Functional and evolutionary analysis of Korean bob-tailed native dog using whole-genome sequencing data

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.

Why do dogs wag their tails?

“…How much of that variation can be explained by genetics? -use whole-genome sequencing data and comparative genomics to investigate whether tail wagging is a genetically linked trait; a logical starting point would be to build on genomic research that has already been conducted on dog tail length [104] and shape [105]. -systematically quantify dog tail wagging parameters when dogs are exposed to social and non-social stimuli and situations (e.g.…”

“…genetics: how much inter-individual phenotypic variation is there in tail wagging? How much of that variation can be explained by genetics?—use whole-genome sequencing data and comparative genomics to investigate whether tail wagging is a genetically linked trait; a logical starting point would be to build on genomic research that has already been conducted on dog tail length [104] and shape [105]. ontogenydevelopment: does tail wagging behaviour in the same individual change from puppyhood to adulthood?…”

PAPipe: A Pipeline for Comprehensive Population Genetic Analysis

“…Because population genetics is based on genetic similarities and differences within and between populations, population genetic analyses generally begin by examining population genetic variant data ( Li et al 2009 ; Van der Auwera et al 2013 ), which represent fundamental inputs in various downstream analyses, such as phylogenetic tree inference, principal component analysis (PCA), and population structure analysis. In many studies, different types of population genetic analyses have been combined in attempts to comprehensively understand the target populations and draw meaningful conclusions ( Baumsteiger et al 2017 ; Lee et al 2017 , 2020a ).…”