Construction of red fox chromosomal fragments from the short-read genome assembly

Halie M. Rando, 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, Anna V Kukekova

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number308
JournalGenes
Volume9
Issue number6
DOIs
StatePublished - Jun 20 2018

Fingerprint

Genome
Chromosomes
Dogs
Genetic Research
Genomics
Cats
Research
Genes

Keywords

  • 10K Genomes Project
  • Canidae
  • Carnivora
  • Chromosome assembly
  • Chromosome evolution
  • Comparative genomics
  • Evolutionary breakpoints
  • Genome assembly
  • Vulpes vulpes

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Rando, H. M., Farré, M., Robson, M. P., Won, N. B., Johnson, J. L., Buch, R., ... Kukekova, A. V. (2018). Construction of red fox chromosomal fragments from the short-read genome assembly. Genes, 9(6), [308]. https://doi.org/10.3390/genes9060308

Construction of red fox chromosomal fragments from the short-read genome assembly. / Rando, Halie M.; Farré, Marta; Robson, Michael P.; Won, Naomi B.; Johnson, Jennifer L.; Buch, Ronak; Bastounes, Estelle R.; Xiang, Xueyan; Feng, Shaohong; Liu, Shiping; Xiong, Zijun; Kim, Jaebum; Zhang, Guojie; Trut, Lyudmila N.; Larkin, Denis M.; Kukekova, Anna V.

In: Genes, Vol. 9, No. 6, 308, 20.06.2018.

Research output: Contribution to journalArticle

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 2018, 'Construction of red fox chromosomal fragments from the short-read genome assembly', Genes, vol. 9, no. 6, 308. https://doi.org/10.3390/genes9060308
Rando HM, Farré M, Robson MP, Won NB, Johnson JL, Buch R et al. Construction of red fox chromosomal fragments from the short-read genome assembly. Genes. 2018 Jun 20;9(6). 308. https://doi.org/10.3390/genes9060308
Rando, Halie M. ; Farré, Marta ; Robson, Michael P. ; Won, Naomi B. ; Johnson, Jennifer L. ; Buch, Ronak ; Bastounes, Estelle R. ; Xiang, Xueyan ; Feng, Shaohong ; Liu, Shiping ; Xiong, Zijun ; Kim, Jaebum ; Zhang, Guojie ; Trut, Lyudmila N. ; Larkin, Denis M. ; Kukekova, Anna V. / Construction of red fox chromosomal fragments from the short-read genome assembly. In: Genes. 2018 ; Vol. 9, No. 6.
@article{109b128324da4b48b56efd9ff2c78390,
title = "Construction of red fox chromosomal fragments from the short-read genome assembly",
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.",
keywords = "10K Genomes Project, Canidae, Carnivora, Chromosome assembly, Chromosome evolution, Comparative genomics, Evolutionary breakpoints, Genome assembly, Vulpes vulpes",
author = "Rando, {Halie M.} and Marta Farr{\'e} and Robson, {Michael P.} and Won, {Naomi B.} and Johnson, {Jennifer L.} and Ronak Buch and Bastounes, {Estelle R.} and Xueyan Xiang and Shaohong Feng and Shiping Liu and Zijun Xiong and Jaebum Kim and Guojie Zhang and Trut, {Lyudmila N.} and Larkin, {Denis M.} and Kukekova, {Anna V}",
year = "2018",
month = "6",
day = "20",
doi = "10.3390/genes9060308",
language = "English (US)",
volume = "9",
journal = "Genes",
issn = "2073-4425",
publisher = "Multidisciplinary Digital Publishing Institute (MDPI)",
number = "6",

}

TY - JOUR

T1 - Construction of red fox chromosomal fragments from the short-read genome assembly

AU - Rando, Halie M.

AU - Farré, Marta

AU - Robson, Michael P.

AU - Won, Naomi B.

AU - Johnson, Jennifer L.

AU - Buch, Ronak

AU - Bastounes, Estelle R.

AU - Xiang, Xueyan

AU - Feng, Shaohong

AU - Liu, Shiping

AU - Xiong, Zijun

AU - Kim, Jaebum

AU - Zhang, Guojie

AU - Trut, Lyudmila N.

AU - Larkin, Denis M.

AU - Kukekova, Anna V

PY - 2018/6/20

Y1 - 2018/6/20

N2 - 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.

AB - 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.

KW - 10K Genomes Project

KW - Canidae

KW - Carnivora

KW - Chromosome assembly

KW - Chromosome evolution

KW - Comparative genomics

KW - Evolutionary breakpoints

KW - Genome assembly

KW - Vulpes vulpes

UR - http://www.scopus.com/inward/record.url?scp=85048827706&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85048827706&partnerID=8YFLogxK

U2 - 10.3390/genes9060308

DO - 10.3390/genes9060308

M3 - Article

AN - SCOPUS:85048827706

VL - 9

JO - Genes

JF - Genes

SN - 2073-4425

IS - 6

M1 - 308

ER -