title: Genome analysis of the domestic dog (Korean Jindo) by massively parallel sequencing.
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.
authors.affiliation: Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.
authors.forename: Ryong Nam
authors.initials: RN
authors.lastname: Kim
authors.forename: Dae-Soo
authors.initials: DS
authors.lastname: Kim
authors.forename: Sang-Haeng
authors.initials: SH
authors.lastname: Choi
authors.forename: Byoung-Ha
authors.initials: BH
authors.lastname: Yoon
authors.forename: Aram
authors.initials: A
authors.lastname: Kang
authors.forename: Seong-Hyeuk
authors.initials: SH
authors.lastname: Nam
authors.forename: Dong-Wook
authors.initials: DW
authors.lastname: Kim
authors.forename: Jong-Joo
authors.initials: JJ
authors.lastname: Kim
authors.forename: Ji-Hong
authors.initials: JH
authors.lastname: Ha
authors.forename: Atsushi
authors.initials: A
authors.lastname: Toyoda
authors.forename: Asao
authors.initials: A
authors.lastname: Fujiyama
authors.forename: Aeri
authors.initials: A
authors.lastname: Kim
authors.forename: Min-Young
authors.initials: MY
authors.lastname: Kim
authors.forename: Kun-Hyang
authors.initials: KH
authors.lastname: Park
authors.forename: Kang Seon
authors.initials: KS
authors.lastname: Lee
authors.forename: Hong-Seog
authors.initials: HS
authors.lastname: Park
mesh_terms: D000818:Animals; D004272:DNA, Mitochondrial / Q000235:genetics*; D004283:Dog Diseases / Q000235:genetics; D004285:Dogs / Q000235:genetics*; D054629:Genome, Mitochondrial / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D054643:INDEL Mutation / Q000235:genetics; D058977:Molecular Sequence Annotation / Q000379:methods; D009687:Nuclear Proteins / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D056910:Republic of Korea; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004272:DNA, Mitochondrial; D009687:Nuclear Proteins