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July 7, 2019

Genetic variation of Pyrenophora teres f. teres isolates in Western Australia and emergence of a Cyp51A fungicide resistance mutation

Genome-wide, unlinked, simple sequence repeat markers were used to examine genetic variation and relationships within Pyrenophora teres f. teres, a common pathogen of barley, in Western Australia. Despite the region’s geographic isolation, the isolates showed relatively high allelic variation compared to similar studies, averaging 7.11 alleles per locus. Principal component, Bayesian clustering and distance differentiation parameters provided evidence for both regional genotypic subdivision together with juxtaposing of isolates possessing different genetic backgrounds. Genotyping of fungicide resistant Cyp51A isolates indicated a single mutation event occurred followed by recombination and long-distance regional dispersal over hundreds of kilometres. Selection of recently emergent favourable alleles such as the Cyp51A mutation and a cultivar virulence may provide an explanation, at least in part, for juxtaposed genotypes. Factors affecting genotypic composition and the movement of new genotypes are discussed in the context of grower practices and pathogen epidemiology, together with the implications for resistance breeding.

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July 7, 2019

Rationally designed perturbation factor drives evolution in Saccharomyces cerevisiae for industrial application.

Saccharomyces cerevisiae strains with favorable characteristics are preferred for application in industries. However, the current ability to reprogram a yeast cell on the genome scale is limited due to the complexity of yeast ploids. In this study, a method named genome replication engineering-assisted continuous evolution (GREACE) was proved efficient in engineering S. cerevisiae with different ploids. Through iterative cycles of culture coupled with selection, GREACE could continuously improve the target traits of yeast by accumulating beneficial genetic modification in genome. The application of GREACE greatly improved the tolerance of yeast against acetic acid compared with their parent strain. This method could also be employed to improve yeast aroma profile and the phenotype could be stably inherited to the offspring. Therefore, GREACE method was efficient in S. cerevisiae engineering and it could be further used to evolve yeast with other specific characteristics.

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July 7, 2019

Genome-wide analysis of the invertase gene family from maize.

The recent release of the maize genome (AGPv4) contains annotation errors of invertase genes and therefore the enzymes are bestly curated manually at the protein level in a comprehensible fashion The synthesis, transport and degradation of sucrose are determining factors for biomass allocation and yield of crop plants. Invertase (INV) is a key enzyme of carbon metabolism in both source and sink tissues. Current releases of the maize genome correctly annotates only two vacuolar invertases (ivr1 and ivr2) and four cell wall invertases (incw1, incw2 (mn1), incw3, and incw4). Our comprehensive survey identified 21 INV isogenes for which we propose a standard nomenclature grouped phylogenetically by amino acid similarity: three vacuolar (INVVR), eight cell wall (INVCW), and ten alkaline/neutral (INVAN) isogenes which form separate dendogram branches due to distinct molecular features. The acidic enzymes were curated for the presence of the DPN tripeptide which is coded by one of the smallest exons reported in plants. Particular attention was placed on the molecular role of INV in vascular tissues such as the nodes, internodes, leaf sheath, husk leaves and roots. We report the expression profile of most members of the maize INV family in nine tissues in two developmental stages, R1 and R3. INVCW7, INVVR2, INVAN8, INVAN9, INVAN10, and INVAN3 displayed the highest absolute expressions in most tissues. INVVR3, INVCW5, INVCW8, and INVAN1 showed low mRNA levels. Expressions of most INVs were repressed from stage R1 to R3, except for INVCW7 which increased significantly in all tissues after flowering. The mRNA levels of INVCW7 in the vegetative stem correlated with a higher transport rate of assimilates from leaves to the cob which led to starch accumulation and growth of the female reproductive organs.

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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.

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July 7, 2019

Complete genome sequence of soil actinobacteria Streptomyces cavourensis TJ430.

A new actinobacteria Streptomyces cavourensis TJ430 was isolated from the mountain soil collected from the southwest of China. In previous study, TJ430 showed striking bactericidal activities and strong ability of antibiotic production. Here, we report complete genome of this bacterium, consisting of 7.6?Mb linear chromosome and 0.2?Mb plasmids. It was predicted 6450 genes in chromosome and 225 genes in plasmids, as well as 12 gene islands in chromosome. Abundant genes have predicted functions in antibiotic metabolism and stress resistance. A whole-genome comparison of S. cavourensis TJ430, S. coelicolor A3(2), and S. lividans 66 indicates that TJ430 has a relatively high degree of strain specificity. The 16S rRNA phylogenetic tree shows the high identities (99.79%) of TJ430 with S. cavourensis DSM40300. TJ430 is a new and rare Streptomyces species, and analysis of its genome helps us to better understand primary metabolism mechanism of this isolate, as well as the evolutionary biology.© 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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July 7, 2019

Evolutionary emergence of drug resistance in Candida opportunistic pathogens.

Fungal infections, such as candidiasis caused by Candida, pose a problem of growing medical concern. In developed countries, the incidence of Candida infections is increasing due to the higher survival of susceptible populations, such as immunocompromised patients or the elderly. Existing treatment options are limited to few antifungal drug families with efficacies that vary depending on the infecting species. In this context, the emergence and spread of resistant Candida isolates are being increasingly reported. Understanding how resistance can evolve within naturally susceptible species is key to developing novel, more effective treatment strategies. However, in contrast to the situation of antibiotic resistance in bacteria, few studies have focused on the evolutionary mechanisms leading to drug resistance in fungal species. In this review, we will survey and discuss current knowledge on the genetic bases of resistance to antifungal drugs in Candida opportunistic pathogens. We will do so from an evolutionary genomics perspective, focusing on the possible evolutionary paths that may lead to the emergence and selection of the resistant phenotype. Finally, we will discuss the potential of future studies enabled by current developments in sequencing technologies, in vitro evolution approaches, and the analysis of serial clinical isolates.

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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.

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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.

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July 7, 2019

Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations

Motivation A long-standing limitation in comparative genomic studies is the dependency on a reference genome, which hinders the spectrum of genetic diversity that can be identified across a population of organisms. This is especially true in the microbial world where genome architectures can significantly vary. There is therefore a need for computational methods that can simultaneously analyze the architectures of multiple genomes without introducing bias from a reference. Results In this article, we present Ptolemy: a novel method for studying the diversity of genome architectures—such as structural variation and pan-genomes—across a collection of microbial assemblies without the need of a reference. Ptolemy is a ‘top-down’ approach to compare whole genome assemblies. Genomes are represented as labeled multi-directed graphs—known as quivers—which are then merged into a single, canonical quiver by identifying ‘gene anchors’ via synteny analysis. The canonical quiver represents an approximate, structural alignment of all genomes in a given collection encoding structural variation across (sub-) populations within the collection. We highlight various applications of Ptolemy by analyzing structural variation and the pan-genomes of different datasets composing of Mycobacterium, Saccharomyces, Escherichia and Shigella species. Our results show that Ptolemy is flexible and can handle both conserved and highly dynamic genome architectures. Ptolemy is user-friendly—requires only FASTA-formatted assembly along with a corresponding GFF-formatted file—and resource-friendly—can align 24 genomes in ~10 mins with four CPUs and <2 GB of RAM.

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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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July 7, 2019

Myxobacteria: Unraveling the potential of a unique microbiome niche

Natural products obtained from microorganisms have been playing an imperative role in drug discovery for decades. Hence, rightfully, microorganisms are considered as the richest source of biochemical remedies. In this review, we represent an unexplored family of bacteria considered to be prolific producers of diverse metabolites. Myxobacteria are gram-negative bacteria which have been reported to produce large families of secondary metabolites with prominent antimicrobial, antifungal, and antitumor activities. Klaus Gerth, Norbert Bedorf, Herbert Irschik, and Hans Reichenbach observed the antifungal activity of Sorangium cellulosum against Mucor hiemalis. In 2006, Hans Reichenbach and his team obtained a novel macrolide cruentaren A from Byssovorax cruenta (myxobacteria). Cruentaren A showed inhibitory activity against yeast and filamentous fungi. It also showed selective inhibitory activity against mitochondrial F-type ATPase. Cruentaren A has been found to be cytotoxic against various human cancer cell lines. In 2007, Reichenbach and his colleagues named an antibiotic produced by Sorangium cellulosum strain Soce895 as thuggacin. This antibiotic acts on the respiration of some bacteria. Other antibiotics from myxobacteria, myxovirescin, and megovalicin show broad-spectrum bactericidal activity. The College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China, evaluated the antitumor property of epothilone, which has shown promise for breast cancer treatment. The study determined high potential and versatile antimicrobial and antitumor secondary metabolites of myxobacteria. In yet another study, Ratjadone A, that exhibited strong antiviral activity against HIV, was obtained from Sorangium cellulosum strain. This compound shows antiviral activity in vitro but has low selectivity. Further search on the derivatives of this compound might help in the future. This is rationale enough to pre-empt that every strain of myxobacteria might be endowed to produce secondary metabolites with novel mechanisms of action which are rarely produced by other microbes. The available data establishes the impact of myxobacterial studies in search for novel metabolites as a front runner in microbiological research and worthy enough to be a thrust area of research in pharmacology.

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July 7, 2019

The molecular basis for the intramolecular migration (NIH shift) of the carboxyl group during para-hydroxybenzoate catabolism.

The NIH shift is a chemical rearrangement in which a substituent on an aromatic ring undergoes an intramolecular migration, primarily during an enzymatic hydroxylation reaction. The molecular mechanism for the NIH shift of a carboxyl group has remained a mystery for 40 years. Here, we elucidate the molecular mechanism of the reaction in the conversion of para-hydroxybenzoate (PHB) to gentisate (GA, 2, 5-dihydroxybenzoate). Three genes (phgABC) from the PHB utilizer Brevibacillus laterosporus PHB-7a encode enzymes (p-hydroxybenzoyl-CoA ligase, p-hydroxybenzoyl-CoA hydroxylase and gentisyl-CoA thioesterase, respectively) catalyzing the conversion of PHB to GA via a route involving CoA thioester formation, hydroxylation concomitant with a 1, 2-shift of the acetyl CoA moiety and thioester hydrolysis. The shift of the carboxyl group was established rigorously by stable isotopic experiments with heterologously expressed phgABC, converting 2, 3, 5, 6-tetradeutero-PHB and [carboxyl-13 C]-PHB to 3, 4, 6-trideutero-GA and [carboxyl-13 C]-GA respectively. This is distinct from the NIH shifts of hydrogen and aceto substituents, where a single oxygenase catalyzes the reaction without the involvement of a thioester. The discovery of this three-step strategy for carboxyl group migration reveals a novel role of the CoA thioester in biochemistry and also illustrates the diversity and complexity of microbial catabolism in the carbon cycle.© 2018 John Wiley & Sons Ltd.

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July 7, 2019

Complete genome sequence of lanthionine-producing Lactobacillus brevis strain 100D8, generated by PacBio sequencing.

Lactobacillus brevis strain 100D8 was isolated from rye silage and showed rapid acidification ability in vitro and antifungal activity against mycotoxin- producing fungi. We report here the complete genome sequence of L. brevis strain 100D8, which has a circular chromosome (2,351,988 bp, 2,304 coding sequences [CDSs]) and three plasmids (45,061 bp, 57 CDSs; 40,740 bp, 40 CDSs; and 39,943 bp, 57 CDSs).

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