scholarly journals Draft Genome Sequence of Methylobacterium sp. ME121, Isolated from Soil as a Mixed Single Colony with Kaistia sp. 32K

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Shun Fujinami ◽  
Kiyoko Takeda-Yano ◽  
Takefumi Onodera ◽  
Katsuya Satoh ◽  
Tetsu Shimizu ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Molecular Mechanisms ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Single Colony

Methylobacterium sp. ME121 was isolated from soil as a mixed single colony with Kaistia sp. 32K, and its growth was enhanced by coculture. Here, we report the draft genome sequence of Methylobacterium sp. ME121, which may contribute to the study of the molecular mechanisms underlying this phenomenon.

scholarly journals Draft Genome Sequence and Transcriptional Analysis of Rosellinia necatrix Infected with a Virulent Mycovirus

2018 ◽  
Vol 108 (10) ◽  
pp. 1206-1211 ◽  
Author(s):  
Takeo Shimizu ◽  
Satoko Kanematsu ◽  
Hajime Yaegashi
Keyword(s):  
Genome Sequence ◽  
Molecular Mechanisms ◽  
Plant Cell Wall ◽  
Draft Genome ◽  
Transcriptional Analysis ◽  
Draft Genome Sequence ◽  
Effective Control ◽  
Economic Losses ◽  
Rosellinia Necatrix ◽  
Cell Wall Degrading Enzymes

Understanding the molecular mechanisms of pathogenesis is useful in developing effective control methods for fungal diseases. The white root rot fungus Rosellinia necatrix is a soilborne pathogen that causes serious economic losses in various crops, including fruit trees, worldwide. Here, using next-generation sequencing techniques, we first produced a 44-Mb draft genome sequence of R. necatrix strain W97, an isolate from Japan, in which 12,444 protein-coding genes were predicted. To survey differentially expressed genes (DEGs) associated with the pathogenesis of the fungus, the hypovirulent W97 strain infected with Rosellinia necatrix megabirnavirus 1 (RnMBV1) was used for a comprehensive transcriptome analysis. In total, 545 and 615 genes are up- and down-regulated, respectively, in R. necatrix infected with RnMBV1. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses of the DEGs suggested that primary and secondary metabolism would be greatly disturbed in R. necatrix infected with RnMBV1. The genes encoding transcriptional regulators, plant cell wall-degrading enzymes, and toxin production, such as cytochalasin E, were also found in the DEGs. The genetic resources provided in this study will accelerate the discovery of genes associated with pathogenesis and other biological characteristics of R. necatrix, thus contributing to disease control.

scholarly journals First Draft Genome Sequence of Xanthomonas axonopodis pv. eucalyptorum, Causal Agent of Bacterial Leaf Blight on Eucalypt

2019 ◽  
Vol 8 (16) ◽  
Author(s):  
Yane F. Neves ◽  
Samuel A. Santos ◽  
Lúcio M. S. Guimarães ◽  
Pedro M. P. Vidigal ◽  
Jorge L. Badel ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Bacterial Blight ◽  
Molecular Mechanisms ◽  
Draft Genome ◽  
Genomic Data ◽  
Leaf Blight ◽  
Bacterial Leaf Blight ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Xanthomonas Axonopodis

Here, we report the annotated draft genome sequence of Xanthomonas axonopodis pv. eucalyptorum pathotype strain LPF602 (synonym Xanthomonas axonopodis BSC45a), isolated from eucalypt leaves showing bacterial blight symptoms in Brazil. The availability of these genomic data will help improve the understanding of the evolution and molecular mechanisms involved in the pathogenesis of this microorganism.

scholarly journals Draft Genome Sequence of Rhizobium sp. Strain TBD182, an Antagonist of the Plant-Pathogenic Fungus Fusarium oxysporum, Isolated from a Novel Hydroponics System Using Organic Fertilizer

2017 ◽  
Vol 5 (11) ◽  
Author(s):  
Yuichiro Iida ◽  
Kazuki Fujiwara ◽  
Nobutaka Someya ◽  
Makoto Shinohara
Keyword(s):  
Fusarium Oxysporum ◽  
Genome Sequence ◽  
Molecular Mechanisms ◽  
Pathogenic Fungus ◽  
Organic Fertilizer ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Fungistatic Activity ◽  
Rhizobium Sp

ABSTRACT Rhizobium sp. strain TBD182, isolated from a novel hydroponics system, is an antagonistic bacterium that inhibits the mycelial growth of Fusarium oxysporum but does not eliminate the pathogen. We report the draft genome sequence of TBD182, which may contribute to elucidation of the molecular mechanisms of its fungistatic activity.

scholarly journals Draft Genome Sequence of Thiobacimonas sp. Strain D13, a Phthalate Ester-Degrading Bacterium Isolated from Deep-Sea Sediments

2019 ◽  
Vol 8 (24) ◽  
Author(s):  
Yang Liu ◽  
Tuyan Luo ◽  
Qiu Lin ◽  
Runying Zeng
Keyword(s):  
Genome Sequence ◽  
Deep Sea ◽  
Molecular Mechanisms ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Phthalate Ester ◽  
Content Type ◽  
Southeastern Pacific ◽  
Degrading Bacterium ◽  
Degradation Ability

Thiobacimonas sp. strain D13, newly isolated from the sediments of the southeastern Pacific, can effectively degrade phthalate ester. Here, we report the 5.22-Mbp draft genome sequence of this strain, which will provide insights into the molecular mechanisms underlying its degradation ability.

scholarly journals Draft Genome Sequence of Ciprofloxacin and Ceftriaxone Resistant Campylobacter jejuni MM26-781 Assigned to Novel ST Isolated From Common Pigeon in Lithuania

2019 ◽  
Vol 15 ◽  
pp. 117693431986846
Author(s):  
Jurgita Aksomaitiene ◽  
Sigita Ramonaite ◽  
Aleksandr Novoslavskij ◽  
Mindaugas Malakauskas ◽  
Egle Kudirkiene
Keyword(s):  
Antibiotic Resistance ◽  
Campylobacter Jejuni ◽  
Genome Sequence ◽  
Molecular Mechanisms ◽  
Draft Genome ◽  
Columba Livia ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Wide Range

Campylobacter jejuni is an important zoonotic pathogen known to be resistant to a wide range of antibiotics worldwide. Campylobacter jejuni may be intrinsically resistant to antibiotics or can acquire antibiotic resistance determinants through gene transfer. However, the knowledge of molecular mechanisms of antimicrobial resistance among Campylobacter isolates from wild birds, especially in Lithuania, is limited. Whole genome sequencing (WGS) is a tool for better understanding the evolutionary and epidemiologic dynamics of C jejuni. This study describes a draft whole genome sequence of C jejuni MM26-781 isolated from a common pigeon ( Columba livia) in Lithuania in 2011 and assigned to ST-6424 (CC179) sequence type. The draft genome sequence contained 1.68 Mb, comprising 1651 coding genes, 40 transfer RNAs, 1 ribosomal RNA, and 69 pseudogenes with an average G + C content of 30.4%. The RAST (Rapid Annotation using Subsystem Technology) pipeline annotated (NCTC11168) a total of 305 subsystems in the genome of C jejuni MM26-781 strain, with most of the genes associated with amino acids and derivatives related to metabolism (18.93%) and protein metabolism (14.43%). The genes and mutations related to antibiotic resistance, including gyrA and gyrB genes associated with quinolone resistance, blaOXA-448 gene (locus tag C9371_07715) associated with resistance to β-lactams, rpoB gene associated with resistance to rifamycin, vgaE gene associated with resistance to streptogramin and efflux system CmeABC ( cmeA, cmeB, cmeC), efflux pump PmrA, and transcriptional regulator CmeR responsible for multidrug resistance in C jejuni MM26-781 chromosome, were identified. Also, the virulence factors, including ciaB, cadF, ceuE, pldA, motB, and bd1A genes, were identified by WGS data analysis.

scholarly journals Draft Genome Sequence of Dicyma pulvinata Strain 414-3, a Mycoparasite of Cladosporium fulvum, Causal Agent of Tomato Leaf Mold

2019 ◽  
Vol 8 (35) ◽  
Author(s):  
Hirotoshi Sushida ◽  
Takuya Sumita ◽  
Yumiko Higashi ◽  
Yuichiro Iida
Keyword(s):  
Genome Sequence ◽  
Molecular Mechanisms ◽  
Draft Genome ◽  
Tomato Leaf ◽  
Draft Genome Sequence ◽  
Cladosporium Fulvum ◽  
Content Type ◽  
Leaf Mold ◽  
Tomato Leaf Mold ◽  
Mycoparasitic Fungus

Dicyma pulvinata strain 414-3, isolated from the surface of a tomato leaf, is a mycoparasitic fungus of Cladosporium fulvum, which causes leaf mold of tomato. We report here the draft genome sequence of strain 414-3, which will contribute to elucidating the molecular mechanisms involved in the mycoparasitism.

scholarly journals Draft Genome Sequence of Escherichia coli XH001, a Producer of l-Threonine in Industry

2011 ◽  
Vol 193 (22) ◽  
pp. 6406-6407 ◽  
Author(s):  
Huilin Yang ◽  
Yuling Liao ◽  
Bin Wang ◽  
Ying Lin ◽  
Li Pan
Keyword(s):  
Escherichia Coli ◽  
Genome Sequence ◽  
Molecular Mechanisms ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
High Quality ◽  
Content Type ◽  
Plasmid Sequence

l-Threonine has been widely used as a supplement in the food, pharmaceutical, and cosmetic industries. Here, we present a high-quality draft annotated genome sequence ofEscherichia coliXH001, a producer ofl-threonine in industry. Its genome and plasmid sequence will provide clues about the molecular mechanisms underlying its beneficial properties.

Draft genome sequence, disease-resistance genes, and phenotype of a Paenibacillus terrae strain (NK3-4) with the potential to control plant diseases

Genome ◽  
2018 ◽  
Vol 61 (10) ◽  
pp. 725-734 ◽  
Author(s):  
Wen Qing Yu ◽  
Gui Ping Zheng ◽  
De Wen Qiu ◽  
Feng Chao Yan ◽  
Wen Zhi Liu ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Molecular Mechanisms ◽  
Polyketide Synthase ◽  
Draft Genome ◽  
Control Plant ◽  
Genomic Analysis ◽  
Protein Component ◽  
Plant Diseases ◽  
Draft Genome Sequence ◽  
Antifungal Protein

Paenibacillus terrae NK3-4 is a plant growth-promoting rhizobacterium that may be useful for controlling plant diseases. We conducted a genomic analysis and identified the genes mediating antimicrobial functions. Additionally, an extracellular antifungal protein component was isolated and identified. The draft genome sequence was assembled into 54 contigs, with 5 458 568 bp and a G+C content of 47%. Moreover, 4 690 015 bp encoded 5090 proteins, 7 rRNAs, and 54 tRNAs. Forty-four genes involved in antimicrobial functions were detected. They mainly encode 19 non-ribosomal peptide synthetases (NRPSs); one polyketide synthase/NRPSs hybrid enzyme; four Zn-dependent metalloproteases; three antilisterial bacteriocin subtilosin biosynthesis proteins (AlbA); four serine proteases; five pectate lyases; three beta-glucanases; and four 1,4-beta-xylanases. These include four novel NRPSs that have not been found in any species of Paenibacillus. Furthermore, five proteins exhibiting antifungal activity were identified from the antifungal extracellular protein component based on MS/MS and the strain NK3-4 predicted protein library. On the basis of these features, we propose that strain NK3-4 represents a promising biocontrol agent for protecting plant from diseases. The draft genome sequence described herein may provide the genetic basis for the characterization of the molecular mechanisms underlying the biocontrol functions. It may also facilitate the development of rational strategies for improving the strain.

scholarly journals Draft Genome Sequence of Stenotrophomonas sp. Strain SbOxS2, an Antimony-Oxidizing Bacterium Isolated from Stibnite Mine Tailing Soil

2020 ◽  
Vol 9 (49) ◽  
Author(s):  
Natsuko Hamamura ◽  
Nobuyoshi Nakajima ◽  
Shigeki Yamamura
Keyword(s):  
Heavy Metal ◽  
Genome Sequence ◽  
Molecular Mechanisms ◽  
Draft Genome ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Mine Tailing ◽  
Draft Genome Sequence ◽  
Protein Coding ◽  
Coding Sequences

ABSTRACT The antimony-oxidizing Stenotrophomonas sp. strain SbOxS2 was isolated from stibnite mine tailing soil. The draft genome sequence of strain SbOxS2 comprises 4.76 Mbp with 4,211 predicted protein-coding sequences. This genome will provide useful information for characterizing the molecular mechanisms associated with heavy metal resistance within the genus Stenotrophomonas.

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