Whole genome sequencing reveals the artificial selection and local environmental adaptability of pigeons ( Columba livia )

Abstract Objective Navigation is the most important feature of homing pigeons, however no integrated response to genetic mechanism of navigation has been reported. The generated data herein represent whole-genome resequencing data for homing pigeon and three other breeds of rock pigeons. Selective sweep analysis between homing pigeon and other breeds of rock pigeon can provide new insight about identification of candidate genes and biological pathways for homing pigeon ability. Data description Whole-genomes sequence data related to 95 birds from four breeds of rock pigeons including, 29 feral pigeons, 24 Shiraz tumblers, 24 Persian high flyers and 18 homing pigeons were provided. More than 6.94 billion short reads with coverage (average ≈7.50 x) and 407.1 Gb data were produced. Whole genome sequencing was carried out on the Illumina Hiseq 2000 platform using a 350 bp library size and 150 bp paired-end read lengths. The whole genome sequencing data have been submitted at the NCBI SRA Database (PRJNA532675). The presented data set can provide useful genomic information to explain the genetic mechanism of navigation ability of homing pigeons and also testing other genetic hypothesis by genomic analysis.

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Whole genome sequencing reveals the impact of recent artificial selection on red sea bream reared in fish farms

Scientific Reports ◽

10.1038/s41598-019-42988-z ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

Author(s):

Bo-Hye Nam ◽

DongAhn Yoo ◽

Young-Ok Kim ◽

Jung Youn Park ◽

Younhee Shin ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Red Sea ◽

Artificial Selection ◽

Sea Bream ◽

Whole Genome ◽

Red Sea Bream ◽

Fish Farms ◽

The Impact

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Darwin’s Fancy Revised: An Updated Understanding of the Genomic Constitution of Pigeon Breeds

Genome Biology and Evolution ◽

10.1093/gbe/evaa027 ◽

2020 ◽

Vol 12 (3) ◽

pp. 136-150

Author(s):

George Pacheco ◽

Hein van Grouw ◽

Michael D Shapiro ◽

Marcus Thomas P Gilbert ◽

Filipe Garrett Vieira

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Phenotypic Diversity ◽

Genotyping By Sequencing ◽

Columba Livia ◽

Whole Genome Sequencing Data ◽

Evolutionary Relationships ◽

Whole Genome ◽

Sequencing Data ◽

Domestic Species

Abstract Through its long history of artificial selection, the rock pigeon (Columba livia Gmelin 1789) was forged into a large number of domestic breeds. The incredible amount of phenotypic diversity exhibited in these breeds has long held the fascination of scholars, particularly those interested in biological inheritance and evolution. However, exploiting them as a model system is challenging, as unlike with many other domestic species, few reliable records exist about the origins of, and relationships between, each of the breeds. Therefore, in order to broaden our understanding of the complex evolutionary relationships among pigeon breeds, we generated genome-wide data by performing the genotyping-by-sequencing (GBS) method on close to 200 domestic individuals representing over 60 breeds. We analyzed these GBS data alongside previously published whole-genome sequencing data, and this combined analysis allowed us to conduct the most extensive phylogenetic analysis of the group, including two feral pigeons and one outgroup. We improve previous phylogenies, find considerable population structure across the different breeds, and identify unreported interbreed admixture events. Despite the reduced number of loci relative to whole-genome sequencing, we demonstrate that GBS data provide sufficient analytical power to investigate intertwined evolutionary relationships, such as those that are characteristic of animal domestic breeds. Thus, we argue that future studies should consider sequencing methods akin to the GBS approach as an optimal cost-effective approach for addressing complex phylogenies.

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Whole Genome Sequencing Reveals Signatures for Artificial Selection for Different Sizes in Japanese Primitive Dog Breeds

Frontiers in Genetics ◽

10.3389/fgene.2021.671686 ◽

2021 ◽

Vol 12 ◽

Author(s):

Guangqi Lyu ◽

Chunyu Feng ◽

Shiyu Zhu ◽

Shuang Ren ◽

Wanyi Dang ◽

...

Keyword(s):

Body Size ◽

Whole Genome Sequencing ◽

Candidate Genes ◽

Genome Sequencing ◽

Artificial Selection ◽

Companion Animals ◽

The Body ◽

Whole Genome ◽

Sliding Windows ◽

Selection For

Body size is an important trait in companion animals. Recently, a primitive Japanese dog breed, the Shiba Inu, has experienced artificial selection for smaller body size, resulting in the “Mame Shiba Inu” breed. To identify loci and genes that might explain the difference in the body size of these Shiba Inu dogs, we applied whole genome sequencing of pooled samples (pool-seq) on both Shiba Inu and Mame Shiba Inu. We identified a total of 13,618,261 unique SNPs in the genomes of these two breeds of dog. Using selective sweep approaches, including FST, Hp and XP-CLR with sliding windows, we identified a total of 12 genomic windows that show signatures of selection that overlap with nine genes (PRDM16, ZNF382, ZNF461, ERGIC2, ENSCAFG00000033351, CCDC61, ALDH3A2, ENSCAFG00000011141, and ENSCAFG00000018533). These results provide candidate genes and specific sites that might be associated with body size in dogs. Some of these genes are associated with body size in other mammals, but 8 of the 9 genes are novel candidate genes that need further study.

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