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Sunday, July 7, 2019

Complete genome sequence of Loktanella vestfoldensis strain SMR4r, a novel strain isolated from a culture of the chain-forming diatom Skeletonema marinoi.

We report here the genome sequence of Loktanella vestfoldensis strain SMR4r, isolated from the marine diatom Skeletonema marinoi strain RO5AC. Its 3,987,360-bp genome consists of a circular chromosome and two circular plasmids, one of which appears to be shared with an S. marinoi-associated Roseovarius species. Copyright © 2018 Töpel et al.

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Sunday, July 7, 2019

Complete genome sequence of the symbiotic strain Bradyrhizobium icense LMTR 13T, isolated from lima bean (Phaseolus lunatus) in Peru.

The complete genome sequence of Bradyrhizobium icense LMTR 13T, a root nodule bacterium isolated from the legume Phaseolus lunatus, is reported here. The genome consists of a circular 8,322,773-bp chromosome which codes for a large and novel symbiotic island as well as genes putatively involved in soil and root colonization. Copyright © 2018 Ormeño-Orrillo et al.

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Sunday, 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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Sunday, 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…

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Sunday, July 7, 2019

Genome sequence resources for the wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici) and the barley stripe rust pathogen (Puccinia striiformis f. sp. hordei)

Puccinia striiformis f. sp. tritici causes devastating stripe (yellow) rust on wheat and P. striiformis f. sp. hordei causes stripe rust on barley. Several P. striiformis f. sp. tritici genomes are available, but no P. striiformis f. sp. hordei genome is available. More genomes of P. striiformis f. sp. tritici and P. striiformis f. sp. hordei are needed to understand the genome evolution and molecular mechanisms of their pathogenicity. We sequenced P. striiformis f. sp. tritici isolate 93-210 and P. striiformis f. sp. hordei isolate 93TX-2, using PacBio and Illumina technologies and RNA sequencing. Their genomic sequences were assembled to…

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Sunday, July 7, 2019

Modular traits of the Rhizobiales root microbiota and their evolutionary relationship with symbiotic Rhizobia.

Rhizobia are a paraphyletic group of soil-borne bacteria that induce nodule organogenesis in legume roots and fix atmospheric nitrogen for plant growth. In non-leguminous plants, species from the Rhizobiales order define a core lineage of the plant microbiota, suggesting additional functional interactions with plant hosts. In this work, genome analyses of 1,314 Rhizobiales isolates along with amplicon studies of the root microbiota reveal the evolutionary history of nitrogen-fixing symbiosis in this bacterial order. Key symbiosis genes were acquired multiple times, and the most recent common ancestor could colonize roots of a broad host range. In addition, root growth promotion is…

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Sunday, July 7, 2019

First description of novel arginine catabolic mobile elements (ACMEs) types IV and V harboring a kdp operon in Staphylococcus epidermidis characterized by whole genome sequencing.

The arginine catabolic mobile element (ACME) was first described in the methicillin-resistant Staphylococcus aureus strain USA300 and is thought to facilitate survival on skin. To date three distinct ACME types have been characterized comprehensively in S. aureus and/or Staphylococcus epidermidis. Type I harbors the arc and opp3 operons encoding an arginine deaminase pathway and an oligopeptide permease ABC transporter, respectively, type II harbors the arc operon only, and type III harbors the opp3 operon only. To investigate the diversity and detailed genetic organization of ACME, whole genome sequencing (WGS) was performed on 32 ACME-harboring oro-nasal S. epidermidis isolates using MiSeq-…

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Sunday, July 7, 2019

Identification of different putative outer membrane electron conduits necessary for Fe(III) citrate, Fe(III) oxide, Mn(IV) oxide, or electrode reduction by Geobacter sulfurreducens.

At least five gene clusters in the Geobacter sulfurreducens genome encode putative “electron conduits” implicated in electron transfer across the outer membrane, each containing a periplasmic multiheme c-type cytochrome, integral outer membrane anchor, and outer membrane redox lipoprotein(s). Markerless single-gene-cluster deletions and all possible multiple-deletion combinations were constructed and grown with soluble Fe(III) citrate, Fe(III) and Mn(IV) oxides, and graphite electrodes poised at +0.24 V and -0.1 V versus the standard hydrogen electrode (SHE). Different gene clusters were necessary for reduction of each electron acceptor. During metal oxide reduction, deletion of the previously described omcBC cluster caused defects, but deletion…

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Sunday, July 7, 2019

Moving forward: recent developments for the ferret biomedical research model.

Since the initial report in 1911, the domestic ferret has become an invaluable biomedical research model. While widely recognized for its utility in influenza virus research, ferrets are used for a variety of infectious and noninfectious disease models due to the anatomical, metabolic, and physiological features they share with humans and their susceptibility to many human pathogens. However, there are limitations to the model that must be overcome for maximal utility for the scientific community. Here, we describe important recent advances that will accelerate biomedical research with this animal model. Copyright © 2018 Albrecht et al.

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Sunday, July 7, 2019

Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size.

The genus Methanosphaera is a well-recognized but poorly characterized member of the mammalian gut microbiome, and distinctive from Methanobrevibacter smithii for its ability to induce a pro-inflammatory response in humans. Here we have used a combination of culture- and metagenomics-based approaches to expand the representation and information for the genus, which has supported the examination of their phylogeny and physiological capacity. Novel isolates of the genus Methanosphaera were recovered from bovine rumen digesta and human stool, with the bovine isolate remarkable for its large genome size relative to other Methanosphaera isolates from monogastric hosts. To substantiate this observation, we then…

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Sunday, July 7, 2019

Immunoglobulin gene analysis as a tool for investigating human immune responses.

The human immunoglobulin repertoire is a hugely diverse set of sequences that are formed by processes of gene rearrangement, heavy and light chain gene assortment, class switching and somatic hypermutation. Early B cell development produces diverse IgM and IgD B cell receptors on the B cell surface, resulting in a repertoire that can bind many foreign antigens but which has had self-reactive B cells removed. Later antigen-dependent development processes adjust the antigen affinity of the receptor by somatic hypermutation. The effector mechanism of the antibody is also adjusted, by switching the class of the antibody from IgM to one of…

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Sunday, July 7, 2019

Complete genome sequence of industrial biocontrol strain Paenibacillus polymyxa HY96-2 and further analysis of Its biocontrol mechanism.

Paenibacillus polymyxa (formerly known as Bacillus polymyxa) has been extensively studied for agricultural applications as a plant-growth-promoting rhizobacterium and is also an important biocontrol agent. Our team has developed the P. polymyxa strain HY96-2 from the tomato rhizosphere as the first microbial biopesticide based on P. polymyxa for controlling plant diseases around the world, leading to the commercialization of this microbial biopesticide in China. However, further research is essential for understanding its precise biocontrol mechanisms. In this paper, we report the complete genome sequence of HY96-2 and the results of a comparative genomic analysis between different P. polymyxa strains. The…

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Sunday, July 7, 2019

sppIDer: a species identification tool to investigate hybrid genomes with high-throughput sequencing.

The genomics era has expanded our knowledge about the diversity of the living world, yet harnessing high-throughput sequencing data to investigate alternative evolutionary trajectories, such as hybridization, is still challenging. Here we present sppIDer, a pipeline for the characterization of interspecies hybrids and pure species, that illuminates the complete composition of genomes. sppIDer maps short-read sequencing data to a combination genome built from reference genomes of several species of interest and assesses the genomic contribution and relative ploidy of each parental species, producing a series of colorful graphical outputs ready for publication. As a proof-of-concept, we use the genus Saccharomyces…

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Sunday, July 7, 2019

Genomic characterization of methylotrophy of Oharaeibacter diazotrophicus strain SM30T.

Oharaeibacter diazotrophicus strain SM30T, isolated from rice rhizosphere, is an aerobic, facultative lanthanide (Ln3+)-utilizing methylotroph and diazotroph that belongs to the Methylocystaceae family. In this research, the complete genome sequence of strain SM30T was determined, and its methylotrophy modules were characterized. The genome consists of one chromosome and two plasmids, comprising a total of 5,004,097 bp, and the GC content was 71.6 mol%. A total of 4497 CDSs, 67 tRNA, and 9 rRNA were encoded. Typical alpha-proteobacterial methylotrophy genes were found: pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH) (mxaF and xoxF1-4), methylotrophy regulatory proteins (mxbDM and mxcQE), PQQ synthesis, H4F pathway, H4MPT…

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