Year: 2018
Type: article
Abstract: ) 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.
Source: Genes
DOI: 10.3390/genes9060308
Institutions: University of Illinois Urbana-Champaign, Royal Veterinary College, China National GeneBank, Konkuk University, University of Copenhagen, Kunming Institute of Zoology, Chinese Academy of Sciences, State Key Laboratory of Genetic Resources and Evolution, Russian Academy of Sciences, Institute of Cytology and Genetics
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,137
Funders: National Science Foundation, U.S. Department of Defense, U.S. Department of Agriculture, American Society for Engineering Education, Siberian Branch, Russian Academy of Sciences, Lundbeckfonden, National Institutes of Health, Directorate for Biological Sciences, University of Illinois at Urbana-Champaign, National Defense Science and Engineering Graduate, Biotechnology and Biological Sciences Research Council, Russian Academy of Sciences, National Institute of General Medical Sciences, Division of Graduate Education, Carl R. Woese Institute for Genomic Biology
Awards: G1304521853, G1329156139, G1533881399, G2032433601, G2142398248, IGERT: Vertically Integrated Training with Genomics, G3225219727, G421919480, G5043544052, Using reference-assisted chromosome assemblies to study chromosome structures and evolution in vertebrates, Molecular Mechanisms of Social Behavior, G7294443060, Genome assembly. chromosomal organization and comparative genomics of multiple bird species: beyond "catalogues of genes", G8761848363
OpenAlex ID: W2809214756