@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.}",
note = "Funding Information: We would like to thank Christopher Fields, Gloria Rendon, and Kathleen Keating from the High Performance Computing in Biology (HPCBio) group for consulting on the execution of the LASTZ alignments and chaining and netting on the Carl R. Woese Institute for Genomic Biology's BioCluster, and David Slater for troubleshooting and advice about BioCluster use. We would also like to thank Julie Lihosit and Qianwen Zhao for their work on the analysis, and Jonathan Beever and Sandra Rodriguez-Zas for their input. Funding for this research was provided by the National Institutes of Health R01 GM120782, Campus Research Board grant from the University of Illinois at Urbana-Champaign, the United States Department of Agriculture Federal Hatch Project (grant number 538922), the Biotechnology and Biological Sciences Research Council, BB/K008226/1 and BB/J010170/1, and the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences (grant number 0324-2018-0016). Halie M. Rando's work on the project was funded through a National Science Foundation (NSF) Integrative Graduate Education and Research Traineeship (IGERT) grant (NSF DGE IGERT-1069157) and by the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program Funding Information: Acknowledgments: We would like to thank Christopher Fields, Gloria Rendon, and Kathleen Keating from the High Performance Computing in Biology (HPCBio) group for consulting on the execution of the LASTZ alignments and chaining and netting on the Carl R. Woese Institute for Genomic Biology{\textquoteright}s BioCluster, and David Slater for troubleshooting and advice about BioCluster use. We would also like to thank Julie Lihosit and Qianwen Zhao for their work on the analysis, and Jonathan Beever and Sandra Rodriguez-Zas for their input. Funding for this research was provided by the National Institutes of Health R01 GM120782, Campus Research Board grant from the University of Illinois at Urbana-Champaign, the United States Department of Agriculture Federal Hatch Project (grant number 538922), the Biotechnology and Biological Sciences Research Council, BB/K008226/1 and BB/J010170/1, and the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences (grant number 0324-2018-0016). Halie M. Rando{\textquoteright}s work on the project was funded through a National Science Foundation (NSF) Integrative Graduate Education and Research Traineeship (IGERT) grant (NSF DGE IGERT-1069157) and by the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program.",
year = "2018",
month = jun,
day = "20",
doi = "10.3390/genes9060308",
language = "English (US)",
volume = "9",
journal = "Genes",
issn = "2073-4425",
publisher = "Multidisciplinary Digital Publishing Institute (MDPI)",
number = "6",
}