scholarly journals Genome Sequence Resource for the Ramie Oomycete Pathogen Phytopythium vexans HF1

2020 ◽  
Vol 33 (11) ◽  
pp. 1270-1273
Author(s):  
Yongting Yu ◽  
Chunsheng Gao ◽  
Tuhong Wang ◽  
Yikun Chen ◽  
Yi Cheng ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Root Rot ◽  
Molecular Mechanisms ◽  
Virulence Genes ◽  
Gc Content ◽  
Damping Off ◽  
Illumina Hiseq ◽  
Antimicrobial Resistance Genes ◽  
Oomycete Pathogen ◽  
Brown Root Rot

The oomycete Phytopythium vexans is a causative agent of patch canker, damping-off, and crown, stem, and root rot in many economically important plants. P. vexans HF1 was isolated in China, where it caused brown root rot of ramie, a fiber crop broadly cultivated in Asia. The genome of HF1 was sequenced by a combination of technologies producing short (Illumina HiSeq X) and long (PacBio RS) reads. The genome is 41.73 Mbp long, assembled into 44 contigs. It has a GC content of 58.17% and contains 13,051 predicted coding genes, including 1,461 putative virulence genes and 220 putative antimicrobial resistance genes. This genome sequence provides a resource for determining the molecular mechanisms of disease development in this pathosystem.

scholarly journals Determination and Structural Analysis of the Whole-Genome Sequence of Fusarium equiseti D25-1

2020 ◽  
Author(s):  
Xueping LI ◽  
Jianhong Li ◽  
Yonghong Qi ◽  
Yonggang Liu ◽  
Minquan Li
Keyword(s):  
Molecular Mechanisms ◽  
Gc Content ◽  
Whole Genome Sequence ◽  
Effective Control ◽  
Sequence Length ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Illumina Hiseq ◽  
Fusarium Equiseti ◽  
Wide Range

Abstract BackgroundFusarium equiseti is a plant pathogen with a wide range of hosts and diverse effects, including probiotic activity. However, the underlying molecular mechanisms remain unclear, hindering its effective control and utilization. In this study, the Illumina HiSeq 4000 and PacBio platforms were used to sequence and assemble the whole genome of Fusarium equiseti D25-1.ResultsThe assembly included 16 fragments with a GC content of 48.01%, gap number of zero, and size of 40,776,005 bp. There were 40,110 exons and 26,281 introns having a total size of 19,787,286 bp and 2,290,434 bp, respectively. The genome had an average copy number of 333, 71, 69, 31, and 108 for tRNAs, rRNAs, sRNAs, snRNAs, and miRNAs, respectively. The total repetitive sequence length was 1,713,918 bp, accounting for 4.2033% of the genome. In total, 13,134 functional genes were annotated, accounting for 94.97% of the total gene number. Toxin-related genes, including two related to zearalenone and 23 related to trichothecene, were identified. A comparative genomic analysis supported the high quality of the F. equiseti assembly, exhibiting good collinearity with the reference strains, 3,483 species-specific genes, and 1,805 core genes. A gene family analysis revealed more than 2,500 single-copy orthologs. F. equiseti was most closely related to Fusarium pseudograminearum based on a phylogenetic analysis at the whole-genome level.ConclusionsOur comprehensive analysis of the whole genome of F. equiseti provides basic data for studies of gene expression, regulatory and functional mechanisms, evolutionary processes, as well as disease prevention and control.

scholarly journals First Genome Sequence of Pasteurella multocida Type B Strain BAUTB2, a Major Pathogen Responsible for Mortality of Bovines in Bangladesh

2018 ◽  
Vol 7 (9) ◽  
Author(s):  
M. Shahjahan Ali Sarker ◽  
M. Tanvir Rahman ◽  
M. Muket Mahmud ◽  
Massimiliano S. Tagliamonte ◽  
Shah M. Ziqrul Haq Chowdhury ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Pasteurella Multocida ◽  
Noncoding Rnas ◽  
Gc Content ◽  
Genome Length ◽  
Type B ◽  
Illumina Hiseq ◽  
Coding Sequences ◽  
Content Type

Here, we report the first genome sequence of Pasteurella multocida BAUTB2 isolated from a buffalo that died from hemorrhagic septicemia in Rajshahi, Bangladesh. Using Illumina HiSeq technology, the BAUTB2 genome length was determined to be 2,439,149 bp, with 40.8% GC content, 2,307 coding sequences (CDS), 6 rRNAs, 51 tRNAs, and 4 noncoding RNAs (ncRNAs).

scholarly journals Complete genome sequence of Sphingomonas paucimobilis AIMST S2, a xenobiotic-degrading bacterium

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Suganniiya K. Ravintheran ◽  
Sumitra Sivaprakasam ◽  
Stella Loke ◽  
Su Yin Lee ◽  
Ravichandran Manickam ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Molecular Mechanisms ◽  
Sphingomonas Paucimobilis ◽  
Growth Promoters ◽  
Illumina Hiseq ◽  
Degrading Bacterium ◽  
Long Reads ◽  
Gene Expression Studies

AbstractComplete genomes of xenobiotic-degrading microorganisms provide valuable resources for researchers to understand molecular mechanisms involved in bioremediation. Despite the well-known ability of Sphingomonas paucimobilis to degrade persistent xenobiotic compounds, a complete genome sequencing is lacking for this organism. In line with this, we report the first complete genome sequence of Sphingomonas paucimobilis (strain AIMST S2), an organophosphate and hydrocarbon-degrading bacterium isolated from oil-polluted soil at Kedah, Malaysia. The genome was derived from a hybrid assembly of short and long reads generated by Illumina HiSeq and MinION, respectively. The assembly resulted in a single contig of 4,005,505 bases which consisted of 3,612 CDS and 56 tRNAs. An array of genes involved in xenobiotic degradation and plant-growth promoters were identified, suggesting its’ potential role as an effective microorganism in bioremediation and agriculture. Having reported the first complete genome of the species, this study will serve as a stepping stone for comparative genome analysis of Sphingomonas strains and other xenobiotic-degrading microorganisms as well as gene expression studies in organophosphate biodegradation.

scholarly journals Influence of selected Rhizoctonia solani isolates on sugar beet seedlings

2016 ◽  
Vol 56 (2) ◽  
pp. 116-121
Author(s):  
Paweł Skonieczek ◽  
Mirosław Nowakowski ◽  
Jacek Piszczek ◽  
Marcin Żurek ◽  
Łukasz Matyka
Keyword(s):  
Sugar Beet ◽  
Rhizoctonia Solani ◽  
Root Rot ◽  
Laboratory Tests ◽  
Anastomosis Group ◽  
Damping Off ◽  
Highly Pathogenic ◽  
Breeding Lines ◽  
Brown Root Rot

Abstract From 2008 to 2010 the levels of sugar beet seedlings infection caused by Rhizoctonia solani were compared in laboratory tests. Seven sugar beet lines were tested: H56, H66, S2, S3, S4, S5 and S6 as well as three control cultivars: Carlos, Esperanza and Janosik. Sugar beet lines with tolerance to rhizoctoniosis and cultivars without tolerance were infected artificially by R. solani isolates: R1, R28a and R28b. These isolates belong to the second anastomosis group (AG), which is usually highly pathogenic to beet roots. The aim of the experiment was to test whether the tolerance of sugar beet genotypes to R. solani AG 2 prevents both root rot, and damping-off of seedlings, induced by the pathogen. Sugar beet lines tolerant to brown root rot in laboratory tests were significantly less sensitive to infection of the seedlings by R. solani AG 2 isolates in comparison to control cultivars. Rhizoctonia solani AG 2 isolates demonstrated considerable differences in pathogenicity against seedlings of sugar beet lines and cultivars. The strongest infection of sugar beet seedlings occurred with the isolate R28b. The greatest tolerance to infection by AG 2 isolates was found for the S5 and S3 breeding lines.

scholarly journals Draft Genome Sequence of Enterobacter hormaechei subsp. steigerwaltii Strain BEI01

2021 ◽  
Vol 10 (28) ◽  
Author(s):  
Soon Keong Wee ◽  
Sharon Cui Mun Chan ◽  
Xue Li Guan ◽  
Eric Peng Huat Yap
Keyword(s):  
Antimicrobial Resistance ◽  
Genome Sequence ◽  
Resistance Genes ◽  
Draft Genome ◽  
Gc Content ◽  
Enterobacter Cloacae ◽  
Metal Resistance ◽  
Content Type ◽  
Antimicrobial Resistance Genes ◽  
Enterobacter Hormaechei

Here, we report the genome sequence of Enterobacter hormaechei subsp. steigerwaltii strain BEI01, originally deposited as a member of the Enterobacter cloacae complex. The genome is 4,900,246 bp in size with a GC content of 55.44%; it contains multidrug antimicrobial resistance genes and several metal resistance gene operons.

scholarly journals Complete genome sequence of an extensively drug resistant (XDR) M. morganii SMM01 isolated from a patient with urinary and fecal incontinence

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Pachi Pulusu Chanakya ◽  
Balaram Khamari ◽  
Manmath Lama ◽  
Arun Sai Kumar Peketi ◽  
Prakash Kumar ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Fecal Incontinence ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Gc Content ◽  
Gene Clusters ◽  
Illumina Hiseq ◽  
Resistance Profile ◽  
Antimicrobial Resistance Profile

Abstract Objective M. morganii is a gram-negative, non-lactose fermenting and an opportunistic pathogen frequently associated with nosocomial infections. Although first isolated in 1906 from a pediatric fecal sample, not many M. morganii isolates have been sequenced. The objective of this work is to determine the complete genome sequence of an XDR M. morganii strain (SMM01) isolated from the urine of a patient with urinary and fecal incontinence and to characterize its antimicrobial resistance profile. Data description Here, we report the complete genome sequence of M. morganii SMM01 generated from the hybrid assembly of Illumina HiSeq X and Nanopore MinION reads. The assembly is 100% complete with genome size of 39,30,130 bp and GC content of 51%. Genomic features include 3617 CDS, 18 rRNAs, 78 tRNAs, 4 ncRNAs and 60 pseudogenes. Antimicrobial resistance profile was characterized by the presence of genes conferring resistance to aminoglycosides, β-lactams, fluoroquinolones, chloramphenicol, and tetracyclines. Secondary metabolite biosynthetic gene clusters like NRPS, T1PKS, thiopeptide, beta-lactone, and bacteriocin were identified. The genome data described here would be the first complete genome of an Indian M. morganii isolate providing crucial information on antimicrobial resistance patterns, paving the way for further comparative genome analyses.

scholarly journals Draft Genome Sequence of Bacillus velezensis 3A-25B, a Strain with Biocontrol Activity against Fungal and Oomycete Root Plant Phytopathogens, Isolated from Grassland Soil

2017 ◽  
Vol 5 (39) ◽  
Author(s):  
Inés Martínez-Raudales ◽  
Yumiko De La Cruz-Rodríguez ◽  
Julio Vega-Arreguín ◽  
Alejandro Alvarado-Gutiérrez ◽  
Atzin Fraire-Mayorga ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Root Rot ◽  
Draft Genome ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Bacillus Velezensis ◽  
Grassland Soil ◽  
Content Type ◽  
Horticultural Crops ◽  
Biocontrol Activity

ABSTRACT Here, we present the draft genome of Bacillus velezensis 3A-25B, which totaled 4.01 Mb with 36 contigs, 3,948 genes, and a GC content of 46.34%. This strain, which demonstrates biocontrol activity against root rot causal phytopathogens in horticultural crops and friendly interactions in roots of pepper plantlets, was obtained from grassland soil in Zacatecas Province, Mexico.

scholarly journals Whole genome sequence analysis of multi drug resistant community associated methicillin resistant Staphylococcus aureus from food fish: detection of clonal lineage ST 28 and its antimicrobial resistance and virulence genes

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11224
Author(s):  
Gopalan Krishnan Sivaraman ◽  
Visnuvinayagam Sivam ◽  
Balasubramanian Ganesh ◽  
Ravikrishnan Elangovan ◽  
Ardhra Vijayan ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Genome Sequence ◽  
Virulence Genes ◽  
Draft Genome ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Drug Resistant ◽  
Methicillin Resistant ◽  
Antimicrobial Resistance Genes ◽  
Food Fish

Methicillin-resistant staphylococcus aureus (MRSA) sequence type 28 (ST 28) and spa type t021 is a CC30, prototype of ST-30, Community Associated-MRSA (CA-MRSA) (lukS-lukF +). It is a multi-drug resistant strain harbouring staphylococcal endotoxins, haemolysins, ureolysin, serine protease, and antimicrobial resistance genes. In this study, we report the draft genome sequence of this MRSA isolated from the most commonly used food fish, ribbon fish (Trichiurus lepturus). The total number of assembled paired-end high-quality reads was 7,731,542 with a total length of  2.8Mb of 2797 predicted genes. The unique ST28/ t021 CA- MRSA in fish is the first report from India, and in addition to antibiotic resistance is known to co-harbour virulence genes, haemolysins, aureolysins and endotoxins. Comprehensive comparative genomic analysis of CA-MRSA strain7 can help further understand their diversity, genetic structure, diversity and a high degree of virulence to aid in fisheries management.

scholarly journals Draft Genome Sequence of Ligilactobacillus salivarius FFIG58, Isolated from the Intestinal Tract of Wakame-Fed Pig

2020 ◽  
Vol 9 (34) ◽  
Author(s):  
Binghui Zhou ◽  
Leonardo Albarracin ◽  
Yuki Masumizu ◽  
Yuhki Indo ◽  
M. Aminul Islam ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Intestinal Tract ◽  
Draft Genome ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
A Genome

ABSTRACT Ligilactobacillus salivarius FFIG58 was isolated from the intestine of a wakame-fed pig and sequenced with an Illumina HiSeq system. FFIG58 genome sequencing revealed a genome size of 1,984,180 bp, with 1,994 protein-coding genes and a GC content of 32.9%. This draft genome sequence will contribute to a better understanding of the porcine gut microbiome.

scholarly journals Whole-Genome Sequence of Bacillus cereus AR156, a Potential Biocontrol Agent with High Soilborne Disease Biocontrol Efficacy and Plant Growth Promotion

2017 ◽  
Vol 5 (35) ◽  
Author(s):  
Chun-Hao Jiang ◽  
Yun Chen ◽  
Fang Yan ◽  
Zhi-Hang Fan ◽  
Jian-Hua Guo
Keyword(s):  
Bacillus Cereus ◽  
Genome Sequence ◽  
Molecular Mechanisms ◽  
Growth Promotion ◽  
Draft Genome ◽  
Gc Content ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Soilborne Disease

ABSTRACT Bacillus cereus AR156 was originally isolated from the forest soil of Zhenjiang, a city in China. To shed new light on the molecular mechanisms underlying the biological control of soilborne pathogens, the whole genome of this strain was sequenced. Here, we report the draft genome sequence of this strain, consisting of a single circularized contig measuring 5.66 Mb, with an average GC content of 35.5% and 5,367 open reading frames.

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