Ontology highlight
ABSTRACT:
PROVIDER: PRJNA726291 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:the current study paints a thorough transcriptome profiles of different skin color groups (white, yellow and brown) in celestial goldfish, and several candidate genes were selected as important functional genes involved in the color variation
2022-12-07 | GSE220201 | GEO
Project description:Many animals exhibit typical color patterns that have been linked to key adaptive functions, yet the developmental mechanisms establishing these crucial designs remain unclear. Here, we surveyed color distribution in the plumage across a large number of passerine finches. Despite extreme apparent pattern diversity, we identified a small set of conserved color regions whose combinatory association can explain all observed patterns. We found these domains are instructed by signals from embryonic somites and lateral plate mesoderm, and through profiling and comparative analyses, produced a molecular map marking putative color domains in the developing skin. This revealed cryptic pre-patterning common to differently colored species, uncovering a simple molecular landscape underlying extensive color pattern variation.
2024-01-18 | GSE165119 | GEO
Project description:As an important cold-water economic fish species, rainbow trout (Oncorhynchus mykiss) exhibits several intra-specific variation in skin pigmentation that can give rise to distinctive phenotypes, and wild-type rainbow trout with black skin (WR) and yellow mutant rainbow trout with yellow skin (YR) are the major two types in the farms, whose distinct skin colors make them suitable model for elucidating the skin pigmentation process. Skin color as a key indicator for selection in rainbow trout farming as well as has a strong visual impact on the consumer when rainbow trout are marketed. Previously, extensive studies have been conducted on skin color in rainbow trout, including the observation of skin spots and the expression analysis of some important pigment genes. However, up to date, no studies have systematically examined the molecular regulation mechanism of skin color difference between WR and YR through a high throughput method. Therefore, the aim of this study was to reveal the molecular regulation mechanism of skin color difference between these two strains at the mRNA and miRNA transcriptome level, and candidate genes, miRNAs and miRNA-mRNA pairs that may be responsible for rainbow trout albinism were obtained.
2021-04-12 | GSE171856 | GEO
Project description:As an important cold-water economic fish species, rainbow trout (Oncorhynchus mykiss) exhibits several intra-specific variation in skin pigmentation that can give rise to distinctive phenotypes, and wild-type rainbow trout with black skin (WR) and yellow mutant rainbow trout with yellow skin (YR) are the major two types in the farms, whose distinct skin colors make them suitable model for elucidating the skin pigmentation process. Skin color as a key indicator for selection in rainbow trout farming as well as has a strong visual impact on the consumer when rainbow trout are marketed. Previously, extensive studies have been conducted on skin color in rainbow trout, including the observation of skin spots and the expression analysis of some important pigment genes. However, up to date, no studies have systematically examined the molecular regulation mechanism of skin color difference between WR and YR through a high throughput method. Therefore, the aim of this study was to reveal the molecular regulation mechanism of skin color difference between these two strains at the mRNA and miRNA transcriptome level, and candidate genes, miRNAs and miRNA-mRNA pairs that may be responsible for rainbow trout albinism were obtained.
2022-04-21 | GSE172482 | GEO
Project description:Rainbow trout (Oncorhynchus mykiss) is a well-known economical fish globally, and its market value and acceptance are greatly influenced by skin color. However, the molecular mechanisms underlying skin color variation in rainbow trout remains largely unknown. In this study, we compared the expression profiles of whole transcriptome in dorsal skin from wild-type (WTrt) and yellow mutant rainbow trout (YMrt) that are F1 generation of WTrt ♂ × YMrt ♀. A total of 115 differentially expressed (DE) mRNAs, 126 lncRNAs, 18 circRNAs and 56 miRNAs were identified, and several core genes (gch1, pts, slc2all, pax7a/pax7b, dgat2, plin6 and pnpla2) involved in pteridine and carotenoid synthesis were significantly upregulated in YMrt. Interestingly, we found that melanogenesis-related genes tyr, dct, mitfa and pmel were also notably elevated in YMrt. Functional enrichment analysis revealed some pigmentation-related GO terms and KEGG pathways, including pteridine-containing compound biosynthetic process, pigment metabolic process, melanosome, melanosome transport, tyrosine metabolism and melanogenesis. Based on competing endogenous RNA analysis, there were 25 and 21 lncRNA-miRNA-mRNA networks targeted to gch1 and mitfa, such as LOC110496571-miR-96-x-gch1, LOC110508587- miR-182-x-gch1, LOC110494316-miR-21-y-mitfa and LOC110526055- miR-182-x-mitfa. Additionally, one (novel_circ_000056), eight (including novel_circ_005436 and novel_circ_005586) and three circRNAs (novel_circ_000382, novel_circ_002592 and novel_circ_005868) were found to regulate dgat2, gch1 and mitfa by targeting 21 miRNAs. This study provides a systematic perspective on the potential functions of these DEmRNAs and ncRNAs, and lays a foundation for further study on the molecular mechanisms governing rainbow trout skin color variation.
2023-12-27 | GSE251664 | GEO
Project description:<p><strong>BACKGROUND:</strong> Reptiles exhibit a wide variety of skin colors, which serve essential roles in survival and reproduction. However, the molecular basis of these conspicuous colors remains unresolved.</p><p><strong>RESULTS:</strong> We investigate color morph-enriched Asian vine snakes (<em>Ahaetulla prasina</em>), to explore the mechanism underpinning color variations. Transmission electron microscopy imaging and metabolomics analysis indicates that chromatophore morphology (mainly iridophores) is the main basis for differences in skin color. Additionally, we assemble a 1.77 Gb high-quality chromosome-anchored genome of the snake. Genome-wide association study and RNA sequencing reveal a conservative amino acid substitution (p.P20S) in <em>SMARCE1</em>, which may be involved in the regulation of chromatophore development initiated from neural crest cells. <em>SMARCE1</em> knockdown in zebrafish and immunofluorescence verify the interactions among <em>SMARCE1</em>, iridophores, and <em>tfec</em>, which may determine color variations in the Asian vine snake.</p><p><strong>CONCLUSIONS:</strong> This study reveals the genetic associations of color variation in Asian vine snakes, providing insights and important resources for a deeper understanding of the molecular and genetic mechanisms related to reptilian coloration.</p>
2023-02-23 | MTBLS6927 | MetaboLights
Project description:Skin color is highly variable in Africans, yet little is known about the underlying molecular mechanism. Here we applied massively parallel reporter assays to screen 1,157 candidate variants influencing skin pigmentation in Africans and identified 165 single-nucleotide polymorphisms showing differential regulatory activities between alleles. We combine Hi-C, genome editing and melanin assays to identify regulatory elements for MFSD12, HMG20B, OCA2, MITF, LEF1, TRPS1, BLOC1S6 and CYB561A3 that impact melanin levels in vitro and modulate human skin color. We found that independent mutations in an OCA2 enhancer contribute to the evolution of human skin color diversity and detect signals of local adaptation at enhancers of MITF, LEF1 and TRPS1, which may contribute to the light skin color of Khoesan-speaking populations from Southern Africa. Additionally, we identified CYB561A3 as a novel pigmentation regulator that impacts genes involved in oxidative phosphorylation and melanogenesis. These results provide insights into the mechanisms underlying human skin color diversity and adaptive evolution.
2023-08-11 | GSE240717 | GEO