scholarly journals Genome Analyses of a New Mycoplasma Species From the scorpion Centruroides vittatus

2018 ◽  
Author(s):  
Tsunemi Yamashita ◽  
Douglas D. Rhoads ◽  
Jeff Pummill
Keyword(s):  
Ribosomal Proteins ◽  
Gc Content ◽  
Fluoroquinolone Resistance ◽  
Mycoplasma Species ◽  
Virulence Determinants ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Centruroides Vittatus ◽  
Genome Analyses ◽  
Single Circular Chromosome

ABSTRACTArthropod Mycoplasma are little known endosymbionts in insects, primarily known as plant disease vectors. Mycoplasma in other arthropods such as arachnids are unknown. We report the first complete Mycoplasma genome sequenced, identified, and annotated from a scorpion, Centruroides vittatus, and designate it as Mycoplasma vittatus. We find the genome is at least a 683,827 bp single circular chromosome with a GC content of 43.7% and with 1,010 protein-coding genes. The putative virulence determinants include 20 genes associated with the virulence operon associated with protein synthesis (SSU ribosomal proteins) and nine genes with fluoroquinolone resistance. Comparative analysis revealed that the M. vittatus genome is smaller than other Mycoplasma genomes and exhibits a higher GC content. Phylogenetic analysis shows M. vittatus as part of the Hominis group of Mycoplasma. As arthropod genomes accumulate, further novel Mycoplasma genomes may be identified and characterized.

scholarly journals Complete Genome Sequence of Enterobacter roggenkampii Strain KQ-01, Isolated from Bacterial Wilt-Resistant Mulberry Cultivar YS283

Plant Disease ◽  
2021 ◽  
pp. PDIS-07-20-1468
Author(s):  
Yinan Zhou ◽  
Hongyu Yang ◽  
Jiping Liu
Keyword(s):  
Ribosomal Rna ◽  
Bacterial Wilt ◽  
Noncoding Rna ◽  
Gc Content ◽  
Wilt Disease ◽  
Circular Chromosome ◽  
Protein Coding ◽  
First Time ◽  
Rna Genes ◽  
Single Circular Chromosome

An Enterobacter roggenkampii strain, named KQ-01, was isolated for the first time from the diseased roots of the bacterial wilt-resistant mulberry (Morus atropurpurea) cultivar YS283 in the western part of Guangxi Zhuang Autonomous Region, China. E. roggenkampii KQ-01 was characterized by a single, circular chromosome of 4,667,006 bp in size, with a 56.16% GC content. In total, 4,396 genes were annotated, of which 4,281 were assigned as protein-coding genes. In addition, 25 ribosomal RNA, 84 transfer RNA, and 6 noncoding RNA genes as well as 34 pseudogenes were predicted. The resource herein presented will help to explore the pathogenetic mechanisms of mulberry wilt disease caused by genus Enterobacter.

scholarly journals The Genome Sequence of the Gram-Positive Sugarcane Pathogen Leifsonia xyli subsp. xyli

2004 ◽  
Vol 17 (8) ◽  
pp. 827-836 ◽  
Author(s):  
Claudia B. Monteiro-Vitorello ◽  
Luis E. A. Camargo ◽  
Marie A. Van Sluys ◽  
João P. Kitajima ◽  
Daniela Truffi ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Gc Content ◽  
Open Reading Frames ◽  
Circular Chromosome ◽  
Free Sugars ◽  
Sugar Transporters ◽  
Living Organisms ◽  
Bacterial Plant Pathogen ◽  
Single Circular Chromosome ◽  
Reading Frames

The genome sequence of Leifsonia xyli subsp. xyli, which causes ratoon stunting disease and affects sugarcane worldwide, was determined. The single circular chromosome of Leifsonia xyli subsp. xyli CTCB07 was 2.6 Mb in length with a GC content of 68% and 2,044 predicted open reading frames. The analysis also revealed 307 predicted pseudogenes, which is more than any bacterial plant pathogen sequenced to date. Many of these pseudogenes, if functional, would likely be involved in the degradation of plant heteropolysaccharides, uptake of free sugars, and synthesis of amino acids. Although L. xyli subsp. xyli has only been identified colonizing the xylem vessels of sugarcane, the numbers of predicted regulatory genes and sugar transporters are similar to those in free-living organisms. Some of the predicted pathogenicity genes appear to have been acquired by lateral transfer and include genes for cellulase, pectinase, wilt-inducing protein, lysozyme, and desaturase. The presence of the latter may contribute to stunting, since it is likely involved in the synthesis of abscisic acid, a hormone that arrests growth. Our findings are consistent with the nutritionally fastidious behavior exhibited by L. xyli subsp. xyli and suggest an ongoing adaptation to the restricted ecological niche it inhabits.

scholarly journals Genome Analyses and Genome-Centered Metatranscriptomics of Methanothermobacter wolfeii Strain SIV6, Isolated from a Thermophilic Production-Scale Biogas Fermenter

2019 ◽  
Vol 8 (1) ◽  
pp. 13
Author(s):  
Julia Hassa ◽  
Daniel Wibberg ◽  
Irena Maus ◽  
Alfred Pühler ◽  
Andreas Schlüter
Keyword(s):  
Microbial Community ◽  
Biogas Production ◽  
Gc Content ◽  
Production Scale ◽  
Circular Chromosome ◽  
Hydrogenotrophic Methanogenesis ◽  
Complex Process ◽  
Indigenous Microbial Community ◽  
Genome Analyses ◽  
And Function

In the thermophilic biogas-producing microbial community, the genus Methanothermobacter was previously described to be frequently abundant. The aim of this study was to establish and analyze the genome sequence of the archaeal strain Methanothermobacter wolfeii SIV6 originating from a thermophilic industrial-scale biogas fermenter and compare it to related reference genomes. The circular chromosome has a size of 1,686,891 bases, featuring a GC content of 48.89%. Comparative analyses considering three completely sequenced Methanothermobacter strains revealed a core genome of 1494 coding sequences and 16 strain specific genes for M. wolfeii SIV6, which include glycosyltransferases and CRISPR/cas associated genes. Moreover, M. wolfeii SIV6 harbors all genes for the hydrogenotrophic methanogenesis pathway and genome-centered metatranscriptomics indicates the high metabolic activity of this strain, with 25.18% of all transcripts per million (TPM) belong to the hydrogenotrophic methanogenesis pathway and 18.02% of these TPM exclusively belonging to the mcr operon. This operon encodes the different subunits of the enzyme methyl-coenzyme M reductase (EC: 2.8.4.1), which catalyzes the final and rate-limiting step during methanogenesis. Finally, fragment recruitment of metagenomic reads from the thermophilic biogas fermenter on the SIV6 genome showed that the strain is abundant (1.2%) within the indigenous microbial community. Detailed analysis of the archaeal isolate M. wolfeii SIV6 indicates its role and function within the microbial community of the thermophilic biogas fermenter, towards a better understanding of the biogas production process and a microbial-based management of this complex process.

scholarly journals The genome ofHyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 °C

Archaea ◽  
2007 ◽  
Vol 2 (2) ◽  
pp. 127-135 ◽  
Author(s):  
Kim Brügger ◽  
Lanming Chen ◽  
Markus Stark ◽  
Arne Zibat ◽  
Peter Redder ◽  
...  
Keyword(s):  
Genome Structure ◽  
Trna Genes ◽  
Growing Up ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Electron Transfer Proteins ◽  
Good Sequence ◽  
High Level ◽  
Large Clusters ◽  
Single Circular Chromosome

Hyperthermus butylicus, a hyperthermophilic neutrophile and anaerobe, is a member of the archaeal kingdom Crenarchaeota. Its genome consists of a single circular chromosome of 1,667,163 bp with a 53.7% G+C content. A total of 1672 genes were annotated, of which 1602 are protein-coding, and up to a third are specific toH. butylicus. In contrast to some other crenarchaeal genomes, a high level of GUG and UUG start codons are predicted. Twocdc6genes are present, but neither could be linked unambiguously to an origin of replication. Many of the predicted metabolic gene products are associated with the fermentation of peptide mixtures including several peptidases with diverse specificities, and there are many encoded transporters. Most of the sulfur-reducing enzymes, hydrogenases and electron-transfer proteins were identified which are associated with energy production by reducing sulfur to H2S. Two large clusters of regularly interspaced repeats (CRISPRs) are present, one of which is associated with a crenarchaeal-typecasgene superoperon; none of the spacer sequences yielded good sequence matches with known archaeal chromosomal elements. The genome carries no detectable transposable or integrated elements, no inteins, and introns are exclusive to tRNA genes. This suggests that the genome structure is quite stable, possibly reflecting a constant, and relatively uncompetitive, natural environment.

scholarly journals Complete Genome Sequence of Kyrpidia sp. Strain EA-1, a Thermophilic Knallgas Bacterium, Isolated from the Azores

2018 ◽  
Vol 6 (3) ◽  
Author(s):  
Johannes Eberhard Reiner ◽  
Christian Jonas Lapp ◽  
Boyke Bunk ◽  
Cathrin Spröer ◽  
Jörg Overmann ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Gc Content ◽  
Hydrothermal Systems ◽  
Circular Chromosome ◽  
Single Circular Chromosome

ABSTRACT Kyrpidia sp. strain EA-1 is a thermophilic hydrogen-oxidizing bacterium isolated from hydrothermal systems at São Miguel Island, Portugal. Here, we present the complete genome sequence of the strain assembled to a single circular chromosome. The genome spans 3,352,175 bp, with a GC content of 58.7%.

scholarly journals Complete Genome Sequence of Marinobacterium aestuarii ST58-10T, a Benzene-Degrading Bacterium Isolated from Estuarine Sediment

2018 ◽  
Vol 7 (11) ◽  
Author(s):  
Kyunghwa Baek ◽  
Seung Seob Bae ◽  
Jaejoon Jung ◽  
Dawoon Chung
Keyword(s):  
Complete Genome Sequence ◽  
Estuarine Sediment ◽  
Aerobic Bacterium ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Degrading Bacterium ◽  
The Republic ◽  
Single Circular Chromosome

Marinobacterium aestuarii ST58-10T was identified as a benzene-degrading aerobic bacterium isolated from estuarine sediment in the Republic of Korea. The genome of strain ST58-10T was found to be composed of a single circular chromosome (5,191,608 bp) with a G+C content of 58.78% and harboring 4,473 protein-coding genes.

scholarly journals Complete Genome of the Chitin-Degrading Bacterium, Paenibacillus xylanilyticus W4

2019 ◽  
Vol 11 (11) ◽  
pp. 3252-3255 ◽  
Author(s):  
Weifang Liao ◽  
Pulin Liu ◽  
Weijie Liao ◽  
Lihong Miao
Keyword(s):  
Complete Genome ◽  
Gc Content ◽  
Circular Chromosome ◽  
Chitin Degradation ◽  
Degrading Bacterium ◽  
Degradation Activity ◽  
Genome Information ◽  
Taxonomic Characterization ◽  
Single Circular Chromosome ◽  
Genome Distance

Abstract Chitinases possess an extraordinary ability to directly hydrolyze highly insoluble chitin polymers to low-molecular-weight chito-oligomers, which possess particular biological functions, such as elicitor action and antitumor activity. A novel strain, Paenibacillus xylanilyticus W4, which was isolated from soil, showed strong chitin degradation activity. Here, we first reported the complete genome information of P. xylanilyticus. Paenibacillus xylanilyticus W4 contains a 5,532,141 bp single circular chromosome with 47.33% GC content. The genome contains 5,996 genes, including 39 rRNA- and 109 tRNA-coding genes. Phylogenetic analysis and Genome-to-Genome Distance revealed its taxonomic characterization into a separate family. Six glycoside hydrolase 18 (GH18) and 2 GH23 enzymes involved in chitin degradation. Although many of the chitinases were conserved in Paenibacillus, several GH18 chitinases share high similarity with Bacillus circulans. The genome information provided here could benefit for understanding the chitin-degrading properties of P. xylanilyticus as well as its potential application in biotechnological and pharmaceutical fields.

scholarly journals Rhizoxin Analogs Contribute to the Biocontrol Activity of a Newly Isolated Pseudomonas Strain

2015 ◽  
Vol 28 (3) ◽  
pp. 333-342 ◽  
Author(s):  
Kasumi Takeuchi ◽  
Naomi Noda ◽  
Yuichi Katayose ◽  
Yoshiyuki Mukai ◽  
Hisataka Numa ◽  
...  
Keyword(s):  
Polyketide Synthase ◽  
Plant Protection ◽  
Whole Genome ◽  
Biosynthesis Gene Cluster ◽  
Circular Chromosome ◽  
Coding Sequences ◽  
Biocontrol Activity ◽  
Protection Efficacy ◽  
Genome Analyses ◽  
Single Circular Chromosome

Two strains of Pseudomonas sp., Os17 and St29, were newly isolated from the rhizosphere of rice and potato, respectively, by screening for 2,4-diacetylphloroglucinol producers. These strains were found to be the same species and were the closest to but different from Pseudomonas protegens among the sequenced pseudomonads, based on 16S ribosomal RNA gene and whole-genome analyses. Strain Os17 was as effective a biocontrol agent as reported for P. protegens Cab57, whereas strain St29 was less effective. The whole-genome sequences of these strains were obtained: the genomes are organized into a single circular chromosome with 6,885,464 bp, 63.5% G+C content, and 6,195 coding sequences for strain Os17; and with 6,833,117 bp, 63.3% G+C content, and 6,217 coding sequences for strain St29. Comparative genome analysis of these strains revealed that the complete rhizoxin analog biosynthesis gene cluster (approximately 79 kb) found in the Os17 genome was absent from the St29 genome. In an rzxB mutant, which lacks the polyketide synthase essential for the production of rhizoxin analogs, the growth inhibition activity against fungal and oomycete pathogens and the plant protection efficacy were attenuated compared with those of wild-type Os17. These findings suggest that rhizoxin analogs are important biocontrol factors of this strain.

scholarly journals Complete Genome Sequence of Blautia producta JCM 1471T

2020 ◽  
Vol 9 (17) ◽  
Author(s):  
Dieter M. Tourlousse ◽  
Mitsuo Sakamoto ◽  
Takamasa Miura ◽  
Koji Narita ◽  
Akiko Ohashi ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Rrna Genes ◽  
Trna Genes ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Coding Sequences ◽  
Content Type ◽  
Single Circular Chromosome

We report a complete genome sequence of Blautia producta JCM 1471T. The genome consists of a single circular chromosome of 6,197,116 bp with a G+C content of 45.7%. The genome was annotated as containing 5 complete sets of rRNA genes, 70 tRNA genes, and 5,516 protein-coding sequences.

scholarly journals Complete Genome Sequence of Mycoplasma bovis Strain XBY01, Isolated from Henan Province, China

2020 ◽  
Vol 9 (15) ◽  
Author(s):  
Qingchun Shen ◽  
Shijing Sun ◽  
Guanlong Xu ◽  
Xuezheng Fan ◽  
Hui Jiang ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Gc Content ◽  
Henan Province ◽  
Mycoplasma Bovis ◽  
Circular Chromosome ◽  
Content Type ◽  
Young Calf ◽  
Single Circular Chromosome

We report the complete genome sequence of Mycoplasma bovis strain XBY01, which was isolated from a severely diseased young calf in Henan Province, China, in 2019. The genome of XBY01 contains a single circular chromosome of 986,067 bp, with a GC content of 29.30%.

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