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Monday, April 27, 2020

Application Note: Microbial multiplexing workflow on the Sequel System

Obtaining microbial genomes with the highest accuracy and contiguity is extremely important when exploring the functional impact of genetic and epigenetic variants on a genome-wide scale. A comprehensive view of the bacterial genome, including genes, regulatory regions, IS elements, phage integration sites, and base modifications is vital to understanding key traits such as antibiotic resistance, virulence, and metabolism. SMRT Sequencing provides complete genomes, often assembled into a single contig. Our streamlined microbial multiplexing procedure for the Sequel System, from library preparation to genome assembly, can be completed with less than 8 hours bench time. Starting with high-quality genomic DNA (gDNA),…

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Tuesday, April 21, 2020

Complete Genome Sequence of strain WHRI 3811, race 1 of Xanthomonas campestris pv. campestris, the Causal Agent of Black Rot of Cruciferous Vegetables.

Xanthomonas campestris pv. campestris (Xcc) is an important bacterial pathogen that causes black rot and brings about enormous production loss for cruciferous vegetables worldwide. Currently, genome sequences for only a few Xcc isolates are available, most of which are draft ones. Based on the next-generation sequencing (NGS) and single-molecule sequencing in real time (SMRT) technologies, we present here the complete genome sequence of strain WHRI 3811, race 1 of Xcc, which is a type strain that has been extensively used. The genome data will contribute to our understanding of Xcc genomic features, and pave the way for research on Xcc-host…

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Tuesday, April 21, 2020

Updated assembly resource of Phytophthora ramorum Pr102 isolate incorporating long reads from PacBio sequencing.

The NA1 clonal lineage of Phytophthora ramorum is responsible for Sudden Oak Death, an epidemic that has devastated California’s coastal forest ecosystems. An NA1 isolate Pr102 derived from coast live oak in California was previously sequenced and reported with 65 Mb assembly containing 12 Mb gaps in 2576 scaffolds. Here we report an improved 70 Mb genome in 1512 scaffolds with 6752 bp gaps after incorporating PacBio P5-C3 longreads. This assembly contains 19494 gene models (average gene length 2515 bp) compared to 16134 genes (average gene length of 1673 bp) in the previous version. We predicted 29 new RXLRs and…

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Tuesday, April 21, 2020

Soil Probiotic Utilizes Plant and Pollinator Transport for Territorial Expansion

Microbe-plant interactions are linked with the core microbiota, and both the plant and the microbial partners depend on one other to thrive in nature. However, why and how the below-ground core microbiota become established aboveground is poorly understood. We tracked the movement of a probiotic Streptomyces endophyte throughout a managed strawberry ecosystem. Probiotics in the rhizosphere and anthosphere were genetically identical, yet these niches were segregated in space and time. The probiotic in the rhizosphere moved upward via the vascular bundle, relocated to aboveground plant parts, and protected against Botrytis cinerea. It also moved from flowers to roots, and among…

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Tuesday, April 21, 2020

Genome data of Fusarium oxysporum f. sp. cubense race 1 and tropical race 4 isolates using long-read sequencing.

Fusarium wilt of banana is caused by the soil-borne fungal pathogen Fusarium oxysporum f. sp. cubense (Foc). We generated two chromosome-level assemblies of Foc race 1 and tropical race 4 strains using single-molecule real-time sequencing. The Foc1 and FocTR4 assemblies had 35 and 29 contigs with contig N50 lengths of 2.08 Mb and 4.28 Mb, respectively. These two new references genomes represent a greater than 100-fold improvement over the contig N50 statistics of the previous short read-based Foc assemblies. The two high-quality assemblies reported here will be a valuable resource for the comparative analysis of Foc races at the pathogenic…

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Tuesday, April 21, 2020

Genome sequence resources for four phytopathogenic fungi from the Colletotrichum orbiculare species complex.

Colletotrichum orbiculare species complex fungi are hemibiotrophic plant pathogens that cause anthracnose of field crops and weeds. Members of this group have genomes that are remarkably expanded relative to other Colletotrichum fungi and compartmentalized into AT-rich, gene poor and GC-rich, gene rich regions. Here we present an updated version of the Colletotrichum orbiculare genome, as well as draft genomes of three other members from the C. orbiculare species complex; the alfalfa pathogen Colletotrichum trifolii, the prickly mallow pathogen Colletotrichum sidae and the burweed pathogen Colletotrichum spinosum. The data reported here will be important for comparative genomics analyses to identify factors…

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Tuesday, April 21, 2020

Defining transgene insertion sites and off-target effects of homology-based gene silencing informs the use of functional genomics tools in Phytophthora infestans.

DNA transformation and homology-based transcriptional silencing are frequently used to assess gene function in Phytophthora. Since unplanned side-effects of these tools are not well-characterized, we used P. infestans to study plasmid integration sites and whether knockdowns caused by homology-dependent silencing spreads to other genes. Insertions occurred both in gene-dense and gene-sparse regions but disproportionately near the 5′ ends of genes, which disrupted native coding sequences. Microhomology at the recombination site between plasmid and chromosome was common. Studies of transformants silenced for twelve different gene targets indicated that neighbors within 500-nt were often co-silenced, regardless of whether hairpin or sense constructs…

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Tuesday, April 21, 2020

The Ptr1 locus of Solanum lycopersicoides confers resistance to race 1 strains of Pseudomonas syringae pv. tomato and to Ralstonia pseudosolanacearum by recognizing the type III effectors AvrRpt2/RipBN.

Race 1 strains of Pseudomonas syringae pv. tomato, which cause bacterial speck disease of tomato, are becoming increasingly common and no simply-inherited genetic resistance to such strains is known. We discovered that a locus in Solanum lycopersicoides, termed Pseudomonas tomato race 1 (Ptr1), confers resistance to race 1 Pst strains by detecting the activity of type III effector AvrRpt2. In Arabidopsis, AvrRpt2 degrades the RIN4 protein thereby activating RPS2-mediated immunity. Using site-directed mutagenesis of AvrRpt2 we found that, like RPS2, activation of Ptr1 requires AvrRpt2 proteolytic activity. Ptr1 also detected the activity of AvrRpt2 homologs from diverse bacteria including one…

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Tuesday, April 21, 2020

Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits.

The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expansion in human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the…

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Tuesday, April 21, 2020

The replication-competent HIV-1 latent reservoir is primarily established near the time of therapy initiation.

Although antiretroviral therapy (ART) is highly effective at suppressing HIV-1 replication, the virus persists as a latent reservoir in resting CD4+ T cells during therapy. This reservoir forms even when ART is initiated early after infection, but the dynamics of its formation are largely unknown. The viral reservoirs of individuals who initiate ART during chronic infection are generally larger and genetically more diverse than those of individuals who initiate therapy during acute infection, consistent with the hypothesis that the reservoir is formed continuously throughout untreated infection. To determine when viruses enter the latent reservoir, we compared sequences of replication-competent viruses…

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Tuesday, April 21, 2020

Rapid transcriptional responses to serum exposure are associated with sensitivity and resistance to antibody-mediated complement killing in invasive Salmonella Typhimurium ST313

Background: Salmonella Typhimurium ST313 exhibits signatures of adaptation to invasive human infection, including higher resistance to humoral immune responses than gastrointestinal isolates. Full resistance to antibody-mediated complement killing (serum resistance) among nontyphoidal Salmonellae is uncommon, but selection of highly resistant strains could compromise vaccine-induced antibody immunity. Here, we address the hypothesis that serum resistance is due to a distinct genotype or transcriptome response in S. Typhimurium ST313.

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Tuesday, April 21, 2020

Draft Genome Sequence of Mesosutterella multiformis JCM 32464T, a Member of the Family Sutterellaceae, Isolated from Human Feces.

Here, we report the draft genome sequence of Mesosutterella multiformis JCM 32464T, a new member of the family Sutterellaceae that was isolated from human feces. The genome assembly comprised 2,621,983?bp, with a G+C content of 56.9%. This genomic analysis will be useful for understanding the metabolic activities of this asaccharolytic bacterium.Copyright © 2019 Ikeyama et al.

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Tuesday, April 21, 2020

Plantibacter flavus, Curtobacterium herbarum, Paenibacillus taichungensis, and Rhizobium selenitireducens Endophytes Provide Host-Specific Growth Promotion of Arabidopsis thaliana, Basil, Lettuce, and Bok Choy Plants.

A collection of bacterial endophytes isolated from stem tissues of plants growing in soils highly contaminated with petroleum hydrocarbons were screened for plant growth-promoting capabilities. Twenty-seven endophytic isolates significantly improved the growth of Arabidopsis thaliana plants in comparison to that of uninoculated control plants. The five most beneficial isolates, one strain each of Curtobacterium herbarum, Paenibacillus taichungensis, and Rhizobium selenitireducens and two strains of Plantibacter flavus were further examined for growth promotion in Arabidopsis, lettuce, basil, and bok choy plants. Host-specific plant growth promotion was observed when plants were inoculated with the five bacterial strains. P. flavus strain M251 increased…

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Tuesday, April 21, 2020

Genome Sequence and Methylation Patterns of Halorubrum sp. Strain BOL3-1, the First Haloarchaeon Isolated and Cultured from Salar de Uyuni, Bolivia.

Halorubrum sp. strain BOL3-1 was isolated from Salar de Uyuni, Bolivia, and sequenced using single-molecule real-time sequencing. Its 3.7-Mbp genome was analyzed for gene content and methylation patterns and incorporated into the Haloarchaeal Genomes Database (http://halo.umbc.edu). The polyextremophilic character and high-elevation environment make the microbe of interest for astrobiology. Copyright © 2019 DasSarma et al.

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