Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2

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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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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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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