Ontology highlight
ABSTRACT:
PROVIDER: PRJEB35221 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| YakSanger.vcf.gz | Vcf | |||
| YakSanger.vcf.gz.tbi | Vcf | |||
| YakWGS.vcf.gz | Vcf | |||
| YakWGS.vcf.gz.tbi | Vcf | |||
| YakMALDI.vcf.gz | Vcf |
Items per page: 5 1 - 5 of 6 |
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Project description:Deciphering the genetics of orange coat color in domestic cats
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Project description:we compared the skin transcriptomes of the black- and white-coated region from the Boer and Macheng Black crossbred goat with black head and white body using the Illumina RNA-Seq method. Six cDNA libraries derived from skin samples of the white coat region (n = 3) and black coat region (n = 3) were constructed from three full-sib goats. On average, we obtained approximately 76.5 and 73.5 million reads for each skin sample of black coat and white coat, respectively, of which 75.39% and 76.05% reads were covered in the genome database. Our study provides insight into the transcriptional regulation of two distinct coat color that might serve as a key resource for understanding coat color pigmentation of goat.
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Project description:We apply developmental and single cell gene expression analysis to fetal skin of domestic cats, together with genetic characterization of Mendelian color variation, to identify when, where, and how, during fetal development, felid color patterns are established. Prior to the appearance of hair follicle placodes, we identify changes in epidermal thickness that represent a signature of color pattern establishment, and that are preceded by a pre-pattern of gene expression in which the secreted Wnt inhibitor encoded by Dickkopf 4 (Dkk4) plays a central role. We also demonstrate that mutations in Dkk4 underlie the Ticked pattern mutation in cats. Our results bring molecular understanding to how the leopard got its spots, suggest that similar mechanisms underlie periodic color pattern and periodic hair follicle spacing, and provide a genomic framework to explore natural selection for diverse pattern types in wild felids.
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Project description:The Sex-linked orange mutation in domestic cats causes variegated patches of reddish/yellow hair and is a defining signature of random X-inactivation in female tortoiseshell and calico cats. Unlike the situation for most coat color genes, there is no apparent homolog for Sex-linked orange in other mammals. We show that Sex-linked orange is caused by a 5 kb deletion that leads to ectopic and melanocyte-specific expression of the Rho GTPase Activating Protein 36 (Arhgap36) gene. Single cell RNA-seq studies from fetal cat skin reveal that red/yellow hair color is caused by reduced expression of melanogenic genes that are normally activated by the Melanocortin 1 receptor (Mc1r)—cyclic adenosine monophosphate (cAMP)—protein kinase A (PKA) pathway, but Mc1r and its ability to stimulate cAMP accumulation is intact. Instead, we show that expression of Arhgap36 in melanocytes leads to reduced levels of the PKA catalytic subunit (PKAC); thus, Sex-linked orange is genetically and biochemically downstream of Mc1r. Our findings resolve a longstanding comparative genetic puzzle, provide in vivo evidence for the ability of Arhgap36 to inhibit PKA, and reveal a molecular explanation for a charismatic color pattern with a rich genetic history.
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Project description:The Sex-linked orange mutation in domestic cats causes variegated patches of reddish/yellow hair and is a defining signature of random X-inactivation in female tortoiseshell and calico cats. Unlike the situation for most coat color genes, there is no apparent homolog for Sex-linked orange in other mammals. We show that Sex-linked orange is caused by a 5 kb deletion that leads to ectopic and melanocyte-specific expression of the Rho GTPase Activating Protein 36 (Arhgap36) gene. Single cell RNA-seq studies from fetal cat skin reveal that red/yellow hair color is caused by reduced expression of melanogenic genes that are normally activated by the Melanocortin 1 receptor (Mc1r)—cyclic adenosine monophosphate (cAMP)—protein kinase A (PKA) pathway, but Mc1r and its ability to stimulate cAMP accumulation is intact. Instead, we show that expression of Arhgap36 in melanocytes leads to reduced levels of the PKA catalytic subunit (PKAC); thus, Sex-linked orange is genetically and biochemically downstream of Mc1r. Our findings resolve a longstanding comparative genetic puzzle, provide in vivo evidence for the ability of Arhgap36 to inhibit PKA, and reveal a molecular explanation for a charismatic color pattern with a rich genetic history.
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Project description:Molecular and genetic characterization of sex-linked orange coat color in the domestic cat [C4F1]
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Project description:Molecular and genetic characterization of sex-linked orange coat color in the domestic cat [C96]
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Project description:Seed coat color in soybean (Glycine max) is determined by the accumulation of flavonoid-derived pigments. However, to date the molecular mechanisms driving natural variation remain poorly defined. This study integrated data from RNA sequencing (RNA-seq) with metabolite profiling via high-performance liquid chromatography (HPLC) to investigate genetic and metabolic differences between black and yellow seed coat soybean lines that share an identical genetic background. Transcriptomic analysis revealed that key anthocyanin biosynthesis genes, including flavanone 3-hydroxylase (F3H-3), anthocyanidin synthase (ANS), UDP-glucose:flavonoid 3-O-glucosyltransferase (UF3GT), UDP-glycosyltransferase (UGT79B6), and glutathione S-transferase (GSTF11), were more highly expressed in black seed coats, where we also observed increased anthocyanin and proanthocyanidin (PA) accumulation and antioxidant activity. In contrast, leucoanthocyanidin reductase (LAR) was strongly expressed in yellow seed coats but did not correspond to PA levels, likely due to the specific expression of laccase (LAC5) in black seeds, which facilitates PA polymerization. Elevated expression of cytochrome P450 enzymes (i.e., CYP73A5, cinnamate 4-hydroxylase; CYP82C4) in yellow seed coats suggested activation of the isoflavone biosynthesis pathway. Further transcriptional profiling also indicated that black-seed-specific MYB transcription factors (i.e., MYB111, MYB113, and MYB17) promoted anthocyanin production. This study is the first to provide evidence that small heat shock proteins (sHSPs) are implicated in the regulation of seed coat pigmentation and stress adaptation. Together, these findings elucidate the genetic and metabolic regulation of seed coat color in soybean and identify candidate genes relevant to functional breeding and genomics research.
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