This is a report of the complete genome sequence of the goatpox virus strain Gorgan, which was obtained directly from a commercial live attenuated vaccine (Caprivac, Jordan Bio-Industries Centre). Copyright © 2016 Mathijs et al.
To date, only 13 genomes of green sulfur bacteria (family Chlorobiaceae) have been sequenced. The sequenced strains do not cover the full phylogenetic diversity of the family. We determined the complete genome sequence of Prosthecochloris sp. strain CIB 2401, thereby increasing the genome information for the poorly represented marine Chlorobiaceae. Copyright © 2016 Nabhan et al.
We report here the complete annotated genome sequence of the Burkholderia stabilis type strain ATCC BAA-67. There were three circular chromosomes with a combined size of 8,527,947 bp and G+C composition of 66.4%. These characteristics closely resemble the genomes of other sequenced members of the Burkholderia cepacia complex. Copyright © 2016 Bugrysheva et al.
Lactobacillus fermentum NCC2970 (CNCM I-5068) is a lactic acid bacterium originating from the Nestle Culture Collection. Here, we disclose its full 1.9-Gb genome sequence comprising one chromosome with no plasmid. Copyright © 2016 Barretto et al.
Sphingobium cloacae JCM 10874(T) can degrade phenolic endocrine-disrupting chemicals, nonylphenol, and octylphenol. Here, we report the complete genome sequence of the JCM 10874(T) strain. Copyright © 2016 Ootsuka et al.
Aminobacter aminovorans is a Gram-negative, pleomorphic rod-shaped, flagellated, and obligately aerobic bacterium that was isolated from soil. Here, we report the complete genome sequence of A. aminovorans KCTC 2477(T), which degrades nitrilotriacetate-metal complexes and iminodiacetate, a metabolic intermediate of nitrilotriacetate. Copyright © 2016 Lee et al.
Pseudomonas citronellolis SJTE-3, isolated from the active sludge of a wastewater treatment plant in China, can utilize a series of environmental estrogens and estrogen-like toxicants. Here, we report its whole-genome sequence, containing one circular chromosome and one circular plasmid. Genes involved in estrogen biodegradation in this bacterium were predicted. Copyright © 2016 Zheng et al.
Burkholderia mallei is a zoonotic agent causing glanders, a notifiable disease in equines. During the past decades glanders emerged, and the Kingdom of Bahrain reported outbreaks to the World Organization of Animal Health in 2010 and 2011. This paper presents the complete genome sequence of the Burkholderia mallei strain 11RR2811 Bahrain1. Copyright © 2016 Elschner et al.
We report here the complete 4.7-Mb genome sequence of Xanthomonas translucens pv. translucens DSM 18974(T), which causes black chaff disease on barley (Hordeum vulgare). Genome data of this X. translucens type strain will improve our understanding of this bacterial species. Copyright © 2016 Jaenicke et al.
Mycobacterium chimaera is a nontuberculous mycobacterial species that causes cardiovascular, pulmonary, and postsurgical infections. Here, we report the first complete genome sequence of M. chimaera This genome is 6.33 Mbp, with a G+C content of 67.56%, and encodes 4,926 protein-coding genes, as well as 74 tRNAs, one ncRNA, and three rRNA genes. Copyright © 2016 Hasan et al.
Here, we report the complete genome sequences of Legionella pneumophila isolates from two collocated outbreaks of Legionnaires’ disease in 2005 and 2008 in Sarpsborg/Fredrikstad, Norway. One clinical and two environmental isolates were sequenced from each outbreak. The genome of all six isolates consisted of a 3.36 Mb-chromosome, while the 2005 genomes featured an additional 68 kb-episome sharing high sequence similarity with the L. pneumophila Lens plasmid. All six genomes contained multiple mobile genetic elements including novel combinations of type-IVA secretion systems. A comparative genomics study will be launched to resolve the genetic relationship between the L. pneumophila isolates. Copyright © 2016 Dybwad et al.
The Stenotrophomonas genus shows great adaptive potential including resistance to multiple antimicrobials, opportunistic pathogenicity, and production of numerous secondary metabolites. Using long-read technology, we report the sequence of a plant-associated Stenotrophomonas strain originating from the citrus phyllosphere that displays a copper resistance phenotype. Copyright © 2016 Richard et al.
Targeted sequencing is commonly used in clinical application of NGS technology since it enables generation of sufficient sequencing depth in the targeted genes of interest and thus ensures the best possible downstream analysis. This notwithstanding, the accurate discovery and annotation of disease causing mutations remains a challenging problem even in such favorable context. The difficulty is particularly salient in the case of third generation sequencing technology, such as PacBio. We present MICADo, a de Bruijn graph based method, implemented in python, that makes possible to distinguish between patient specific mutations and other alterations for targeted sequencing of a cohort of patients. MICADo analyses NGS reads for each sample within the context of the data of the whole cohort in order to capture the differences between specificities of the sample with respect to the cohort. MICADo is particularly suitable for sequencing data from highly heterogeneous samples, especially when it involves high rates of non-uniform sequencing errors. It was validated on PacBio sequencing datasets from several cohorts of patients. The comparison with two widely used available tools, namely VarScan and GATK, shows that MICADo is more accurate, especially when true mutations have frequencies close to backgound noise. The source code is available at http://github.com/cbib/MICADo.
Several species of the genus Dickeya provoke soft rot and blackleg diseases on a wide range of plants and crops. Dickeya solani has been identified as the causative agent of diseases outbreaks on potato culture in Europe for the last decade. Here, we report the complete genome of the D. solani IPO 2222(T). Using PacBio and Illumina technologies, a unique circular chromosome of 4,919,833 bp was assembled. The G?+?C content reaches 56% and the genomic sequence contains 4,059 predicted proteins. The ANI values calculated for D. solani IPO 2222(T) vs. other available D. solani genomes was over 99.9% indicating a high genetic homogeneity within D. solani species.
The whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) is among the 100 worst invasive species in the world. As one of the most important crop pests and virus vectors, B. tabaci causes substantial crop losses and poses a serious threat to global food security. We report the 615-Mb high-quality genome sequence of B. tabaci Middle East-Asia Minor 1 (MEAM1), the first genome sequence in the Aleyrodidae family, which contains 15,664 protein-coding genes. The B. tabaci genome is highly divergent from other sequenced hemipteran genomes, sharing no detectable synteny. A number of known detoxification gene families, including cytochrome P450s and UDP-glucuronosyltransferases, are significantly expanded in B. tabaci. Other expanded gene families, including cathepsins, large clusters of tandemly duplicated B. tabaci-specific genes, and phosphatidylethanolamine-binding proteins (PEBPs), were found to be associated with virus acquisition and transmission and/or insecticide resistance, likely contributing to the global invasiveness and efficient virus transmission capacity of B. tabaci. The presence of 142 horizontally transferred genes from bacteria or fungi in the B. tabaci genome, including genes encoding hopanoid/sterol synthesis and xenobiotic detoxification enzymes that are not present in other insects, offers novel insights into the unique biological adaptations of this insect such as polyphagy and insecticide resistance. Interestingly, two adjacent bacterial pantothenate biosynthesis genes, panB and panC, have been co-transferred into B. tabaci and fused into a single gene that has acquired introns during its evolution.The B. tabaci genome contains numerous genetic novelties, including expansions in gene families associated with insecticide resistance, detoxification and virus transmission, as well as numerous horizontally transferred genes from bacteria and fungi. We believe these novelties likely have shaped B. tabaci as a highly invasive polyphagous crop pest and efficient vector of plant viruses. The genome serves as a reference for resolving the B. tabaci cryptic species complex, understanding fundamental biological novelties, and providing valuable genetic information to assist the development of novel strategies for controlling whiteflies and the viruses they transmit.
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