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

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.

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Whole-genome sequence assembly of Pediococcus pentosaceus LI05 (CGMCC 7049) from the human gastrointestinal tract and comparative analysis with representative sequences from three food-borne strains

Gut Pathogens ◽

10.1186/s13099-014-0036-y ◽

2014 ◽

Vol 6 (1) ◽

Cited By ~ 13

Author(s):

Long-Xian Lv ◽

Yu-Dong Li ◽

Xin-Jun Hu ◽

Hai-Yan Shi ◽

Lan-Juan Li

Keyword(s):

Comparative Analysis ◽

Gastrointestinal Tract ◽

Genome Sequence ◽

Sequence Assembly ◽

Whole Genome Sequence ◽

Whole Genome ◽

Human Gastrointestinal Tract ◽

Pediococcus Pentosaceus ◽

Genome Sequence Assembly ◽

Food Borne

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Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2

Genome Research ◽

10.1101/gr.828403 ◽

2003 ◽

Vol 13 (1) ◽

pp. 91-96 ◽

Cited By ~ 197

Author(s):

D. B. Jaffe

Keyword(s):

Genome Sequence ◽

Sequence Assembly ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequence Assembly ◽

Mammalian Genomes

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Accuracy and coverage assessment of Oryctolagus cuniculus (rabbit) genes encoding immunoglobulins in the whole genome sequence assembly (OryCun2.0) and localization of the IGH locus to chromosome 20

Immunogenetics ◽

10.1007/s00251-013-0722-9 ◽

2013 ◽

Vol 65 (10) ◽

pp. 749-762 ◽

Cited By ~ 12

Author(s):

E. Michael Gertz ◽

Alejandro A. Schäffer ◽

Richa Agarwala ◽

Amélie Bonnet-Garnier ◽

Claire Rogel-Gaillard ◽

...

Keyword(s):

Genome Sequence ◽

Oryctolagus Cuniculus ◽

Sequence Assembly ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequence Assembly ◽

Igh Locus ◽

Chromosome 20 ◽

Genes Encoding

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

Microbiology Resource Announcements ◽

10.1128/mra.00145-21 ◽

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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Limitations of next-generation genome sequence assembly

Nature Methods ◽

10.1038/nmeth.1527 ◽

2010 ◽

Vol 8 (1) ◽

pp. 61-65 ◽

Cited By ~ 442

Author(s):

Can Alkan ◽

Saba Sajjadian ◽

Evan E Eichler

Keyword(s):

Genome Sequence ◽

Sequence Assembly ◽

Next Generation ◽

Genome Sequence Assembly

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Developing a 670k genotyping array to tag ∼2M SNPs across 24 horse breeds

10.1101/112979 ◽

2017 ◽

Author(s):

Robert J. Schaefer ◽

Mikkel Schubert ◽

Ernest Bailey ◽

Danika L. Bannasch ◽

Eric Barrey ◽

...

Keyword(s):

Genome Sequence ◽

High Density ◽

Genotype Imputation ◽

Whole Genome Sequence ◽

Probe Design ◽

Candidate Snps ◽

Genotype Data ◽

Domestic Horse ◽

Whole Genome ◽

Next Generation

AbstractBackgroundTo date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array.ResultsUsing whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of ∼5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix, now Thermo Fisher Scientific) a set of ∼2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of ∼670 thousand SNPs (MNEc670k), was designed for genotype imputation.ConclusionsHere, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse.

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Draft Whole-Genome Sequence of the Purple Photosynthetic Bacterium Rhodopseudomonas palustris XCP

Microbiology Resource Announcements ◽

10.1128/mra.00855-18 ◽

2018 ◽

Vol 7 (4) ◽

Cited By ~ 3

Author(s):

Amiera Rayyan ◽

Terry Meyer ◽

John Kyndt

Keyword(s):

Genome Sequence ◽

Rhodopseudomonas Palustris ◽

Photosynthetic Bacterium ◽

Whole Genome Sequence ◽

Whole Genome ◽

Content Type ◽

Wide Range ◽

Purple Photosynthetic Bacterium

Rhodopseudomonas palustris is known for its versatile metabolic capabilities and has been proposed for a wide range of innovative applications. Here, we report the genome sequence of strain XCP, as well as a whole-genome nucleotide comparison of R. palustris strains, which indicates the need for further differentiation of the known strains.

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Draft Genome Sequence of Ciprofloxacin and Ceftriaxone Resistant Campylobacter jejuni MM26-781 Assigned to Novel ST Isolated From Common Pigeon in Lithuania

Evolutionary Bioinformatics ◽

10.1177/1176934319868469 ◽

2019 ◽

Vol 15 ◽

pp. 117693431986846

Author(s):

Jurgita Aksomaitiene ◽

Sigita Ramonaite ◽

Aleksandr Novoslavskij ◽

Mindaugas Malakauskas ◽

Egle Kudirkiene

Keyword(s):

Antibiotic Resistance ◽

Campylobacter Jejuni ◽

Genome Sequence ◽

Molecular Mechanisms ◽

Draft Genome ◽

Columba Livia ◽

Draft Genome Sequence ◽

Whole Genome Sequence ◽

Whole Genome ◽

Wide Range

Campylobacter jejuni is an important zoonotic pathogen known to be resistant to a wide range of antibiotics worldwide. Campylobacter jejuni may be intrinsically resistant to antibiotics or can acquire antibiotic resistance determinants through gene transfer. However, the knowledge of molecular mechanisms of antimicrobial resistance among Campylobacter isolates from wild birds, especially in Lithuania, is limited. Whole genome sequencing (WGS) is a tool for better understanding the evolutionary and epidemiologic dynamics of C jejuni. This study describes a draft whole genome sequence of C jejuni MM26-781 isolated from a common pigeon ( Columba livia) in Lithuania in 2011 and assigned to ST-6424 (CC179) sequence type. The draft genome sequence contained 1.68 Mb, comprising 1651 coding genes, 40 transfer RNAs, 1 ribosomal RNA, and 69 pseudogenes with an average G + C content of 30.4%. The RAST (Rapid Annotation using Subsystem Technology) pipeline annotated (NCTC11168) a total of 305 subsystems in the genome of C jejuni MM26-781 strain, with most of the genes associated with amino acids and derivatives related to metabolism (18.93%) and protein metabolism (14.43%). The genes and mutations related to antibiotic resistance, including gyrA and gyrB genes associated with quinolone resistance, blaOXA-448 gene (locus tag C9371_07715) associated with resistance to β-lactams, rpoB gene associated with resistance to rifamycin, vgaE gene associated with resistance to streptogramin and efflux system CmeABC ( cmeA, cmeB, cmeC), efflux pump PmrA, and transcriptional regulator CmeR responsible for multidrug resistance in C jejuni MM26-781 chromosome, were identified. Also, the virulence factors, including ciaB, cadF, ceuE, pldA, motB, and bd1A genes, were identified by WGS data analysis.

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

PROCEEDINGS ON APPLIED BOTANY GENETICS AND BREEDING ◽

10.30901/2227-8834-2021-2-63-71 ◽

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).

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