scholarly journals Draft Genome Sequence of Anoxybacillus sp. Strain UARK-01, a New Thermophilic Lignin-Utilizing Bacterium Isolated from Soil in Arkansas, USA

2017 ◽  
Vol 5 (30) ◽  
Author(s):  
Thamir H. Alkahem Albalawi ◽  
Douglas D. Rhoads ◽  
Ravi D. Barabote
Keyword(s):  
United States ◽  
Genome Sequence ◽  
De Novo ◽  
Draft Genome ◽  
Illumina Miseq ◽  
The United States ◽  
Soil Bacterium ◽  
Lignocellulose Degradation ◽  
Illumina Miseq Platform ◽  
Miseq Platform

ABSTRACT The draft genome of Anoxybacillus sp. strain UARK-01, a novel lignin-utilizing thermophilic soil bacterium, represents the first sequence of an Anoxybacillus isolate from the United States. The genome was sequenced using the Illumina MiSeq platform, de novo assembled using SeqMan NGen, and annotated at NCBI. The genome sequence revealed genes for laccase and lignocellulose degradation enzymes.

scholarly journals Draft Genome Sequences of Two Novel Salmonella enterica subsp. enterica Strains Isolated from Low-Moisture Foods with Applications in Food Safety Research

2018 ◽  
Vol 6 (13) ◽  
Author(s):  
Devon R. Radford ◽  
Carlos G. Leon-Velarde ◽  
Shu Chen ◽  
Amir M. Hamidi Oskouei ◽  
Sampathkumar Balamurugan
Keyword(s):  
Salmonella Enterica ◽  
De Novo ◽  
Draft Genome ◽  
Illumina Miseq ◽  
Consensus Method ◽  
Genome Sequences ◽  
Content Type ◽  
Illumina Miseq Platform ◽  
Safety Research ◽  
Miseq Platform

ABSTRACT The genomes of two strains of Salmonella enterica subsp. enterica serovar Cubana and serovar Muenchen, isolated from dry hazelnuts and chia seeds, respectively, were sequenced using the Illumina MiSeq platform, assembled de novo using the overlap-layout-consensus method, and aligned to their respective most identical sequence genome scaffolds using MUMMER and BLAST searches.

scholarly journals Draft Genome Sequence of Lactobacillus reuteri Strain LR CGMCC 11154, Isolated from the Feces of Healthy Weaned Piglets

2019 ◽  
Vol 8 (3) ◽  
Author(s):  
Ting Yu ◽  
Xi Yang ◽  
Zhilin Wang ◽  
Cui Zhu ◽  
Jinlong Bei ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Lactobacillus Reuteri ◽  
Draft Genome ◽  
Illumina Miseq ◽  
Probiotic Bacterium ◽  
Whole Genome ◽  
Weaned Piglets ◽  
Content Type ◽  
Illumina Miseq Platform ◽  
Miseq Platform

Lactobacillus reuteri strain LR CGMCC 11154, which was isolated from the feces of healthy weaned piglets, was experimentally proven to be a probiotic bacterium. The whole genome was sequenced on the Illumina Miseq platform to obtain the draft genome, which consists of 120 contigs totaling 1.9 Mbp encoding 1,854 genes.

scholarly journals Draft Genome Sequences ofAnaplasma phagocytophilum,A. marginale, andA. ovisIsolates from Different Hosts

2018 ◽  
Vol 6 (5) ◽  
Author(s):  
Sandra Diaz-Sanchez ◽  
Angélica Hernández-Jarguín ◽  
Isabel G. Fernández de Mera ◽  
Pilar Alberdi ◽  
Erich Zweygarth ◽  
...  
Keyword(s):  
United States ◽  
Genome Sequence ◽  
Anaplasma Phagocytophilum ◽  
Draft Genome ◽  
Anaplasma Marginale ◽  
The United States ◽  
Genome Sequences ◽  
Anaplasma Ovis ◽  
First Report

ABSTRACTHere, we report the draft genome sequences of isolates ofAnaplasma phagocytophilum,Anaplasma marginale, andAnaplasma ovis. The genomes ofA. phagocytophilum(human),A. marginale(cattle), andA. ovis(goat) isolates from the United States were sequenced and characterized. This is the first report of anA. ovisgenome sequence.

scholarly journals Draft Genome Sequence of a New Zealand Isolate of Mycoplasma ovipneumoniae

2020 ◽  
Vol 9 (10) ◽  
Author(s):  
B. J. Bridgeman ◽  
S. K. Gupta ◽  
A. Murray ◽  
V. S. R. Dukkipati ◽  
E. Altermann ◽  
...  
Keyword(s):  
New Zealand ◽  
Genome Sequence ◽  
De Novo ◽  
Draft Genome ◽  
Illumina Miseq ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Mycoplasma Ovipneumoniae

The genome of New Zealand Mycoplasma ovipneumoniae isolate 90 was sequenced and assembled using an Illumina MiSeq system and combining the built-in Geneious de novo and Velvet de novo assemblers. The 1,031,345-bp-long genome harbored 711 genes with a coding percentage of 86.6.

scholarly journals Draft Genome Sequence of Pasteurella multocida Isolate P1062, Isolated from Bovine Respiratory Disease

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Juan E. Abrahante ◽  
Samuel S. Hunter ◽  
Samuel K. Maheswaran ◽  
Melissa J. Hauglund ◽  
Fred M. Tatum ◽  
...  
Keyword(s):  
United States ◽  
Respiratory Disease ◽  
Genome Sequence ◽  
Pasteurella Multocida ◽  
Bovine Respiratory Disease ◽  
Draft Genome ◽  
The United States ◽  
Draft Genome Sequence

Here, we report the draft genome of Pasteurella multocida isolate P1062 recovered from pneumonic bovine lung in the United States in 1959.

scholarly journals Draft Genome Sequence and intraspecific diversification of the wild crop relative Brassica cretica Lam. using demographic model selection

2019 ◽  
Author(s):  
Antonis Kioukis ◽  
Vassiliki A. Michalopoulou ◽  
Laura Briers ◽  
Stergios Pirintsos ◽  
David J. Studholme ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Sequence Data ◽  
Plant Genetic Resources ◽  
Crop Improvement ◽  
Draft Genome ◽  
Illumina Miseq ◽  
Crop Wild Relatives ◽  
Demographic Model ◽  
Sequencing Data

AbstractCrop wild relatives contain great levels of genetic diversity, representing an invaluable resource for crop improvement. Many of their traits have the potential to help crops become more resistant and resilient, and adapt to the new conditions that they will experience due to climate change. An impressive global effort occurs for the conservation of various wild crop relatives and facilitates their use in crop breeding for food security.The genus Brassica is listed in Annex I of the International Treaty on Plant Genetic Resources for Food and Agriculture. Brassica oleracea (or wild cabbage) is a species native to coastal southern and western Europe that has become established as an important human food crop plant because of its large reserves stored over the winter in its leaves.Brassica cretica Lam. is a wild relative crop in the brassica group and B. cretica subsp. nivea has been suggested as a separate subspecies. The species B. cretica has been proposed as a potential gene donor to a number of crops in the brassica group, including broccoli, Brussels sprout, cabbage, cauliflower, kale, swede, turnip and oilseed rape.Here, we present the draft de novo genome assemblies of four B. cretica individuals, including two B. cretica subsp. nivea and two B. cretica.De novo assembly of Illumina MiSeq genomic shotgun sequencing data yielded 243,461 contigs totalling 412.5 Mb in length, corresponding to 122 % of the estimated genome size of B. cretica (339 Mb). According to synteny mapping and phylogenetic analysis of conserved genes, B. cretica genome based on our sequence data reveals approximately 30.360 proteins.Furthermore, our demographic analysis based on whole genome data, suggests that distinct populations of B. cretica are not isolated. Our findings suggest that the classification of the B. cretica in distinct subspecies is not supported from the genome sequence data we analyzed.

scholarly journals Draft Genome Sequence Resource for Phyllachora maydis—An Obligate Pathogen That Causes Tar Spot of Corn with Recent Economic Impacts in the United States

2020 ◽  
Vol 33 (7) ◽  
pp. 884-887
Author(s):  
Darcy E. P. Telenko ◽  
Tiffanna J. Ross ◽  
Sujoung Shim ◽  
Qinhu Wang ◽  
Raksha Singh
Keyword(s):  
United States ◽  
Genome Sequence ◽  
Repetitive Sequences ◽  
Draft Genome ◽  
The United States ◽  
Effector Proteins ◽  
Protein Coding ◽  
Corn Breeding ◽  
Tar Spot ◽  
Obligate Pathogen

Phyllachora maydis is an important fungal pathogen that causes tar spot of corn and has led to significant yield loss in the United States and other countries. P. maydis is an obligate biotroph belonging to the Sordariomycetes class of Ascomycota. Due to the challenges posed by their obligate nature, there is no genome sequence available in the Phyllachora genus. P. maydis isolate PM01 was collected from a corn field in Indiana and the genome was determined by next-generation sequencing. The assembly size is 45.7 Mb, with 56.46% repetitive sequences. There are 5,992 protein-coding genes and 59 are predicted as effector proteins. This genome resource will increase our understanding of genomic features of P. maydis and will assist in studying the corn–P. maydis interaction and identifying potential resistant candidates for corn breeding programs.

scholarly journals Genomic Analysis of Xanthomonas oryzae Isolates from Rice Grown in the United States Reveals Substantial Divergence from Known X. oryzae Pathovars

2011 ◽  
Vol 77 (12) ◽  
pp. 3930-3937 ◽  
Author(s):  
L. R. Triplett ◽  
J. P. Hamilton ◽  
C. R. Buell ◽  
N. A. Tisserat ◽  
V. Verdier ◽  
...  
Keyword(s):  
United States ◽  
Genome Sequence ◽  
Draft Genome ◽  
The United States ◽  
Xanthomonas Oryzae ◽  
Draft Genome Sequence ◽  
Diagnostic Tools ◽  
Putative Gene ◽  
Content Type ◽  
The U.S

ABSTRACTThe speciesXanthomonas oryzaeis comprised of two designated pathovars, both of which cause economically significant diseases of rice in Asia and Africa. AlthoughX. oryzaeis not considered endemic in the United States, anX. oryzae-like bacterium was isolated from U.S. rice and southern cutgrass in the late 1980s. The U.S. strains were weakly pathogenic and genetically distinct from characterizedX. oryzaepathovars. In the current study, a draft genome sequence from two U.S.Xanthomonasstrains revealed that the U.S. strains form a novel clade within theX. oryzaespecies, distinct from all strains known to cause significant yield loss. Comparative genome analysis revealed several putative gene clusters specific to the U.S. strains and supported previous reports that the U.S. strains lack transcriptional activator-like (TAL) effectors. In addition to phylogenetic and comparative analyses, the genome sequence was used for designing robust U.S. strain-specific primers, demonstrating the usefulness of a draft genome sequence in the rapid development of diagnostic tools.

scholarly journals Draft Genome Sequence of Mycobacterium virginiense Strain GF75, Isolated from the Mud of a Swine Farm in Japan

2018 ◽  
Vol 6 (17) ◽  
Author(s):  
Toshihiro Ito ◽  
Fumito Maruyama ◽  
Kotaro Sawai ◽  
Keiko Nozaki ◽  
Keiko Otsu ◽  
...  
Keyword(s):  
United States ◽  
Genome Sequence ◽  
Draft Genome ◽  
The United States ◽  
Draft Genome Sequence ◽  
Swine Farm ◽  
Content Type

ABSTRACT Mycobacterium virginiense , a newly described species of the Mycobacterium terrae complex, is a cause of tenosynovitis and osteomyelitis in the United States. Here, we report the 4,849,424-bp draft genome sequence of M. virginiense strain GF75, isolated from a mud sample taken from a Japanese swine farm.

scholarly journals Genome Sequence of a Salmonella enterica subsp. enterica Serovar Corvallis Strain Isolated from Human Blood

2019 ◽  
Vol 8 (44) ◽  
Author(s):  
Emily L. McCutchen ◽  
Madeline Galac ◽  
Curtis Kapsak ◽  
Steven H. Hinrichs ◽  
Peter C. Iwen ◽  
...  
Keyword(s):  
United States ◽  
Genome Sequence ◽  
Human Blood ◽  
Salmonella Enterica ◽  
Draft Genome ◽  
The United States ◽  
Multidrug Resistant ◽  
Content Type ◽  
Avian Populations ◽  
By Products

Salmonella enterica subsp. enterica serovar Corvallis is commonly reported in avian populations and avian by-products. We report the draft genome sequence of a multidrug-resistant S. Corvallis strain (NPHL 15376). To our knowledge, this is the first reported case of this serovar isolated from human blood in the United States.

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