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.

scholarly journals PSVII-39 Late-Breaking Abstract: Enhancing production and Aleutian disease resilience in mink through advanced genomics

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 342-342
Author(s):  
Younes Miar ◽  
Graham Plastow ◽  
Zhiquan Wang ◽  
Mehdi Sargolzaei
Keyword(s):  
Genome Sequence ◽  
Genetic Relationships ◽  
American Mink ◽  
Sequence Assembly ◽  
Whole Genome Sequence ◽  
High Price ◽  
Whole Genome ◽  
Next Generation ◽  
Genome Sequence Assembly ◽  
Wide Range

Abstract The fur industry is one of the oldest and the most historically significant industries in Canada. The industry has used American mink (Neovison vison) as the major source of fur for decades because of their high-quality fur and wide range of colours. This project will seek to (1) create the first accurate whole-genome sequence assembly of mink using next-generation sequencing technology to help understanding the biology and evolution of the order Carnivora, (2) design a robust and informative SNP assay for genomics discovery in mink, (3) discover genome structure and signature of selection as well as identify new genetic variants explaining variation in economically important traits, and (4) identify the genetic relationships among these traits including feed efficiency, Aleutian disease resilience, fur quality, reproductive performance, growth rate and pelt size. One hundred mink DNA samples from the Canadian Centre for Fur Animal Research at Dalhousie Agriculture Campus (Truro, Nova Scotia), and one breeding population (Millbank Fur Farm Limited, Rockwood, Ontario) were sequenced using next-generation whole-genome sequencing with more than 30x coverage to create the first SNP assay for American mink. A DNA panel composed of these sequenced mink from five color-types were assembled to identify the most homozygous individual as the reference animal for whole-genome sequence assembly development. The phenotypic data and DNA samples from 3,323 animals were collected and will be genotyped using the customized assay. The ultimate objective is to develop new tools for implementation of marker assisted selection or genomic selection in mink breeding programs for development of superior, highly efficient, and healthy animals. This approach will help improve the overall performance of the North American mink industry, which is now in difficulty due to several economic factors such as the high price of feed, declining price of fur and prevalence of diseases.

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 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 IdentifyingStreptococcus pneumoniaegenes associated with invasive disease using pangenome-based whole genome sequence typing

2018 ◽  
Author(s):  
Uri Obolski ◽  
Andrea Gori ◽  
José Lourenço ◽  
Craig Thompson ◽  
Robin Thompson ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Pneumococcal Disease ◽  
Learning Algorithm ◽  
Invasive Disease ◽  
Whole Genome Sequence ◽  
Data Sets ◽  
Whole Genome ◽  
Upper Respiratory Tract ◽  
Pneumococcal Carriage ◽  
Upper Respiratory

AbstractStreptococcus pneumoniaeis a normal commensal of the upper respiratory tract but can also invade the bloodstream or CSF (cerebrospinal fluid), causing invasive pneumococcal disease (IPD). In this study, we attempt to identify genes associated with IPD by applying a random forest machine-learning algorithm to whole genome sequence (WGS) data. We find 43 genes consistently associated with IPD across three geographically distinct WGS data sets of pneumococcal carriage isolates. Of these genes, 23 genes have previously shown to be directly relevant to IPD, while the other 18 are uncharacterized.

scholarly journals Genome assembly of Vitis rotundifolia Michx. using third-generation sequencing (Oxford Nanopore Technologies)

2021 ◽  
Vol 182 (2) ◽  
pp. 63-71
Author(s):  
M. M. Agakhanov ◽  
E. A. Grigoreva ◽  
E. K. Potokina ◽  
P. S. Ulianich ◽  
Y. V. Ukhatova
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
De Novo ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Third Generation ◽  
Vitis Rotundifolia ◽  
Third Generation Sequencing ◽  
Genome Sequence Assembly ◽  
Generation Sequencing

The immune North American grapevine species Vitis rotundifolia Michaux (subgen. Muscadinia Planch.) is regarded as a potential donor of disease resistance genes, withstanding such dangerous diseases of grapes as powdery and downy mildews. The cultivar ‘Dixie’ is the only representative of this species preserved ex situ in Russia: it is maintained by the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR) in the orchards of its branch, Krymsk Experiment Breeding Station. Third-generation sequencing on the MinION platform was performed to obtain information on the primary structure of the cultivar’s genomic DNA, employing also the results of Illumina sequencing available in databases. A detailed description of the technique with modifications at various stages is presented, as it was used for grapevine genome sequencing and whole-genome sequence assembly. The modified technique included the main stages of the original protocol recommended by the MinION producer: 1) DNA extraction; 2) preparation of libraries for sequencing; 3) MinION sequencing and bioinformatic data processing; 4) de novo whole-genome sequence assembly using only MinION data or hybrid assembly (MinION+Illumina data); and 5) functional annotation of the whole-genome assembly. Stage 4 included not only de novo sequencing, but also the analysis of the available bioinformatic data, thus minimizing errors and increasing precision during the assembly of the studied genome. The DNA isolated from the leaves of cv. ‘Dixie’ was sequenced using two MinION flow cells (R9.4.1).

scholarly journals Mining Whole Genome Sequence data to efficiently attribute individuals to source populations

2020 ◽  
Author(s):  
Francisco J. Pérez-Reche ◽  
Ovidiu Rotariu ◽  
Bruno S. Lopes ◽  
Ken J. Forbes ◽  
Norval J.C. Strachan
Keyword(s):  
Genome Sequence ◽  
Sequence Data ◽  
Large Data ◽  
Biological Species ◽  
Whole Genome Sequence ◽  
Data Sets ◽  
Whole Genome ◽  
Computationally Efficient ◽  
Proteomic Data ◽  
Source Populations

ABSTRACTWhole genome sequence (WGS) data could transform our ability to attribute individuals to source populations. However, methods that effectively mine these data are yet to be developed. We present a minimal multilocus distance (MMD) method which rapidly deals with these large data sets as well as methods for optimally selecting loci. This was applied on WGS data to determine the source of human campylobacteriosis, the geographical origin of diverse biological species including humans and proteomic data to classify breast cancer tumours. The MMD method provides a highly accurate attribution which is computationally efficient for extended genotypes. These methods are generic, easy to implement for WGS and proteomic data and have wide application.

scholarly journals TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Cécile Monat ◽  
Sudharsan Padmarasu ◽  
Thomas Lux ◽  
Thomas Wicker ◽  
Heidrun Gundlach ◽  
...  
Keyword(s):  
Open Source ◽  
Genome Sequence ◽  
Sequence Data ◽  
Sequence Assembly ◽  
Sequencing Data ◽  
Chromosome Conformation ◽  
Assembly Algorithm ◽  
Genome Sequence Assembly ◽  
Mate Pair ◽  
Genomic Studies

AbstractChromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We present TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluate the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and construct an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.

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