Variation of Comb Color is Caused by a Free Combination of Two CNVs Located on Chromosome 20 in Lueyang Black-Bone Chicken
This dataset provides comprehensive genomic and transcriptomic data on Lueyang black-bone chickens, focusing on the genetic variation of comb color, a trait influenced by hyperpigmentation (fibromelanosis). These data offer a combination of broad population-level sequencing and high-resolution genomic analysis to investigate the genetic underpinnings of pigmentation variation, specifically the novel structural variation (SV) that contributes to the fibromelanosis phenotype.1.Long Fragment Sequencing Data:This dataset includes long-read sequencing data from a single Lueyang black-bone chicken (sample: 3rdGen_Sample_FB1). The long-read sequencing provides high-quality, detailed information about genomic regions relevant to pigmentation and structural variations, including a novel 16 kb SV, located in the FM gene locus, that is associated with the fibromelanosis phenotype.2.Whole-Genome Sequencing (WGS) Data of F0 Generation:This includes whole-genome sequencing data from 235 individuals in the F0 generation (founder population) of Lueyang black-bone chickens. With an average clean data size of 8.69GB per sample, this dataset provides high-quality sequence data that enables the identification of genetic variations across the population. The sequencing depth provides a broad understanding of the general genetic landscape, allowing the identification of genetic factors contributing to comb color variation and hyperpigmentation.3.Lower Coverage Whole Genome Sequencing Data of F1 Generation:The F1 generation consists of 1374 samples with a lower average sequencing depth (1.4GB of clean data per sample). This dataset provides broader genetic information across the F1 population, enabling the identification of common genetic variations. It helps to explore how these variations, combined with structural variations such as the novel 16 kb SV, might influence comb color phenotypes and fibromelanosis.4.Transcriptome Data:This dataset includes transcriptome sequencing (RNA-Seq) data for 16 individual chickens (32 samples in total, covering both comb and dorsal skin tissues). The average clean data per sample is 6.87GB. These transcriptomic data are crucial for exploring gene expression patterns related to pigmentation and melanogenesis, particularly genes like GPNMB, MLANA, SLC24A5, TYR, and DCT. These genes are potential key regulators of comb color variation and are linked to melanocyte content in the comb.5.Whole-Genome Sequencing (WGS) Data of 16 Individual Chickens:This dataset includes high-depth whole-genome sequencing data from 16 individual chickens, each with different comb color types, with an average clean data size of 10.17GB per sample. The sequencing depth (7.4x) provides higher resolution for analyzing specific genomic regions, particularly those related to pigmentation variation and gene expression. This dataset aids in understanding how different combinations of structural variations, including the novel SV, influence melanocyte content and melanin deposition levels, which are critical factors in comb color variation.Together, these datasets provide a comprehensive resource for studying the genetic mechanisms underlying comb color variation and fibromelanosis in Lueyang black-bone chickens. By integrating low-coverage whole-genome sequencing (lcWGS) with whole-genome sequencing (WGS), we are able to identify both common and novel structural variations, shedding light on the role of SVs in pigmentation and providing new insights for the breeding and study of hyperpigmentation in chickens.