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Friday, July 19, 2019

Recently published Streptomyces genome sequences.

Many readers of this journal will need no introduction to the bacterial genus Streptomyces, which includes several hundred species, many of which produce biotechnologically useful secondary metabolites. The last 2 years have seen numerous publications describing Streptomyces genome sequences (Table?1), mostly as short genome announcements restricted to just 500 words and therefore allowing little description and analysis. Our aim in this current manuscript is to survey these recent publications and to dig a little deeper where appropriate. The genus Streptomyces is now one of the most highly sequenced, with 19 finished genomic sequences (Table?2) and a further 125 draft assemblies…

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Friday, July 19, 2019

Targeted single molecule sequencing methodology for ovarian hyperstimulation syndrome.

One of the most significant issues surrounding next generation sequencing is the cost and the difficulty assembling short read lengths. Targeted capture enrichment of longer fragments using single molecule sequencing (SMS) is expected to improve both sequence assembly and base-call accuracy but, at present, there are very few examples of successful application of these technologic advances in translational research and clinical testing. We developed a targeted single molecule sequencing (T-SMS) panel for genes implicated in ovarian response to controlled ovarian hyperstimulation (COH) for infertility.Target enrichment was carried out using droplet-base multiplex polymerase chain reaction (PCR) technology (RainDance®) designed to yield…

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Sunday, July 7, 2019

Construction of a reference genetic map of Raphanus sativus based on genotyping by whole-genome resequencing.

This manuscript provides a genetic map of Raphanus sativus that has been used as a reference genetic map for an ongoing genome sequencing project. The map was constructed based on genotyping by whole-genome resequencing of mapping parents and F 2 population. Raphanus sativus is an annual vegetable crop species of the Brassicaceae family and is one of the key plants in the seed industry, especially in East Asia. Assessment of the R. sativus genome provides fundamental resources for crop improvement as well as the study of crop genome structure and evolution. With the goal of anchoring genome sequence assemblies of…

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Sunday, July 7, 2019

Nonribosomal peptide synthase gene clusters for lipopeptide biosynthesis in Bacillus subtilis 916 and their phenotypic functions.

Bacillus cyclic lipopeptides (LPs) have been well studied for their phytopathogen-antagonistic activities. Recently, research has shown that these LPs also contribute to the phenotypic features of Bacillus strains, such as hemolytic activity, swarming motility, biofilm formation, and colony morphology. Bacillus subtilis 916 not only coproduces the three families of well-known LPs, i.e., surfactins, bacillomycin Ls (iturin family), and fengycins, but also produces a new family of LP called locillomycins. The genome of B. subtilis 916 contains four nonribosomal peptide synthase (NRPS) gene clusters, srf, bmy, fen, and loc, which are responsible for the biosynthesis of surfactins, bacillomycin Ls, fengycins, and…

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Sunday, July 7, 2019

Analysis of a draft genome sequence of Kitasatospora cheerisanensis KCTC 2395 producing bafilomycin antibiotics.

Kitasatospora cheerisanensis KCTC 2395, producing bafilomycin antibiotics belonging to plecomacrolide group, was isolated from a soil sample at Mt. Jiri, Korea. The draft genome sequence contains 8.04 Mb with 73.6% G+C content and 7,810 open reading frames. All the genes for aerial mycelium and spore formations were confirmed in this draft genome. In phylogenetic analysis of MurE proteins (UDP-N-acetylmuramyl-L-alanyl-D-glutamate:DAP ligase) in a conserved dcw (division of cell wall) locus, MurE proteins of Kitasatospora species were placed in a separate clade between MurEs of Streptomyces species incorporating LL-diaminopimelic acid (DAP) and MurEs of Saccharopolyspora erythraea as well as Mycobacterium tuberculosis ligating…

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Sunday, July 7, 2019

Active site and laminarin binding in glycoside hydrolase family 55.

The Carbohydrate Active Enzyme (CAZy) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo-ß-1,3-glucanases. The founding structure in the GH55 is PcLam55A from the white rot fungus Phanerochaete chrysosporium (Ishida, T., Fushinobu, S., Kawai, R., Kitaoka, M., Igarashi, K., and Samejima, M. (2009) Crystal structure of glycoside hydrolase family 55 ß-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J. Biol. Chem. 284, 10100-10109). Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies, implicate Glu-502 as the catalytic…

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Sunday, July 7, 2019

Complete genome sequence of Rhodococcus sp. B7740, a carotenoid-producing bacterium isolated from the Arctic Sea.

Rhodococcus sp. B7740 was isolated from Arctic seawater and selected for its capacity to synthesize carotenoids. Here, we report the complete genome sequence of Rhodococcus sp. B7740 to provide the genetic basis for a better understanding of its carotenoid-accumulating capabilities, and we describe the major features of the genome. Copyright © 2015 Zhang et al.

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Sunday, July 7, 2019

Draft genome sequence of marine actinomycete Streptomyces sp. strain NTK 937, producer of the benzoxazole antibiotic caboxamycin.

Streptomyces sp. strain NTK 937 is the producer of the benzoxazole antibiotic caboxamycin, which has been shown to exert inhibitory activity against Gram-positive bacteria, cytotoxic activity against several human tumor cell lines, and inhibition of the enzyme phosphodiesterase. In this genome announcement, we present a draft genome sequence of Streptomyces sp. NTK 937 in which we identified at least 35 putative secondary metabolite biosynthetic gene clusters. Copyright © 2014 Olano et al.

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Sunday, July 7, 2019

Draft genome sequence of Kitasatospora cheerisanensis KCTC 2395, which produces plecomacrolide against phytopathogenic fungi.

Kitasatospora cheerisanensis KCTC 2395, which produces antifungal metabolites with bafilomycin derivatives, including bafilomycin C1-amide, was isolated from a soil sample at Mt. Jiri, South Korea. Here, we report its draft genome sequence, which contains 8.04 Mb with 73.6% G+C content and 7,810 protein-coding genes. Copyright © 2014 Hwang et al.

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Sunday, July 7, 2019

Complete genome sequence of the sugar cane endophyte Pseudomonas aurantiaca PB-St2, a disease-suppressive bacterium with antifungal activity toward the plant pathogen Colletotrichum falcatum.

The endophytic bacterium Pseudomonas aurantiaca PB-St2 exhibits antifungal activity and represents a biocontrol agent to suppress red rot disease of sugar cane. Here, we report the completely sequenced 6.6-Mb genome of P. aurantiaca PB-St2. The sequence contains a repertoire of biosynthetic genes for secondary metabolites that putatively contribute to its antagonistic activity and its plant-microbe interactions.

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Sunday, July 7, 2019

Complete genome sequence of Cellulophaga lytica HI1 using PacBio Single-Molecule Real-Time Sequencing.

We report here the complete genome sequence of Cellulophaga lytica HI1 isolated from a seawater table located at the Kewalo Marine Laboratory (Honolulu, HI). This is the first complete de novo genome assembly of C. lytica HI1 using PacBio single-molecule real-time (SMRT) sequencing, which resulted in a single scaffold of 3.8 Mb. Copyright © 2014 Asahina and Hadfield.

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Sunday, July 7, 2019

Draft genome sequence of Pantoea agglomerans R190, a producer of antibiotics against phytopathogens and foodborne pathogens.

Pantoea agglomerans R190, isolated from an apple orchard, showed antibacterial activity against various spoilage bacteria, including Pectobacterium carotovorum subsp. carotovorum, and foodborne pathogens such as Escherichia coli O157:H7. Here, we report the genome sequence of P. agglomerans R190. This report will raise the value of P. agglomerans as an agent for biocontrol of disease. Copyright © 2014. Published by Elsevier B.V.

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