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July 7, 2019  |  

Velez bacillusL-1The pear Botrytis cinerea and Penicillium bacteria of suppression role evaluation and all Genome Analysis

[Objective] Clear Velez bacillus(Bacillus S rDNA Sequence) L-1The pear Botrytis cinerea and Penicillium bacteria of suppression role clear Bacteria L-1Sterile fermentation broth antagonistic activity of stability and may be of Antagonistic mechanism. [Methods] by in vitro determination, living determination and pathogenic bacteria mycelium morphology observation evaluation StrainL-1The pear Botrytis cinerea and Penicillium bacteria of antagonistic activity. To pear Botrytis cinerea bacteria for try pathogenic bacteria use Oxford Cup method determination StrainL-1Sterile fermentation broth antagonistic activity of stability. UsePacbio rsiiThree generations sequencing technology determinationL-1Of all gene sequence will all gene sequence and gene protein sequence databaseBLASTComparison Analysis prediction StrainL-1May be of secondary metabolism product and potential of role mechanism. [Results] The StrainL-1The pear Botrytis cinerea and Penicillium bacteria of living inhibition rate respectively92.88%And77.47%Can caused by pathogenic bacteria mycelium enlargement, deformity. StrainL-1In10% NaClOf culture medium in can still normal growth its sterile fermentation broth high temperature resistant, acid, alkali, UV irradiation and protease degradation on pathogenic bacteria has stability of antagonistic activity. All gene sequence analysis results showed that strainL-1Yes112A Gene Involved in the many kinds of carbon source of metabolism can use many kinds of carbon source the growth; containing involved in spermidine, trehalose and strain stress resistance related compounds synthesis of gene; secondary metabolism prediction results display:L-1Containing SynthesisSurfactin,Fengycin,Bacillibactin,Bacillaene,Macolactin,Difficidin,BacilysinAnd many kinds of peptide chitosan and polyketide sugar resistance compounds of gene cluster and can degradation pathogenic bacteria cell wallß-1,3-Glucanase and chitinase related of gene; in addition StrainL-1Containing generation acetoin and can induced Plant Resistance of gene. [Conclusion] StrainL-1Can effective antagonistic many kinds of pear of after disease resistance strong antagonistic activity stability prediction StrainL-1Can by producing many kinds of antagonistic activity compounds and cell wall hydrolysis enzymes and induced Plant Resistance implementation disease prevention effect has very big of application potential.

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July 7, 2019  |  

The ß-lactamase gene profile and a plasmid-carrying multiple heavy metal resistance genes of Enterobacter cloacae.

In this work, by high-throughput sequencing, antibiotic resistance genes, including class A (blaCTX-M, blaZ, blaTEM, blaVEB, blaKLUC, and blaSFO), class C (blaSHV, blaDHA, blaMIR, blaAZECL-29, and blaACT), and class D (blaOXA) ß-lactamase genes, were identified among the pooled genomic DNA from 212 clinical Enterobacter cloacae isolates. Six blaMIR-positive E. cloacae strains were identified, and pulsed-field gel electrophoresis (PFGE) showed that these strains were not clonally related. The complete genome of the blaMIR-positive strain (Y546) consisted of both a chromosome (4.78?Mb) and a large plasmid pY546 (208.74?kb). The extended-spectrum ß-lactamases (ESBLs) (blaSHV-12 and blaCTX-M-9a) and AmpC (blaMIR) were encoded on the chromosome, and the pY546 plasmid contained several clusters of genes conferring resistance to metals, such as copper (pco), arsenic (ars), tellurite (ter), and tetrathionate (ttr), and genes encoding many divalent cation transporter proteins. The comparative genomic analyses of the whole plasmid sequence and of the heavy metal resistance gene-encoding regions revealed that the plasmid sequences of Klebsiella pneumoniae (such as pKPN-332, pKPN-3967, and pKPN-262) shared the highest similarity with those of pY546. It may be concluded that a variety of ß-lactamase genes present in E. cloacae which confer resistance to ß-lactam antibiotics and the emergence of plasmids carrying heavy metal resistance genes in clinical isolates are alarming and need further surveillance.

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July 7, 2019  |  

Alignment-free genome comparison enables accurate geographic sourcing of white oak DNA.

The application of genomic data and bioinformatics for the identification of restricted or illegally-sourced natural products is urgently needed. The taxonomic identity and geographic provenance of raw and processed materials have implications in sustainable-use commercial practices, and relevance to the enforcement of laws that regulate or restrict illegally harvested materials, such as timber. Improvements in genomics make it possible to capture and sequence partial-to-complete genomes from challenging tissues, such as wood and wood products.In this paper, we report the success of an alignment-free genome comparison method, [Formula: see text] that differentiates different geographic sources of white oak (Quercus) species with a high level of accuracy with very small amount of genomic data. The method is robust to sequencing errors, different sequencing laboratories and sequencing platforms.This method offers an approach based on genome-scale data, rather than panels of pre-selected markers for specific taxa. The method provides a generalizable platform for the identification and sourcing of materials using a unified next generation sequencing and analysis framework.

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July 7, 2019  |  

Hardwood tree genomics: Unlocking woody plant biology.

Woody perennial angiosperms (i.e., hardwood trees) are polyphyletic in origin and occur in most angiosperm orders. Despite their independent origins, hardwoods have shared physiological, anatomical, and life history traits distinct from their herbaceous relatives. New high-throughput DNA sequencing platforms have provided access to numerous woody plant genomes beyond the early reference genomes of Populus and Eucalyptus, references that now include willow and oak, with pecan and chestnut soon to follow. Genomic studies within these diverse and undomesticated species have successfully linked genes to ecological, physiological, and developmental traits directly. Moreover, comparative genomic approaches are providing insights into speciation events while large-scale DNA resequencing of native collections is identifying population-level genetic diversity responsible for variation in key woody plant biology across and within species. Current research is focused on developing genomic prediction models for breeding, defining speciation and local adaptation, detecting and characterizing somatic mutations, revealing the mechanisms of gender determination and flowering, and application of systems biology approaches to model complex regulatory networks underlying quantitative traits. Emerging technologies such as single-molecule, long-read sequencing is being employed as additional woody plant species, and genotypes within species, are sequenced, thus enabling a comparative (“evo-devo”) approach to understanding the unique biology of large woody plants. Resource availability, current genomic and genetic applications, new discoveries and predicted future developments are illustrated and discussed for poplar, eucalyptus, willow, oak, chestnut, and pecan.

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July 7, 2019  |  

De novo genome assembly of the olive fruit fly (Bactrocera oleae) developed through a combination of linked-reads and long-read technologies

Long-read sequencing has greatly contributed to the generation of high quality assemblies, albeit at a high cost. It is also not always clear how to combine sequencing platforms. We sequenced the genome of the olive fruit fly (Bactrocera oleae), the most important pest in the olive fruits agribusiness industry, using Illumina short-reads, mate-pairs, 10x Genomics linked-reads, Pacific Biosciences (PacBio), and Oxford Nanopore Technologies (ONT). The 10x linked-reads assembly gave the most contiguous assembly with an N50 of 2.16 Mb. Scaffolding the linked-reads assembly using long-reads from ONT gave a more contiguous assembly with scaffold N50 of 4.59 Mb. We also present the most extensive transcriptome datasets of the olive fly derived from different tissues and stages of development. Finally, we used the Chromosome Quotient method to identify Y-chromosome scaffolds and show that the long-reads based assembly generates very highly contiguous Y-chromosome assembly.

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July 7, 2019  |  

The complete genome sequence of a marine sponge-associated bacteria, Bacillus safensis KCTC 12796BP, which produces the anti-allergic compounds

The full genome sequence of Bacillus safensis KCTC 12796BP which had been isolated from the marine sponge in the seawater of Jeju Island, was determined by Pac-Bio next- generation sequencing system. A circular chromosome in the length of 3,935,874 bp was obtained in addition to a circular form of plasmid having 36,690 bp. The G + C content of chromosome was 41.4%, and that of plasmid was 37.3%. The number of deduced CDSs in the chromosome was 3,980, whereas 36 CDS regions were determined in a plasmid. Among the deduced CDSs in chromosome, 81 tRNA genes and 24 rRNA genes in addition to one tmRNA were allocated. More than 30 CDSs for sporulation, 16 CDSs for spore coat, and 20 CDSs for germination were also assigned in the chromosome. Several genes for capsular polysaccharide biosynthesis and for flagella biosynthesis and chemotaxis in addition to genes for osmotic tolerance through glycine-choline betaine pathway were also identified. Above all, the biosynthetic gene cluster for anti- allergic compounds seongsanamides were found among two non-ribosomal peptide synthetase (NRPS) gene clusters for secondary metabolites.

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