scholarly journals Genome Sequence of Streptococcus agalactiae Strain H002, Serotype III, Isolated in China from a Pregnant Woman

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Rui Wang ◽  
Liping Li ◽  
Fuguang Luo ◽  
Wanwen Liang ◽  
Xi Gan ◽  
...  
Keyword(s):  
Pregnant Woman ◽  
Genome Sequence ◽  
Streptococcus Agalactiae ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Genomic Studies ◽  
Important Addition

Here, we report the first whole-genome sequence of Streptococcus agalactiae strain H002, serotype III, isolated in China from a woman 32 weeks pregnant. This sequence represents an important addition to the published genomes and will promote comparative genomic studies of S. agalactiae spp. isolated from diverse regions, particularly when compared with Chinese strains.

scholarly journals Whole-Genome Sequence ofEscherichia coliSerotype O157:H7 Strain EDL932 (ATCC 43894)

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Gaylen A. Uhlich ◽  
George C. Paoli ◽  
Chin-Yi Chen ◽  
Bryan J. Cottrell ◽  
Xinmin Zhang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genome Sequence ◽  
Shiga Toxin ◽  
Whole Genome Sequence ◽  
Hemorrhagic Colitis ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Outbreak Strain ◽  
E Coli ◽  
Genomic Studies

The genome sequence ofEscherichia coliserotype O157:H7 EDL933, a ground beef isolate from a 1983 hemorrhagic colitis outbreak, is a standard reference for comparative genomic studies of Shiga toxin-producingE. colistrains. Here, we report the genome sequence of a patient stool isolate from that outbreak, strain EDL932.

scholarly journals Draft Genome Sequence of an InvasiveStreptococcus agalactiaeIsolate Lacking Pigmentation

2016 ◽  
Vol 4 (1) ◽  
Author(s):  
Pallavi Singh ◽  
David M. Aronoff ◽  
H. Dele Davies ◽  
Shannon D. Manning
Keyword(s):  
Genome Sequence ◽  
Streptococcus Agalactiae ◽  
Draft Genome ◽  
Pigment Production ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome

This report provides the whole-genome sequence ofStreptococcus agalactiaeisolate GB00037 isolated from a newborn in Calgary, Canada. This serotype V isolate is unique because it lacks pigment production previously shown to be critical forS. agalactiaevirulence.

scholarly journals Complete Genome Sequence of Streptococcus agalactiae GD201008-001, Isolated in China from Tilapia with Meningoencephalitis

2012 ◽  
Vol 194 (23) ◽  
pp. 6653-6653 ◽  
Author(s):  
Guangjin Liu ◽  
Wei Zhang ◽  
Chengping Lu
Keyword(s):  
Genome Sequence ◽  
Streptococcus Agalactiae ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Genetic Basis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Host Tropism

ABSTRACTThis work describes a whole-genome sequence ofStreptococcus agalactiaestrain GD201008-001, a pathogen causing meningoencephalitis in cultural tilapia in China. The genome sequence provides opportunities to understand the piscine GBS pathogenicity and its genetic basis associated with host tropism.

Comparison of three species of Elizabethkingia genus by whole-genome sequence analysis

2021 ◽  
Vol 368 (5) ◽  
Author(s):  
Chen Yang ◽  
Zhe Liu ◽  
Shuai Yu ◽  
Kun Ye ◽  
Xin Li ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genomic Analysis ◽  
Information Storage ◽  
Whole Genome Sequence ◽  
Neonatal Meningitis ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Significant Finding ◽  
Beta Lactams ◽  
Clusters Of Orthologous Groups

Abstract Elizabethkingia are found to cause severe neonatal meningitis, nosocomial pneumonia, endocarditis and bacteremia. However, there are few studies on Elizabethkingia genus by comparative genomic analysis. In this study, three species of Elizabethkingia were found: E. meningoseptica, E. anophelis and E. miricola. Resistance genes and associated proteins of seven classes of antibiotics including beta-lactams, aminoglycosides, macrolides, tetracyclines, quinolones, sulfonamides and glycopeptides, as well as multidrug resistance efflux pumps were identified from 20 clinical isolates of Elizabethkingia by whole-genome sequence. Genotype and phenotype displayed a good consistency in beta-lactams, aminoglycosides and glycopeptides, while contradictions exhibited in tetracyclines, quinolones and sulfonamides. Virulence factors and associated genes such as hsp60 (htpB), exopolysaccharide (EPS) (galE/pgi), Mg2+ transport (mgtB/mgtE) and catalase (katA/katG) existed in all clinical and reference strains. The functional analysis of the clusters of orthologous groups indicated that ‘metabolism’ occupied the largest part in core genome, ‘information storage and processing’ was the largest group in both accessory genome and unique genome. Abundant mobile elements were identified in E. meningoseptica and E. anophelis. The most significant finding in our study was that a single clone of E. anophelis had been circulating within diversities of departments in a clinical setting for nearly 18 months.

scholarly journals Whole Genome Sequence of the Commercially Relevant Mushroom Strain Agaricus bisporus var. bisporus ARP23

2019 ◽  
Vol 9 (10) ◽  
pp. 3057-3066 ◽  
Author(s):  
Eoin O’Connor ◽  
Jamie McGowan ◽  
Charley G. P. McCarthy ◽  
Aniça Amini ◽  
Helen Grogan ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Agaricus Bisporus ◽  
Genomic Analysis ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Protein Coding ◽  
Single Strain ◽  
Protein Coding Genes ◽  
Starting Point

Agaricus bisporus is an extensively cultivated edible mushroom. Demand for cultivation is continuously growing and difficulties associated with breeding programs now means strains are effectively considered monoculture. While commercial growing practices are highly efficient and tightly controlled, the over-use of a single strain has led to a variety of disease outbreaks from a range of pathogens including bacteria, fungi and viruses. To address this, the Agaricus Resource Program (ARP) was set up to collect wild isolates from diverse geographical locations through a bounty-driven scheme to create a repository of wild Agaricus germplasm. One of the strains collected, Agaricus bisporus var. bisporus ARP23, has been crossed extensively with white commercial varieties leading to the generation of a novel hybrid with a dark brown pileus commonly referred to as ‘Heirloom’. Heirloom has been successfully implemented into commercial mushroom cultivation. In this study the whole genome of Agaricus bisporus var. bisporus ARP23 was sequenced and assembled with Illumina and PacBio sequencing technology. The final genome was found to be 33.49 Mb in length and have significant levels of synteny to other sequenced Agaricus bisporus strains. Overall, 13,030 putative protein coding genes were located and annotated. Relative to the other A. bisporus genomes that are currently available, Agaricus bisporus var. bisporus ARP23 is the largest A. bisporus strain in terms of gene number and genetic content sequenced to date. Comparative genomic analysis shows that the A. bisporus mating loci in unifactorial and unsurprisingly highly conserved between strains. The lignocellulolytic gene content of all A. bisporus strains compared is also very similar. Our results show that the pangenome structure of A. bisporus is quite diverse with between 60–70% of the total protein coding genes per strain considered as being orthologous and syntenically conserved. These analyses and the genome sequence described herein are the starting point for more detailed molecular analyses into the growth and phenotypical responses of Agaricus bisporus var. bisporus ARP23 when challenged with economically important mycoviruses.

scholarly journals Whole-genome sequence analyses of Glaesserella parasuis isolates reveals extensive genomic variation and diverse antibiotic resistance determinants

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9293
Author(s):  
Xiulin Wan ◽  
Xinhui Li ◽  
Todd Osmundson ◽  
Chunling Li ◽  
He Yan
Keyword(s):  
Antibiotic Resistance ◽  
Genetic Variation ◽  
Genome Sequence ◽  
Resistance Genes ◽  
Genomic Variation ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Broad Host Range ◽  
Whole Genome ◽  
Resistance Determinants

Background Glaesserella parasuis (G. parasuis) is a respiratory pathogen of swine and the etiological agent of Glässer’s disease. The structural organization of genetic information, antibiotic resistance genes, potential pathogenicity, and evolutionary relationships among global G. parasuis strains remain unclear. The aim of this study was to better understand patterns of genetic variation, antibiotic resistance factors, and virulence mechanisms of this pathogen. Methods The whole-genome sequence of a ST328 isolate from diseased swine in China was determined using Pacbio RS II and Illumina MiSeq platforms and compared with 54 isolates from China sequenced in this study and 39 strains from China and eigtht other countries sequenced by previously. Patterns of genetic variation, antibiotic resistance, and virulence mechanisms were investigated in relation to the phylogeny of the isolates. Electrotransformation experiments were performed to confirm the ability of pYL1—a plasmid observed in ST328—to confer antibiotic resistance. Results The ST328 genome contained a novel Tn6678 transposon harbouring a unique resistance determinant. It also contained a small broad-host-range plasmid pYL1 carrying aac(6’)-Ie-aph(2”)-Ia and blaROB-1; when transferred to Staphylococcus aureus RN4220 by electroporation, this plasmid was highly stable under kanamycin selection. Most (85.13–91.74%) of the genetic variation between G. parasuis isolates was observed in the accessory genomes. Phylogenetic analysis revealed two major subgroups distinguished by country of origin, serotype, and multilocus sequence type (MLST). Novel virulence factors (gigP, malQ, and gmhA) and drug resistance genes (norA, bacA, ksgA, and bcr) in G. parasuis were identified. Resistance determinants (sul2, aph(3”)-Ib, norA, bacA, ksgA, and bcr) were widespread across isolates, regardless of serovar, isolation source, or geographical location. Conclusions Our comparative genomic analysis of worldwide G. parasuis isolates provides valuable insight into the emergence and transmission of G. parasuis in the swine industry. The result suggests the importance of transposon-related and/or plasmid-related gene variations in the evolution of G. parasuis.

scholarly journals Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes

2015 ◽  
Vol 112 (11) ◽  
pp. E1257-E1262 ◽  
Author(s):  
Yan-Bo Sun ◽  
Zi-Jun Xiong ◽  
Xue-Yan Xiang ◽  
Shi-Ping Liu ◽  
Wei-Wei Zhou ◽  
...  
Keyword(s):  
De Novo ◽  
Structural Evolution ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Protein Coding ◽  
Comparable Rate ◽  
Evolutionary Studies ◽  
Genomic Studies ◽  
The Difference

The development of efficient sequencing techniques has resulted in large numbers of genomes being available for evolutionary studies. However, only one genome is available for all amphibians, that of Xenopus tropicalis, which is distantly related from the majority of frogs. More than 96% of frogs belong to the Neobatrachia, and no genome exists for this group. This dearth of amphibian genomes greatly restricts genomic studies of amphibians and, more generally, our understanding of tetrapod genome evolution. To fill this gap, we provide the de novo genome of a Tibetan Plateau frog, Nanorana parkeri, and compare it to that of X. tropicalis and other vertebrates. This genome encodes more than 20,000 protein-coding genes, a number similar to that of Xenopus. Although the genome size of Nanorana is considerably larger than that of Xenopus (2.3 vs. 1.5 Gb), most of the difference is due to the respective number of transposable elements in the two genomes. The two frogs exhibit considerable conserved whole-genome synteny despite having diverged approximately 266 Ma, indicating a slow rate of DNA structural evolution in anurans. Multigenome synteny blocks further show that amphibians have fewer interchromosomal rearrangements than mammals but have a comparable rate of intrachromosomal rearrangements. Our analysis also identifies 11 Mb of anuran-specific highly conserved elements that will be useful for comparative genomic analyses of frogs. The Nanorana genome offers an improved understanding of evolution of tetrapod genomes and also provides a genomic reference for other evolutionary studies.

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