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Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly

Rando, Halie, Farré, Marta, Robson, Michael, Won, Naomi, Johnson, Jennifer, Buch, Ronak, Bastounes, Estelle, Xiang, Xueyan, Feng, Shaohong, Liu, Shiping, and others. (2018) Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly. Genes, 9 (6). p. 308. ISSN 2073-4425. E-ISSN 2073-4425. (doi:10.3390/genes9060308) (KAR id:70042)

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Abstract

The genome of a red fox (Vulpes vulpes) was recently sequenced and assembled using next-generation sequencing (NGS). The assembly is of high quality, with 94X coverage and a scaffold N50 of 11.8 Mbp, but is split into 676,878 scaffolds, some of which are likely to contain assembly errors. Fragmentation and misassembly hinder accurate gene prediction and downstream analysis such as the identification of loci under selection. Therefore, assembly of the genome into chromosome-scale fragments was an important step towards developing this genomic model. Scaffolds from the assembly were aligned to the dog reference genome and compared to the alignment of an outgroup genome (cat) against the dog to identify syntenic sequences among species. The program Reference-Assisted Chromosome Assembly (RACA) then integrated the comparative alignment with the mapping of the raw sequencing reads generated during assembly against the fox scaffolds. The 128 sequence fragments RACA assembled were compared to the fox meiotic linkage map to guide the construction of 40 chromosomal fragments. This computational approach to assembly was facilitated by prior research in comparative mammalian genomics, and the continued improvement of the red fox genome can in turn offer insight into canid and carnivore chromosome evolution. This assembly is also necessary for advancing genetic research in foxes and other canids.

Item Type: Article
DOI/Identification number: 10.3390/genes9060308
Uncontrolled keywords: Vulpes vulpes; comparative genomics; chromosome assembly; 10K Genomes Project; evolutionary breakpoints; Carnivora; Canidae; chromosome evolution; genome assembly
Divisions: Faculties > Sciences > School of Biosciences
Depositing User: M. Farre-Belmonte
Date Deposited: 12 Nov 2018 14:03 UTC
Last Modified: 30 May 2019 08:18 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/70042 (The current URI for this page, for reference purposes)
Farré, Marta: https://orcid.org/0000-0001-9170-5767
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