scholarly journals Whole-genome sequence and methylome profiling of the almond (Prunus dulcis [Mill.] D.A.Webb) cultivar Nonpareil

2021 ◽  
Author(s):  
Katherine M. D'Amico-Willman ◽  
Wilberforce Z. Ouma ◽  
Tea Meulia ◽  
Gina M. Sideli ◽  
Thomas M. Gradziel ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Cytosine Methylation ◽  
Gene Prediction ◽  
Prunus Dulcis ◽  
The United States ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Sequencing Data ◽  
Oxford Nanopore ◽  
Epigenetic Signatures

Almond (Prunus dulcis [Mill.] D.A. Webb) is an economically important, specialty nut crop grown almost exclusively in the United States. Breeding and improvement efforts worldwide have led to the development of key, productive cultivars, including Nonpareil, which is the most widely grown almond cultivar. Thus far, genomic resources for this species have been limited, and a whole-genome assembly for Nonpareil is not currently available despite its economic importance and use in almond breeding worldwide. We generated a 615.89X coverage genome sequence using Illumina, PacBio, and optical mapping technologies. Gene prediction revealed 27,487 genes using MinION Oxford nanopore and Illumina RNA sequencing, and genome annotation found that 68% of predicted models are associated with at least one biological function. Further, epigenetic signatures of almond, namely DNA cytosine methylation, have been implicated in a variety of phenotypes including self-compatibility, bud dormancy, and development of non-infectious bud failure. In addition to the genome sequence and annotation, this report also provides the complete methylome of several key almond tissues, including leaf, flower, endocarp, mesocarp, fruit skin, and seed coat. Comparisons between methylation profiles in these tissues revealed differences in genome-wide weighted percent methylation and chromosome-level methylation enrichment. The raw sequencing data are available on NCBI Sequence Read Archive, and the complete genome sequence and annotation files are available on NCBI Genbank. All data can be used without restriction.

scholarly journals MTBseq: a comprehensive pipeline for whole genome sequence analysis of Mycobacterium tuberculosis complex isolates

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5895 ◽  
Author(s):  
Thomas Andreas Kohl ◽  
Christian Utpatel ◽  
Viola Schleusener ◽  
Maria Rosaria De Filippo ◽  
Patrick Beckert ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Mycobacterium Tuberculosis ◽  
Genome Sequence ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome Sequencing Data ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
Sequencing Data ◽  
Desktop Computer

Analyzing whole-genome sequencing data of Mycobacterium tuberculosis complex (MTBC) isolates in a standardized workflow enables both comprehensive antibiotic resistance profiling and outbreak surveillance with highest resolution up to the identification of recent transmission chains. Here, we present MTBseq, a bioinformatics pipeline for next-generation genome sequence data analysis of MTBC isolates. Employing a reference mapping based workflow, MTBseq reports detected variant positions annotated with known association to antibiotic resistance and performs a lineage classification based on phylogenetic single nucleotide polymorphisms (SNPs). When comparing multiple datasets, MTBseq provides a joint list of variants and a FASTA alignment of SNP positions for use in phylogenomic analysis, and identifies groups of related isolates. The pipeline is customizable, expandable and can be used on a desktop computer or laptop without any internet connection, ensuring mobile usage and data security. MTBseq and accompanying documentation is available from https://github.com/ngs-fzb/MTBseq_source.

scholarly journals Genome Sequence Data of the Soybean Pathogen Stagonosporopsis vannaccii: A Resource for Studies on Didymellaceae Evolution

2020 ◽  
Vol 33 (8) ◽  
pp. 1022-1024
Author(s):  
Giovanni Cafà ◽  
Thaís Regina Boufleur ◽  
Renata Rebellato Linhares de Castro ◽  
Nelson Sidnei Massola ◽  
Riccardo Baroncelli
Keyword(s):  
Comparative Genomics ◽  
Genome Sequence ◽  
Plant Pathogens ◽  
Sequence Data ◽  
Gene Prediction ◽  
Whole Genome Sequence ◽  
Future Research ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Associated Species

The genus Stagonosporopsis is classified within the Didymellaceae family and has around 40 associated species. Among them, several species are important plant pathogens responsible for significant losses in economically important crops worldwide. Stagonosporopsis vannaccii is a newly described species pathogenic to soybean. Here, we present the draft whole-genome sequence, gene prediction, and annotation of S. vannaccii isolate LFN0148 (also known as IMI 507030). To our knowledge, this is the first genome sequenced of this species and represents a new useful source for future research on fungal comparative genomics studies.

scholarly journals Genome sequence resource for Stagonosporopsis cucurbitacearum, a cause of gummy stem blight disease of watermelon

2021 ◽  
Author(s):  
Fahao Wang ◽  
Jiahui Qi ◽  
Miao Tian ◽  
Yizhou Gao ◽  
Xiaohui Xiong ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Related Species ◽  
Southern China ◽  
Gene Prediction ◽  
Pathogenic Mechanism ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Stem Blight ◽  
Gummy Stem Blight ◽  
Blight Disease

Gummy stem blight (GSB), which is caused by three related species of Stagonosporopsis, is a worldwide devastating disease of cucurbit crops including watermelon. Previously S. cucurbitacearum was reported to be the major fungal cause of watermelon GSB in Southern China, where it causes a significant decrease in watermelon yield. Here, we present the draft whole genome sequence, gene prediction and annotation of S. cucurbitacearum strain DBTL4, isolated from diseased watermelon plants. To our knowledge, this is the first publicly available genome sequence of this species, and knowledge of this genome sequence will help further understand the pathogenic mechanism of S. cucurbitacearum to cucurbit plants.

scholarly journals Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf

2016 ◽  
Vol 2 (7) ◽  
pp. e1501714 ◽  
Author(s):  
Bridgett M. vonHoldt ◽  
James A. Cahill ◽  
Zhenxin Fan ◽  
Ilan Gronau ◽  
Jacqueline Robinson ◽  
...  
Keyword(s):  
United States ◽  
Genome Sequence ◽  
North American ◽  
Sequence Data ◽  
The United States ◽  
Geographic Range ◽  
Whole Genome Sequence ◽  
Gray Wolf ◽  
Whole Genome ◽  
Eastern Wolf

Protection of populations comprising admixed genomes is a challenge under the Endangered Species Act (ESA), which is regarded as the most powerful species protection legislation ever passed in the United States but lacks specific provisions for hybrids. The eastern wolf is a newly recognized wolf-like species that is highly admixed and inhabits the Great Lakes and eastern United States, a region previously thought to be included in the geographic range of only the gray wolf. The U.S. Fish and Wildlife Service has argued that the presence of the eastern wolf, rather than the gray wolf, in this area is grounds for removing ESA protection (delisting) from the gray wolf across its geographic range. In contrast, the red wolf from the southeastern United States was one of the first species protected under the ESA and was protected despite admixture with coyotes. We use whole-genome sequence data to demonstrate a lack of unique ancestry in eastern and red wolves that would not be expected if they represented long divergent North American lineages. These results suggest that arguments for delisting the gray wolf are not valid. Our findings demonstrate how a strict designation of a species under the ESA that does not consider admixture can threaten the protection of endangered entities. We argue for a more balanced approach that focuses on the ecological context of admixture and allows for evolutionary processes to potentially restore historical patterns of genetic variation.

scholarly journals Whole-Genome Sequence of Photobacterium damselae subsp. piscicida Strain 91-197, Isolated from Hybrid Striped Bass (Morone sp.) in the United States

2017 ◽  
Vol 5 (29) ◽  
Author(s):  
Yuki Teru ◽  
Jun-ichi Hikima ◽  
Tomoya Kono ◽  
Masahiro Sakai ◽  
Tomokazu Takano ◽  
...  
Keyword(s):  
United States ◽  
Genome Sequence ◽  
Striped Bass ◽  
The United States ◽  
Whole Genome Sequence ◽  
Economic Damage ◽  
Whole Genome ◽  
Content Type ◽  
Photobacterium Damselae ◽  
Causative Bacterium

ABSTRACT Photobacterium damselae subsp. piscicida is a causative bacterium of fish pasteurellosis, which has caused serious economic damage to aquaculture farms worldwide. Here, the whole-genome sequence of P. damselae subsp. piscicida 91-197, isolated in the United States, suggests that this genome consists of two chromosomes and two plasmids.

scholarly journals Whole genome sequence and gene annotation resource for Didymella bellidis, associated with tea leaf spot

Plant Disease ◽  
2020 ◽  
Author(s):  
Xue Wang ◽  
Xian Wu ◽  
Shilong Jiang ◽  
Qiaoxiu Yin ◽  
Dongxue Li ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Leaf Spot ◽  
Sequence Data ◽  
Gene Annotation ◽  
Gene Prediction ◽  
Guizhou Province ◽  
Whole Genome Sequence ◽  
Phytopathogenic Fungus ◽  
Future Research ◽  
Whole Genome

Didymella bellidis is a phytopathogenic fungus that causes leaf spot on tea plants (Camellia sinensis), which negatively affects the productivity and quality of tea leaves in Guizhou Province, China. D. bellidis isolate GZYQYQX2B was sequenced using Pacific Biosciences and Illumina technologies, and assembled into a whole genome of 35.5 Mbp. Transcripts of D. bellidis isolate GZYQYQX2B were predicted from the assembled genome and were further validated by RNA sequence data. In total, 10,731 genes were predicted by integrating three approaches, namely ab initio and homology-based gene prediction, as well as transcriptomics data. The whole-genome sequence of D. bellidis will provide a resource for future research on trait-specific genes of the pathogen and host-pathogen interactions.

scholarly journals Population and Whole Genome Sequence Based Characterization of Invasive Group A Streptococci Recovered in the United States during 2015

mBio ◽  
2017 ◽  
Vol 8 (5) ◽  
Author(s):  
Sopio Chochua ◽  
Ben J. Metcalf ◽  
Zhongya Li ◽  
Joy Rivers ◽  
Saundra Mathis ◽  
...  
Keyword(s):  
United States ◽  
Genome Sequence ◽  
The United States ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Group A Streptococci ◽  
Phylogenetic Clustering ◽  
Streptolysin O ◽  
Group A

ABSTRACTGroup A streptococci (GAS) are genetically diverse. Determination of strain features can reveal associations with disease and resistance and assist in vaccine formulation. We employed whole-genome sequence (WGS)-based characterization of 1,454 invasive GAS isolates recovered in 2015 by Active Bacterial Core Surveillance and performed conventional antimicrobial susceptibility testing. Predictions were made for genotype, GAS carbohydrate, antimicrobial resistance, surface proteins (M family, fibronectin binding, T, R28), secreted virulence proteins (Sda1, Sic, exotoxins), hyaluronate capsule, and an upregulatedngaoperon (encodes NADase and streptolysin O) promoter (Pnga3). Sixty-four M protein gene (emm) types were identified among 69 clonal complexes (CCs), including one CC ofStreptococcus dysgalactiaesubsp.equisimilis.emmtypes predicted the presence or absence of activesofdeterminants and were segregated intosof-positive orsof-negative genetic complexes. Only one “emmtype switch” between strains was apparent.sof-negative strains showed a propensity to cause infections in the first quarter of the year, whilesof+strain infections were more likely in summer. Of 1,454 isolates, 808 (55.6%) were Pnga3 positive and 637 (78.9%) were accounted for by typesemm1,emm89, andemm12. Theoretical coverage of a 30-valent M vaccine combined with an M-related protein (Mrp) vaccine encompassed 98% of the isolates. WGS data predicted that 15.3, 13.8, 12.7, and 0.6% of the isolates were nonsusceptible to tetracycline, erythromycin plus clindamycin, erythromycin, and fluoroquinolones, respectively, with only 19 discordant phenotypic results. Close phylogenetic clustering ofemm59isolates was consistent with recent regional emergence. This study revealed strain traits informative for GAS disease incidence tracking, outbreak detection, vaccine strategy, and antimicrobial therapy.IMPORTANCEThe current population-based WGS data from GAS strains causing invasive disease in the United States provide insights important for prevention and control strategies. Strain distribution data support recently proposed multivalent M type-specific and conserved M-like protein vaccine formulations that could potentially protect against nearly all invasive U.S. strains. The three most prevalent clonal complexes share key polymorphisms in thengaoperon encoding two secreted virulence factors (NADase and streptolysin O) that have been previously associated with high strain virulence and transmissibility. We find thatStreptococcus pyogenesis phylogenetically subdivided into loosely defined multilocus sequence type-based clusters consisting of solelysof-negative orsof-positive strains; withsof-negative strains demonstrating differential seasonal preference for infection, consistent with the recently demonstrated differential seasonal preference based on phylogenetic clustering of full-length M proteins. This might relate to the differences in GAS strain compositions found in different geographic settings and could further inform prevention strategies.

scholarly journals Whole-Genome Sequence Analysis of CTX-M Containing Escherichia coli Isolates from Retail Meats and Cattle in the United States

2018 ◽  
Vol 24 (7) ◽  
pp. 939-948 ◽  
Author(s):  
Daniel A. Tadesse ◽  
Cong Li ◽  
Sampa Mukherjee ◽  
Chih-Hao Hsu ◽  
Sonya Bodeis Jones ◽  
...  
Keyword(s):  
United States ◽  
Escherichia Coli ◽  
Sequence Analysis ◽  
Genome Sequence ◽  
The United States ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Analysis ◽  
Retail Meats

scholarly journals RNA Sequencing Data Sets and Their Whole-Genome Sequence Assembly of Dengue Virus from Three Serial Passages in Vero Cells

2021 ◽  
Vol 10 (17) ◽  
Author(s):  
Thidathip Wongsurawat ◽  
Nuntaya Punyadee ◽  
Piroon Jenjaroenpun ◽  
Dumrong Mairiang ◽  
Nattaya Tangthawornchaikul ◽  
...  
Keyword(s):  
Dengue Virus ◽  
Rna Sequencing ◽  
Genome Sequence ◽  
Vero Cells ◽  
Sequence Assembly ◽  
Whole Genome Sequence ◽  
Data Sets ◽  
Whole Genome ◽  
Sequencing Data ◽  
Genome Sequence Assembly

ABSTRACT We present RNA sequencing data sets and their genome sequence assembly for dengue virus that was isolated from a patient with dengue hemorrhagic fever and serially propagated in Vero cells. RNA sequencing data obtained from the first, third, and fifth passages and their corresponding whole-genome sequences are provided in this work.

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