Journal Article

Genome Analysis of the Domestic Dog (Korean Jindo) by Massively Parallel Sequencing

Ryong Nam Kim, Dae-Soo Kim, Sang-Haeng Choi, Byoung-Ha Yoon, Aram Kang, Seong-Hyeuk Nam, Dong-Wook Kim, Jong-Joo Kim, Ji-Hong Ha, Atsushi Toyoda, Asao Fujiyama, Aeri Kim, Min-Young Kim, Kun-Hyang Park, Kang Seon Lee and Hong-Seog Park

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 19, issue 3, pages 275-288
Published in print June 2012 | ISSN: 1340-2838
Published online April 2012 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/dss011

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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.

Keywords: genome sequencing; Jindo dog; massively parallel sequencing

Journal Article.  5638 words.  Illustrated.

Subjects: Genetics and Genomics

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