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July 7, 2019

Complete genome sequence of Rhizobium sp. strain 11515TR, isolated from tomato rhizosphere in the Philippines.

Rhizobium sp. strain 11515TR was isolated from the rhizosphere of to- mato in Laguna, Philippines. The 7.07-Mb complete genome comprises three repli- cons, one chromosome, and two plasmids, with a G?C content of 59.4% and 6,720 protein-coding genes. The genome encodes gene clusters supporting rhizosphere processes, plant symbiosis, and secondary bioactive metabolites.


July 7, 2019

Near- complete genome sequences of Streptomyces sp. strains AC1-42T and AC1-42W, isolated from bat guano from Cabalyorisa Cave, Mabini, Pangasinan, Philippines.

Streptomyces sp. strains AC1-42T and AC1-42W, isolated from bat guano from Cabalyorisa Cave, Mabini, Pangasinan, Philippines, are active against Bacillus subtilis subsp. subtilis KCTC 3135T. The near-complete genome sequences reported here represent a possible source of ribosomally synthesized, posttranslationally mod- ified peptides, such as lantipeptides, bacteriocins, linaridin, and a lasso peptide.


July 7, 2019

Complete genome sequence of Lactococcus lactis subsp. lactis SLPE1-3, a novel lactic acid bacterium causing postharvest decay of the mushroom Pleurotus eryngii

Lactococcus lactis subsp. lactis is a pathogenic bacterium causing postharvest decay of the cultivated mushroom Pleurotus eryngii, whose pathogenic mechanism is little known. Sequencing of its complete genome is a prerequisite for revealing the molecular mechanism of infection. In this research, the complete genome of SLPE1-3 was obtained using the Single Molecular Real Time (SMRT) sequencing strategy. The genome was analyzed both structurally and functionally. The complete genome of SLPE1-3 consists of a single, circular chromosome (2,522,493 bp; 34.91% GC content) without any plasmid. The results showed the feasibility and superiority of SMRT in bacterial complete-genome research. The genome of SLPE1-3 has the specific features of L. lactis subsp. lactis not just in the phylogenesis and genome structure, but also in functional classification. Compared with L. lactis subsp. lactis IL1403, L. lactis subsp. cremoris MG1363 and L. lactis subsp. lactis KF147, 23 peculiar genes were identified in SLPE1-3 which were involved in lipid metabolism, cell wall biogenesis and some functional enzymes. In addition, 37 potential genes relating to antifungal function were filtered for further mechanism research.


July 7, 2019

Genome resequencing and analysis of d-lactic acid fermentation ability of Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293

Genome resequencing of D-lactic acid-producing Leuconostoc mesenteroides ATCC 8293 revealed 28 base errors in the version published in the 2017. Based on the revised genome annotation, four genes encoding putative D- lactate dehydrogenases were identified. The transcriptional expression of each gene was analyzed at different growth phases and the functionality of each gene was studied in Escherichia coli. Bioreactor studies indicated that L. mesenteroides ATCC 8293 produced D-lactic acid and ethanol at a ratio of 1.7:1 (g/g) regardless of the glucose concentration.


July 7, 2019

Traditional Norwegian kveik are a genetically distinct group of domesticated Saccharomyces cerevisiae brewing yeasts.

The widespread production of fermented food and beverages has resulted in the domestication of Saccharomyces cerevisiae yeasts specifically adapted to beer production. While there is evidence beer yeast domestication was accelerated by industrialization of beer, there also exists a farmhouse brewing culture in western Norway which has passed down yeasts referred to as kveik for generations. This practice has resulted in ale yeasts which are typically highly flocculant, phenolic off flavor negative (POF-), and exhibit a high rate of fermentation, similar to previously characterized lineages of domesticated yeast. Additionally, kveik yeasts are reportedly high-temperature tolerant, likely due to the traditional practice of pitching yeast into warm (>28°C) wort. Here, we characterize kveik yeasts from 9 different Norwegian sources via PCR fingerprinting, whole genome sequencing of selected strains, phenotypic screens, and lab-scale fermentations. Phylogenetic analysis suggests that kveik yeasts form a distinct group among beer yeasts. Additionally, we identify a novel POF- loss-of-function mutation, as well as SNPs and CNVs potentially relevant to the thermotolerance, high ethanol tolerance, and high fermentation rate phenotypes of kveik strains. We also identify domestication markers related to flocculation in kveik. Taken together, the results suggest that Norwegian kveik yeasts are a genetically distinct group of domesticated beer yeasts with properties highly relevant to the brewing sector.


July 7, 2019

Genomics, GPCRs and new targets for the control of insect pests and vectors.

The pressing need for new pest control products with novel modes of action has spawned interest in small molecules and peptides targeting arthropod GPCRs. Genome sequence data and tools for reverse genetics have enabled the prediction and characterization of GPCRs from many invertebrates. We review recent work to identify, characterize and de-orphanize arthropod GPCRs, with a focus on studies that reveal exciting new functional roles for these receptors, including the regulation of metabolic resistance. We explore the potential for insecticides targeting Class A biogenic amine-binding and peptide-binding receptors, and consider the innovation required to generate pest-selective leads for development, within the context of new PCR-targeting products to control arthropod vectors of disease.Copyright © 2018. Published by Elsevier Inc.


July 7, 2019

DNA sequences and predicted protein structures of prot6E and sefA genes for Salmonella ser. Enteritidis detection

Genes prot6E and sefA are used as targets for detection of Salmonella enterica subsp. enterica serovar Enteritidis (Salmonella ser. Enteritidis). We investigated variations in these genes across 64 different Salmonella ser. Enteritidis strains isolated from egg and chicken samples, then used Whole Genome Sequence (WGS) data to model the structures of their protein products. Isolates were sequenced using Illumina technologies. Based on the resulting phylogenetic tree, our isolates clustered in 2 distinct clades. All isolates carried prot6E and sefA. Comparative genomic analyses indicated two non-synonymous mutations (Glycine ? Serine and Valine ? Isoleucine) of prot6E in 11 isolates (9 egg samples, 2 chicken samples). However, SWISS-MODEL was unable to clearly model the protein structure of these two mutations. We identified one non-synonymous mutation (Valine ? Glutamic Acid) in the sefA gene in 4 isolates from egg samples. The model for the protein structure of this mutant gene was clearly different from that of the other isolates studied herein. Circular maps of plasmid genomes from two PacBio platform-sequenced Salmonella ser. Enteritidis isolates revealed prot6E gene was located on the tail of the plasmid. Based on the biosynthesis of amino acids – Reference pathway in the KEGG pathway Database, the transition of amino acid from sefA Var. was a transversion from essential amino acid to non-essential amino acid, while that of prot6E Var.1 happened between the conditionally non-essential amino acid, and prot6E Var. 2 occurred between essential amino acids. Properties of these mutated amino acids, such as side-chain polarity or charge, may contribute to the occurrence and rate of mutations in prot6E and sefA. These insights can be used to improve detection methods for Salmonella ser. Enteritidis.


July 7, 2019

Omics in weed science: A perspective from genomics, transcriptomics, and metabolomics approaches

Modern high-throughput molecular and analytical tools offer exciting opportunities to gain a mechanistic understanding of unique traits of weeds. During the past decade, tremendous progress has been made within the weed science discipline using genomic techniques to gain deeper insights into weedy traits such as invasiveness, hybridization, and herbicide resistance. Though the adoption of newer “omics” techniques such as proteomics, metabolomics, and physionomics has been slow, applications of these omics platforms to study plants, especially agriculturally important crops and weeds, have been increasing over the years. In weed science, these platforms are now used more frequently to understand mechanisms of herbicide resistance, weed resistance evolution, and crop–weed interactions. Use of these techniques could help weed scientists to further reduce the knowledge gaps in understanding weedy traits. Although these techniques can provide robust insights about the molecular functioning of plants, employing a single omics platform can rarely elucidate the gene-level regulation and the associated real-time expression of weedy traits due to the complex and overlapping nature of biological interactions. Therefore, it is desirable to integrate the different omics technologies to give a better understanding of molecular functioning of biological systems. This multidimensional integrated approach can therefore offer new avenues for better understanding of questions of interest to weed scientists. This review offers a retrospective and prospective examination of omics platforms employed to investigate weed physiology and novel approaches and new technologies that can provide holistic and knowledge-based weed management strategies for future.


July 7, 2019

Complete genome sequence of an efficient vitamin D3-hydroxylating bacterium, Pseudonocardia autotrophica NBRC 12743.

Pseudonocardia autotrophica NBRC 12743 contains a cytochrome P450 vitamin D3hydroxylase, and it is used as a biocatalyst for the commercial produc- tion of hydroxyvitamin D3, a valuable compound for medication. Here, we report the complete genome sequence of P. autotrophica NBRC 12743, which could be useful for improving the productivity of hydroxyvitamin D3.


July 7, 2019

Near-complete genome sequence of Ralstonia solanacearum T523, a phylotype I tomato phytopathogen isolated from the Philippines.

Ralstonia solanacearum strain T523 is the major phytopathogen causing tomato bacterial wilt in the Philippines. Here, we report the complete chromosome and draft megaplasmid genomes with predicted gene inventories supporting rhizo- sphere processes, extensive plant virulence effectors, and the production of bioac- tive signaling metabolites, such as ralstonin, micacocidin, and homoserine lactone.


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