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Volume 9
Issue 6
10.3390/genes9060308
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Article

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

by
Halie M. Rando
1,2,
Marta Farré
3,
Michael P. Robson
4,
Naomi B. Won
2,
Jennifer L. Johnson
2,
Ronak Buch
4,
Estelle R. Bastounes
2,
Xueyan Xiang
5,
Shaohong Feng
5,
Shiping Liu
5,
Zijun Xiong
5,
Jaebum Kim
6,
Guojie Zhang
5,7,8,
Lyudmila N. Trut
9,
Denis M. Larkin
3 and
Anna V. Kukekova
2,*
1
Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
2
Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
3
Department of Comparative Biomedical Science, Royal Veterinary College, London NW1 0TU, UK
4
Department of Computer Science, College of Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
5
China National Genebank, BGI -Shenzhen, Shenzhen 518083, Guangdong, China
6
Department of Stem Cell and Regenerative Biology, Konkuk University, Seoul 05029, Korea
7
Section for Ecology and Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark
8
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
9
Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia
*
Author to whom correspondence should be addressed.
Genes 2018, 9(6), 308; https://doi.org/10.3390/genes9060308
Received: 17 March 2018 / Revised: 19 May 2018 / Accepted: 4 June 2018 / Published: 20 June 2018
(This article belongs to the Section Animal Genetics and Genomics)
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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.
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Keywords: Vulpes vulpes; comparative genomics; chromosome assembly; 10K Genomes Project; evolutionary breakpoints; Carnivora; Canidae; chromosome evolution; genome assembly Vulpes vulpes; comparative genomics; chromosome assembly; 10K Genomes Project; evolutionary breakpoints; Carnivora; Canidae; chromosome evolution; genome assembly
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MDPI and ACS Style

Rando, H.M.; Farré, M.; Robson, M.P.; Won, N.B.; Johnson, J.L.; Buch, R.; Bastounes, E.R.; Xiang, X.; Feng, S.; Liu, S.; Xiong, Z.; Kim, J.; Zhang, G.; Trut, L.N.; Larkin, D.M.; Kukekova, A.V. Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly. Genes 2018, 9, 308. https://doi.org/10.3390/genes9060308

AMA Style

Rando HM, Farré M, Robson MP, Won NB, Johnson JL, Buch R, Bastounes ER, Xiang X, Feng S, Liu S, Xiong Z, Kim J, Zhang G, Trut LN, Larkin DM, Kukekova AV. Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly. Genes. 2018; 9(6):308. https://doi.org/10.3390/genes9060308

Chicago/Turabian Style

Rando, Halie M., Marta Farré, Michael P. Robson, Naomi B. Won, Jennifer L. Johnson, Ronak Buch, Estelle R. Bastounes, Xueyan Xiang, Shaohong Feng, Shiping Liu, Zijun Xiong, Jaebum Kim, Guojie Zhang, Lyudmila N. Trut, Denis M. Larkin, and Anna V. Kukekova. 2018. "Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly" Genes 9, no. 6: 308. https://doi.org/10.3390/genes9060308

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