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Complete Genome Sequence of the Type Strain Pectobacterium punjabenseSS95, Isolated from a Potato Plant with Blackleg Symptoms. Sarfraz, S and Oulghazi, S and Cigna, J and Sahi, ST and Riaz, K andTufail, MR and Fayyaz, A and Naveed, K and Hameed, A and Lopez-Roques, Cand Vandecasteele, C and Faure, D Pectobacterium punjabense is a newly described species causing blackleg disease in potato plants. Therefore, by the combination of long (Oxford Nanopore Technologies, MinION) and short (Illumina MiSeq) reads, we sequenced the complete genome of P. punjabense SS95T, which contains a circular chromosome of 4.793 Mb wi... |
Sizing, stabilising, and cloning repeat-expansions for gene targeting constructs. Nair RR, Tibbit C, Thompson D, McLeod R, Nakhuda A, Simon MM, Baloh RH, Fisher EMC, Isaacs AM, Cunningham TJ Aberrant microsatellite repeat-expansions at specific loci within the human genome cause several distinct, heritable, and predominantly neurological, disorders. Creating models for these diseases poses a challenge, due to the instability of such repeats in bacterial vectors, especially with large repeat expansions. ... |
Tandem gene duplications drive divergent evolution of caffeine and crocin biosynthetic pathways in plants. Xu Z, Pu X, Gao R, Demurtas OC, Fleck SJ, Richter M, He C, Ji A, Sun W, Kong J, Hu K, Ren F, Song J, Wang Z, Gao T, Xiong C, Yu H, Xin T, Albert VA, Giuliano G, Chen S, Song J BACKGROUND: Plants have evolved a panoply of specialized metabolites that increase their environmental fitness. Two examples are caffeine, a purine psychotropic alkaloid, and crocins, a group of glycosylated apocarotenoid pigments. Both classes of compounds are found in a handful of distantly related plant genera (C... |
Nanopore Sequencing and Its Clinical Applications. Sun X, Song L, Yang W, Zhang L, Liu M, Li X, Tian G, Wang W Nanopore sequencing is a method for determining the order and modifications of DNA/RNA nucleotides by detecting the electric current variations when DNA/RNA oligonucleotides pass through the nanometer-sized hole (nanopore). Nanopore-based DNA analysis techniques have been commercialized by Oxford Nanopore Techn... |
Condition-dependent co-regulation of genomic clusters of virulence factors in the grapevine trunk pathogen Neofusicoccum parvum Massonnet M. et al. The ascomycete Neofusicoccum parvum, one of the causal agents of Botryosphaeria dieback, is a destructive wood-infecting fungus and a serious threat to grape production worldwide. The capability of colonizing woody tissue combined with the secretion of phytotoxic compounds is thought to underlie its pathogenicity an... |
Complete genome of Staphylococcus aureus Tager 104 provides evidence of its relation to modern systemic hospital-acquired strains Richard W. DavisIV, Andrew D. Brannen, Mohammad J. Hossain, Scott Monsma, Paul E. Bock, Matthias Nahrendorf, David Mead, Michael Lodes, Mark R. Liles and Peter Panizzi
Background
Staphylococcus aureus (S. aureus) infections range in severity due to expression of certain virulence factors encoded on mobile genetic elements (MGE). As such, characterization of these MGE, as well as single nucleotide polymorphisms, is of high clinical and microbiological importance. To und... |
Complete Genome Sequences of Four Escherichia coli ST95 Isolates from Bloodstream Infections Craig M. Stephens, Jeffrey M. Skerker, Manraj S. Sekhon, Adam P. Arkin, Lee W. Rileyd Finished genome sequences are presented for four Escherichia coli strains isolated from bloodstream infections at San Francisco General Hospital. These strains provide reference sequences for four major fimH-identified sublineages within the multilocus sequence type (MLST) ST95 group, and provide insights into patho... |
Diversification of bacterial genome content through distinct mechanisms over different timescales. Croucher NJ, Coupland PG, Stevenson AE, Callendrello A, Bentley SD, Hanage WP Bacterial populations often consist of multiple co-circulating lineages. Determining how such population structures arise requires understanding what drives bacterial diversification. Using 616 systematically sampled genomes, we show that Streptococcus pneumoniae lineages are typically characterized by combinations ... |
Emergence of scarlet fever Streptococcus pyogenes emm12 clones in Hong Kong is associated with toxin acquisition and multidrug resistance Mark R Davies, Matthew T Holden, Paul Coupland, Jonathan H K Chen, Carola Venturini, Timothy C Barnett, Nouri L Ben Zakour, Herman Tse, Gordon Dougan, Kwok-Yung Yuen & Mark J Walker A scarlet fever outbreak began in mainland China and Hong Kong in 2011 (refs. 1–6). Macrolide- and tetracycline-resistant Streptococcus pyogenes emm12 isolates represent the majority of clinical cases. Recently, we identified two mobile genetic elements that were closely associated with emm12 ou... |
Microevolution of Burkholderia pseudomallei during an acute infection. Limmathurotsakul D, Holden MT, Coupland P, Price EP, Chantratita N, Wuthiekanun V, Amornchai P, Parkhill J, Peacock SJ We used whole-genome sequencing to evaluate 69 independent colonies of Burkholderia pseudomallei isolated from seven body sites of a patient with acute disseminated melioidosis. Fourteen closely related genotypes were found, providing evidence for the rapid in vivo diversification of B. pseudomallei after inoculatio... |