, morphology, abiotic stress tolerance and extreme heterosis 3,4 . Although genetic studies have proven informative, few genes underlying specific QTLs have been cloned, largely because of the lack of a S. pennellii genome sequence. To support QTL analyses, we sequenced the genome of S. pennellii using Illumina sequencing with ~190-fold coverage ( Fig. 1 and Supplementary Tables 1-5). The initial assembly size was 942 Mb, with a scaffold N50 value of 1.7 Mb and N90 value of 0.43 Mb (Table 1 and Supplementary Tables 6 and 7). We estimated the total genome size to be about 1.2 Gb using a k-mer-based analysis ( Supplementary Fig. 1 and Supplementary Table 8), in accordance with previous estimations 3,4 . We anchored 97.1% of the genome assembly to chromosomes using genetic maps and restriction site-associated DNA sequencing (RAD-seq)-based markers from the IL population 5 (Supplementary Note). Comparison of the assembly to publicly available BAC sequences indicated an accuracy of >99.9%, and a satisfactory accuracy of gap-filled regions was shown by realigning reads (Supplementary Fig. 2 and Supplementary Table 9). Of the 307,350 S. lycopersicum and 7,812 S. pennellii publicly available ESTs, 93% and >96% could be aligned to the genome, respectively (Supplementary Table 10), indicating comprehensive coverage of the gene-rich regions. We predicted 32,273 high-confidence genes and a potential set of 44,966 protein-coding genes and checked these
To understand the origin and emergence of pathogenic bacteria, knowledge of the genetic inventory from their nonpathogenic relatives is a prerequisite. Therefore, the 2.11-megabase genome sequence of Wolinella succinogenes, which is closely related to the pathogenic bacteria Helicobacter pylori and Campylobacter jejuni, was determined. Despite being considered nonpathogenic to its bovine host, W. succinogenes holds an extensive repertoire of genes homologous to known bacterial virulence factors. Many of these genes have been acquired by lateral gene transfer, because part of the virulence plasmid pVir and an N-linked glycosylation gene cluster were found to be syntenic between C. jejuni and genomic islands of W. succinogenes. In contrast to other hostadapted bacteria, W. succinogenes does harbor the highest density of bacterial sensor kinases found in any bacterial genome to date, together with an elaborate signaling circuitry of the GGDEF family of proteins. Because the analysis of the W. succinogenes genome also revealed genes related to soil-and plant-associated bacteria such as the nif genes, W. succinogenes may represent a member of the epsilon proteobacteria with a life cycle outside its host.Helicobacter ͉ Campylobacter ͉ epsilon proteobacteria ͉ bacterial pathogenicity
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