We report the complete mitochondrial genome sequence of the freshwater diatom Asterionella formosa. The large 61.9?kb circular sequence encodes 34 proteins and 25 tRNAs that are universally conserved in other sequenced diatoms. We fully resolved a unique 24?kb region containing highly conserved repeated sequence units, possibly collocating with an origin of replication.
The genome of Paenalcaligenes hominis, isolated from a paraplegic patient with neurogenic bladder, was sequenced with the Pacific Biosciences RSII platform. The genome size is 2.68 Mb and includes 3,096 annotated coding sequences, including genes associated with quinone cofactors, which play crucial roles in the virulence of Gram-negative bacteria. Copyright © 2017 Mukhopadhyay et al.
Mycobacterium avium subsp. hominissuis is an environmentally acquired bacterium known to cause pulmonary and soft tissue infections, lymphadenitis, and disseminated disease in humans. We report here the complete genome sequence of strain H87, isolated from an indoor water sample, as a single circular chromosome of 5,626,623 bp with a G+C content of 68.8%. Copyright © 2017 Zhao et al.
Staphylococcus aureus causes a variety of human diseases ranging in severity. The pathogenicity of S. aureus can be partially attributed to the acquisition of mobile genetic elements. In this report, we provide two complete genome sequences from human clinical S. aureus isolates. Copyright © 2017 Hau et al.
Flavobacteriales bacterium strain UJ101 was isolated from a xanthid crab species collected from the East Sea of Korea. Here, we report the complete genome sequence of strain UJ101 for the study of major metabolic pathways related to microbial species from marine invertebrate species. Copyright © 2017 Yang et al.
Amycolatopsis orientalis CPCC200066 is an actinomycete exploited commercially in China for the production of norvancomycin, an important glycopeptide antibiotic structurally close to the well-known vancomycin. The availability of the complete genome sequence of CPCC200066 would greatly strengthen our understanding of the regulation pattern of norvancomycin biosynthesis and ultimately improve its production, as well as potentiate discoveries of novel bioactive compounds. Here we report the complete genome sequence of A. orientalis CPCC200066, a circular chromosome consisting of 9,490,992bp. Forty putative secondary metabolite biosynthetic gene clusters, including norvancomycin, were predicted, covering 20.3% of the whole genome. To facilitate genetic manipulation of this strain, an efficient transformation system was established by constructing a novel integrative vector pIMBT1, which could be transferred into CPCC200066 by electroporation with high efficiency. FBT1 attB sites were also identified in other known Amycolatopsis genomes, indicating pIMBT1’s prospect to be a novel vector for genus Amycolatopsis. Copyright © 2017 Elsevier B.V. All rights reserved.
Microbiologically induced calcium carbonate precipitation shows the potential for use in bioremediation and construction consolidation, but the efficiency of this process must be improved. Lysinibacillus sphaericus LMG 22257 is a gram-positive ureolytic strain that has recently been applied for consolidating construction by mediating calcium carbonate precipitation. The complete genome sequence of L. sphaericus LMG 22257 is 3,436,578 base pairs with a GC content of 38.99%. The urea degradation pathway and genes related to extracellular polymeric substance biosynthesis were also identified. The strain can tolerate high alkalinity (pH up to 10) and high urea concentration (up to 3M). These findings provide insights into the microbiologically induced carbonate precipitation and extend the application of the metabolic potential of L. sphaericus LMG 22257 for bioremediation. Copyright © 2017 Elsevier B.V. All rights reserved.
Pseudomonas aeruginosa DN1 was isolated from a petroleum-contaminated soil from Changqing Oilfield with its capability to degrade high molecular weight polycyclic aromatic hydrocarbons (HMW PAHs) and crude oil. Herein, the whole genome sequence analysis of P. aeruginosa strain DN1 was reported, consisting of a size of 6,641,902 bp chromosome assembled genome (67.09 mol% G + C content) and a 317,349 bp plasmid assembled genome (57.01 mol% G + C content). According to the genome information, strain DN1 encodes various genes related to degradation of aliphatic hydrocarbons and aromatic compounds. In addition, DN1 contains gene clusters for biosynthesis and regulation of biosurfactant rhamnolipids. These genes may serve as a basis of further elucidation of the genetic background of this promising strain, and provide insights into investigating the metabolic and regulatory mechanisms of hydrocarbon biodegradation.
The plant growth-promoting rhizobacterium Pseudomonas protegens H78, which was isolated from the rhizosphere of oilseed rape in Shanghai, can produce a large array of antibiotics with a broad spectrum of activities. Here, we report the annotated complete genome sequence of P. protegens H78. Copyright © 2017 Huang et al.
Although clustering of genes from the same metabolic pathway is a widespread phenomenon, the evolution of the polysaccharide biosynthetic gene cluster remains poorly understood. To determine the evolution of this pathway, we identified a scattered production pathway of the polysaccharide sanxan by Sphingomonas sanxanigenens NX02, and compared the distribution of genes between sphingan-producing and other Sphingomonadaceae strains. This allowed us to determine how the scattered sanxan pathway developed, and how the polysaccharide gene cluster evolved. Our findings suggested that the evolution of microbial polysaccharide biosynthesis gene clusters is a lengthy cyclic process comprising cluster 1???scatter???cluster 2. The sanxan biosynthetic pathway proved the existence of a dispersive process. We also report the complete genome sequence of NX02, in which we identified many unstable genetic elements and powerful secretion systems. Furthermore, nine enzymes for the formation of activated precursors, four glycosyltransferases, four acyltransferases, and four polymerization and export proteins were identified. These genes were scattered in the NX02 genome, and the positive regulator SpnA of sphingans synthesis could not regulate sanxan production. Finally, we concluded that the evolution of the sanxan pathway was independent. NX02 evolved naturally as a polysaccharide producing strain over a long-time evolution involving gene acquisitions and adaptive mutations.
Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.
We report here the complete genome sequence of a panresistant Pseudomonas aeruginosa strain, isolated from a patient with respiratory failure in Canada. No carbapenemase genes were identified. Carbapenem resistance is attributable to a frameshift in the oprD gene; the basis for colistin resistance remains undetermined. Copyright © 2017 Xiong et al.
USA300 is a predominant community-associated methicillin-resistant Staphylococcus aureus strain causing significant morbidity and mortality. We present here the full annotated genome of a USA300 hypervirulent clinical strain, USA300-C2406, isolated from a patient with a lethal case of necrotizing pneumonia, to gain a better understanding of USA300 hypervirulence. Copyright © 2017 McClure and Zhang.
Four complete genome sequences of genetically distinct Paenibacillus larvae strains have been determined. Pacific BioSciences single-molecule real-time (SMRT) sequencing technology was used as the sole method of sequence determination and assembly. The chromosomes exhibited a G+C content of 44.1 to 44.2% and a molecular size range of 4.29 to 4.67 Mbp. Copyright © 2017 Dingman.
Legionella is a highly diverse genus of intracellular bacterial pathogens that cause Legionnaire’s disease (LD), an often severe form of pneumonia. Two L. micdadei sp. clinical isolates, obtained from patients hospitalized with LD from geographically distinct areas, were sequenced using PacBio SMRT cell technology, identifying incomplete phage regions, which may impact virulence. Copyright © 2017 Osborne et al.
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