Genome analysis of the domestic dog (Korean Jindo) by massively parallel sequencing

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Title
Genome analysis of the domestic dog (Korean Jindo) by massively parallel sequencing
Author(s)
Ryong Nam Kim; Dae Soo Kim; Sang-Haeng Choi; Byoungha Yoon; Aram Kang; Seong-Hyeuk Nam; Dong-Wook Kim; J J Kim; J H Ha; A Toyoda; A Fujiyama; Aeri Kim; Min-Young Kim; Kun Hyang Park; Kang-Seon Lee; Hong-Seog Park
Bibliographic Citation
DNA Research, vol. 19, no. 3, pp. 275-287
Publication Year
2012
Abstract
Although pioneering sequencing projects have shed light on the boxer and poodle genomes, a number of challenges need to be met before the sequencing and annotation of the dog genome can be considered complete. Here, we present the DNA sequence of the Jindo dog genome, sequenced to 45-fold average coverage using Illumina massively parallel sequencing technology. A comparison of the sequence to the reference boxer genome led to the identification of 4 675 437 single nucleotide polymorphisms (SNPs, including 3 346 058 novel SNPs), 71 642 indels and 8131 structural variations. Of these, 339 non-synonymous SNPs and 3 indels are located within coding sequences (CDS). In particular, 3 non-synonymous SNPs and a 26-bp deletion occur in the TCOF1 locus, implying that the difference observed in cranial facial morphology between Jindo and boxer dogs might be influenced by those variations. Through the annotation of the Jindo olfactory receptor gene family, we found 2 unique olfactory receptor genes and 236 olfactory receptor genes harbouring non-synonymous homozygous SNPs that are likely to affect smelling capability. In addition, we determined the DNA sequence of the Jindo dog mitochondrial genome and identified Jindo dog-specific mtDNA genotypes. This Jindo genome data upgrade our understanding of dog genomic architecture and will be a very valuable resource for investigating not only dog genetics and genomics but also human and dog disease genetics and comparative genomics.
Keyword
genome sequencingJindo dogmassively parallel sequencing
ISSN
1340-2838
Publisher
Oxford Univ Press
DOI
http://dx.doi.org/10.1093/dnares/dss011
Type
Article
Appears in Collections:
Division of Bio Technology Innovation > Core Research Facility & Analysis Center > 1. Journal Articles
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