Abstract
Rapid and cost effective production of large-scale genome data through next-generation sequencing has enabled population-level studies of various organisms to identify their genotypic differences and phenotypic consequences. This is also used to study indigenous animals with historical and economical values, although they are less studied than model organisms. The objective of this study was to perform functional and evolutionary analysis of Korean bob-tailed native dog Donggyeong with distinct tail and agility phenotype using whole-genome sequencing data by using population and comparative genomics approaches. Based on the uniqueness of non-synonymous single nucleotide polymorphisms obtained from next-generation sequencing data, Donggyeong dog-specific genes/proteins and their functions were identified by comparison with 12 other dog breeds and six other related species. These proteins were further divided into subpopulation-specific ones with different tail length and protein interaction-level signatures were investigated. Finally, the trajectory of shaping protein interactions of subpopulation-specific proteins during evolution was uncovered. This study expands our knowledge of Korean native dogs. Our results also provide a good example of using whole-genome sequencing data for population-level analysis in closely related species.
Highlights
Rapid advances in next-generation sequencing technologies has enabled the analysis of animal populations at the DNA sequence level[1]
Genomic features of three different Donggyeong dog populations based on tail length were determined and the evolution of protein interactions compared to related dog breeds and related species was analyzed
Using sequencing data generated from multiple individuals of selected dog breeds and related species, single nucleotide polymorphisms (SNPs) were identified and Donggyeong dog-specific genes were obtained based on the existence of unique non-synonymous SNPs only present in the population of Donggyeong dog
Summary
Rapid advances in next-generation sequencing technologies has enabled the analysis of animal populations at the DNA sequence level[1]. Genomic features of three different Donggyeong dog populations based on tail length (long, short, and non-tail) were determined and the evolution of protein interactions compared to related dog breeds (a total of 12 breeds) and related species (a total of 10 species) was analyzed. Using sequencing data generated from multiple individuals of selected dog breeds and related species, single nucleotide polymorphisms (SNPs) were identified and Donggyeong dog-specific genes were obtained based on the existence of unique non-synonymous SNPs only present in the population of Donggyeong dog. Functional and variant analyses were performed for Donggyeong dog-specific genes These Donggyeong dog-specific genes were further classified by considering the uniqueness of non-synonymous SNPs separately in different Donggyeong dog populations with different tail lengths. Our results provide a good example of using whole-genome sequencing data for population-level analysis in closely related species
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