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Asset Tag: SMRT Sequencing

July 7, 2019

Genome sequence of Pseudomonas chlororaphis Lzh-T5, a plant growth-promoting rhizobacterium with antimicrobial activity.

Pseudomonas chlororaphis Lzh-T5 is a plant growth-promoting rhizobacterium (PGPR) with antimicrobial activity isolated from tomato rhizosphere in the city of Dezhou, Shandong Province, China. Here, the draft genome sequence of P. chlororaphis Lzh-T5 is reported, and several functional genes related to antifungal antibiotics and siderophore biosynthesis have been found in the genome. Copyright © 2018 Li et al.

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July 7, 2019

Genome sequences of two cyanobacterial strains, toxic green Microcystis aeruginosa KW (KCTC 18162P) and nontoxic brown Microcystis sp. strain MC19, under xenic culture conditions.

Bloom-forming cyanobacteria pose concerns for the environment and the health of humans and animals by producing toxins and thus lowering water quality. Here, we report near-complete genome sequences of two Microcystis strains under xenic culture conditions, which were originally isolated from two separate freshwater reservoirs from the Republic of Korea. Copyright © 2018 Jeong et al.

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July 7, 2019

Complete genome sequence of Lelliottia nimipressuralis type strain SGAir0187, isolated from tropical air collected in Singapore.

Lelliottia nimipressuralis type strain SGAir0187 was isolated from tropical air samples collected in Singapore. The genome was assembled with an average coverage of 180-fold using Pacific Biosciences long reads and Illumina MiSeq paired-end reads. The genome measures 4.8?Mb and contains 4,424 protein-coding genes, 83 tRNAs, and 25 rRNAs. Copyright © 2018 Heinle et al.

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July 7, 2019

Complete genome sequence of Acinetobacter indicus type strain SGAir0564 isolated from tropical air collected in Singapore.

Acinetobacter indicus (Gammaproteobacteria) is a strict aerobic nonmotile bacterium. The strain SGAir0564 was isolated from air samples collected in Singapore. The complete genome is 3.1 Mb and was assembled using a combination of short and long reads. The genome contains 2,808 protein-coding genes, 80 tRNAs, and 21 rRNA subunits. Copyright © 2018 Vettath et al.

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July 7, 2019

Genome sequence of Bacillus cereus strain TG1-6, a plant-beneficial rhizobacterium that is highly salt tolerant.

The complete genome sequence of Bacillus cereus strain TG1-6, which is a highly salt-tolerant rhizobacterium that enhances plant tolerance to drought stress, is reported here. The sequencing process was performed based on a combination of pyrosequencing and single-molecule sequencing. The complete genome is estimated to be approximately 5.42?Mb, containing a total of 5,610 predicted protein-coding DNA sequences (CDSs). Copyright © 2018 Vílchez et al.

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July 7, 2019

Complete genome sequence of Staphylococcus haemolyticus type strain SGAir0252.

Staphylococcus haemolyticus is a coagulase-negative staphylococcal species that is part of the skin microbiome and an opportunistic human pathogen. The strain SGAir0252 was isolated from tropical air samples collected in Singapore, and its complete genome comprises one chromosome of 2.63?Mb and one plasmid of 41.6?kb. Copyright © 2018 Premkrishnan et al.

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July 7, 2019

First detection of a blaCTX-M-15-carrying plasmid in Vibrio alginolyticus.

Vibrio alginolyticus is a gram-negative halophilic bacterium, widely distributed in sea-water and seafood all over the world and is the main pathogenic bacteria of marine animals such as fish, shrimp and shellfish. Besides, it is also an important human pathogen causing eye, ear and wound infections, as well as gastroenteritis, septicemia, and necrotizing fasciitis [1]. Resistance to extended-spectrum cephalosporins is rarely ob- served in V. alginolyticus. Here, we report for the first time the identification of a foodborne V. alginolyticus strain Vb0506 carrying plasmid encoding blaCTX-M-15.

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July 7, 2019

Complete genome sequence of Colwellia hornerae PAMC 20917, a cold-active enzyme-producing bacterium isolated from the Arctic Ocean sediment

Psychrophilic bacteria are considered a source of cold-active enzymes that can be used in industrial applications. The Arctic bacterium Colwellia hornerae PAMC 20917 strain has been isolated from the offshore sediment near Ny-Ålesund, Svalbard. The optimal growth temperature of the strain was 10?°C on marine agar. The cell lysate showed alkaline phosphatase activities. Analysis of the enzymatic properties showed that the alkaline phosphatase was cold-active and thermolabile. To explore useful cold-active industrial enzymes further, the entire genome of the PAMC 20917 strain was sequenced. The genome of the strain contained 4,684,314 nucleotides, with 37.87% G+C content. Genome mining analysis revealed that, in the complete genome sequence, three proteins were annotated as alkaline phosphatases. The genome of PAMC 20917 encodes cold shock proteins and an ice-binding protein that inhibits the growth of ice, allowing the bacterium to adapt to cold environments. This genome information may be useful for understanding mechanisms of adaptation to cold stress.

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July 7, 2019

Identification of repetitive DNA sequences in the Chrysanthemum boreale genome

We previously revealed that the Chrysanthemum boreale genome is highly repetitive; however, the types and nucleotide sequences of repetitive DNA in this diploid wild chrysanthemum are not known. Here, we characterized repetitive DNA sequences in the C. boreale genome by analysing genomic sequences obtained by Illumina sequencing and confirmed their repetitive nature by conducting fluorescence in situ hybridization (FISH) analyses. Annotation of the obtained DNA sequences revealed that microsatellite-containing genomic sequences exhibited similarity with genomic sequences in Chrysanthemum morifolium, indicating sequence conservation of repetitive DNA sequences between the two Chrysanthemum species. Two superfamilies of repetitive DNA, Copia and Gypsy, belonging to the long-terminal repeat (LTR) class of retrotransposons, are abundant in the C. boreale genome. We propose that Copia and Gypsy retroelements contribute to the current genome architecture of C. boreale. Whole genome sequencing, which is currently in progress, will reveal the extent to which these repetitive DNA sequences contribute.

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July 7, 2019

Identification of Pseudomonas mosselii BS011 gene clusters required for suppression of Rice Blast Fungus Magnaporthe oryzae.

Pseudomonas is a Gram-negative, rod-shaped bacteria. Many members of this genus displayed remarkable physiological and metabolic activity against different plant pathogens. However, Pseudomonas mosselii has not yet been characterized in biocontrol against plant disease. Here we isolated a strain of P. mosselii BS011 from the rhizosphere soil of rice plants, and the isolate showed strong inhibitory activity against the rice blast fungus Magnaporthe oryzae. Further we sequenced the complete genome of BS011, which consist of 5.75?Mb with a circular chromosome, 5,170 protein-coding genes, 23 rRNA and 78 tRNA operons. Bioinformatic analysis revealed that seven gene clusters may be involved in the biosynthesis of metabolites. Gene deletion experiments demonstrated that the gene cluster c-xtl is required for inhibitory activity against M. oryzae. Bioassay showed that the crude extract from BS011 fermentation sample significantly inhibited the development of M. oryzae at a concentration of 10?µg/ml. Besides, we illustrated that the crude extract of BS011 impaired the appressorial formation in a dose dependent manner. Collectively our results revealed that P. mosselii BS011 is a promising biocontrol agent and the gene cluster c-xtl is essential for inhibiting the development of M. oryzae. Copyright © 2018. Published by Elsevier B.V.

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July 7, 2019

Phylogeny of dermatophytes with genomic character evaluation of clinically distinct Trichophyton rubrum and T. áviolaceum

Trichophyton rubrum and T. violaceum are prevalent agents of human dermatophyte infections, the former being found on glabrous skin and nail, while the latter is confined to the scalp. The two species are phenotypically different but are highly similar phylogenetically. The taxonomy of dermatophytes is currently being reconsidered on the basis of molecular phylogeny. Molecular species definitions do not always coincide with existing concepts which are guided by ecological and clinical principles. In this article, we aim to bring phylogenetic and ecological data together in an attempt to develop new species concepts for anthropophilic dermatophytes. Focus is on the T. rubrum complex with analysis of rDNA ITS supplemented with LSU, TUB2, TEF3 and ribosomal protein L10 gene sequences. In order to explore genomic differences between T. rubrum and T. violaceum, one representative for both species was whole genome sequenced. Draft sequences were compared with currently available dermatophyte genomes. Potential virulence factors of adhesins and secreted proteases were predicted and compared phylogenetically. General phylogeny showed clear gaps between geophilic species of Arthroderma, but multilocus distances between species were often very small in the derived anthropophilic and zoophilic genus Trichophyton. Significant genome conservation between T. rubrum and T. violaceum was observed, with a high similarity at the nucleic acid level of 99.38 % identity. Trichophyton violaceum contains more paralogs than T. rubrum. About 30 adhesion genes were predicted among dermatophytes. Seventeen adhesins were common between T. rubrum and T. violaceum, while four were specific for the former and eight for the latter. Phylogenetic analysis of secreted proteases reveals considerable expansion and conservation among the analyzed species. Multilocus phylogeny and genome comparison of T. rubrum and T. violaceum underlined their close affinity. The possibility that they represent a single species exhibiting different phenotypes due to different localizations on the human body is discussed.

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July 7, 2019

The case for not masking away repetitive DNA

In the course of analyzing whole-genome data, it is common practice to mask or filter out repetitive regions of a genome, such as transposable elements and endogenous retroviruses, in order to focus only on genes and thus simplify the results. This Commentary is a plea from one member of the Mobile DNA community to all gene-centric researchers: please do not ignore the repetitive fraction of the genome. Please stop narrowing your findings by only analyzing a minority of the genome, and instead broaden your analyses to include the rich biology of repetitive and mobile DNA. In this article, I present four arguments supporting a case for retaining repetitive DNA in your genome-wide analysis.

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