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 language | English (US) |
|---|---|
| Article number | 308 |
| Journal | Genes |
| Volume | 9 |
| Issue number | 6 |
| DOIs | |
| State | Published - Jun 20 2018 |
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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
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 journal › Article
}
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 -