MiRNA analyses of genetic factors and the role of carotenoid accumulation in adductor muscles of QN Orange scallops
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PROVIDER: PRJNA1044795 | ENA |
REPOSITORIES: ENA
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Project description:QN Orange scallop was interspecific hybrids with orange adductor muscles. Previous studies shown the accumulation of carotenoids was present in QN Orange scallops. In this study, analysis of miRNA expression profiles was performed to explore possibly regulatory patterns in carotenoid accumulation in adductor muscles of QN Orange scallops. Based on small RNA sequencing, a total of 3289 miRNAs and 91 differential expression miRNAs were identified between white and orange adductor muscles, respectively. GO and KEGG enrichment analysis of target genes of DE miRNA enriched in the transmembrane transporter activity-related pathways, kinase activity-related pathways, signal transduction-related pathways, ABC transporters, Retinol metabolism, lipid related metabolism and calcium signaling pathway.
2024-11-10 | GSE248569 | GEO
Project description:QN Orange scallops is new strain with carotenoid deposition in orange adductor muscle, which provided suitable model for studying carotenoid accumulation. The present study was conducted to further understand the role of VPS29 in carotenoids deposition process via RNA interference (RNAi) of VPS29. Transcriptomic analysis revealed 534 differentially expressed genes (DEGs) between the groups without and with RNAi, among which were 288 upregulated and 246 were downregulated. Among these DGEs, genes related to carotenoids biosynthesis decrease in the expression of low-density lipoprotein receptor domain class (LDLR), cytochrome P450 (CYP 450), Niemann Pick C1-like 1 (NPC1L1) and ATP binding cassette transporter (ABC transporter) were identified. These results indicated that VPS29 played a vital role on carotenoids deposition by regulating other genes.
2019-10-09 | GSE138590 | GEO
Project description:In this study, a cross species hybridization (CSH) approach was used to evaluate whole transcriptome changes during carotenoid accumulation in the storage root of carrot (Daucus carota). Carotenoids are isoprenoid compounds providing red, yellow and orange color to plants. Previous gene expression analyses of carotenoid accumulation in non-model plant species have primarily used a candidate gene approach. Since global transcriptome analyses require extensive genome sequence, in the absence of these genomic resources an alternate approach uses platforms developed for model plant species. To assess transcriptome patterns associated with carotenoid pigmentation in carrot storage root, two carrot sibling inbred lines, B8788, true breeding for orange color and B8750, true breeding for white root color, were hybridized to the Medicago Affymetrix GeneChip microarray. Near isogenic recombinant inbred lines B8788 and B8750, derived from a cross between white rooted wild carrot (QAL) and orange-rooted B493 were used for comparative analyzes to minimize background genetic differences. B8788 is true breeding for orange color whereas B8750 is true breeding for white storage root color. Carrots were grown in three pots for each genotype under greenhouse conditions and carrots were selected arbitrarily from these pots for harvest. Roots were harvested at approximately 11 weeks post planting when carotenoid accumulation becomes apparent in the storage root. Storage root tissue from sixteen individual carrot roots was pooled into three one-gram tissue pools of four carrots for each genotype.
2014-08-13 | E-GEOD-49873 | biostudies-arrayexpress
Project description:In this study, a cross species hybridization (CSH) approach was used to evaluate whole transcriptome changes during carotenoid accumulation in the storage root of carrot (Daucus carota). Carotenoids are isoprenoid compounds providing red, yellow and orange color to plants. Previous gene expression analyses of carotenoid accumulation in non-model plant species have primarily used a candidate gene approach. Since global transcriptome analyses require extensive genome sequence, in the absence of these genomic resources an alternate approach uses platforms developed for model plant species. To assess transcriptome patterns associated with carotenoid pigmentation in carrot storage root, two carrot sibling inbred lines, B8788, true breeding for orange color and B8750, true breeding for white root color, were hybridized to the Medicago Affymetrix GeneChip microarray.
2014-08-13 | GSE49873 | GEO
Project description:Boihai Red is new strains of inter-specific hybridizing the bay scallop (Argopecten irradians irradians) with the Peruvian scallop (Argopecten purpuratus). Orange color variant of adductor muscle have been developed through successive selective breeding in this strain. In the present study,proteomic were conducted on orange and white adductor muscle tissues.Notably, 74 differentially expressed proteins (DEPs) were identified by lable free proteomics, including 36 up and 38 down regulated. In DEGs, apolipophorin, CYP450 and tyrosinase were expressed highly in orange adductor muscle tissues, which related to carotenoids or melanin. In DEPs, high expression of VPS and TIF in orange adductor muscle tissues indicated that proteins outside the carotenoid pathway might also affect carotenoid biosynthesis. In addition, RAB11A related to melanin was also expressed highly in orange adductor muscle tissues at protein level. It is probable that not only carotenoids, but also melanin act on orange color of adductor muscle. This study provides valuable genetic resources for understanding underlying mechanisms and pathways of adductor muscle color.
2019-11-12 | PXD011708 | Pride
Project description:Transcriptome analysis of adductor muscle with VPS29 RNAi in QN Orange scallops
| PRJNA576474 | ENA
Project description:We performed the first quantitative proteomics analysis of differences between striated (fast) and catch (slow) adductor muscle in Yesso scallop (Patinopecten yessoensis), with the goal to uncover muscle specific genes and proteins, as well as enzymes of metabolic pathways in fast and slow adductor muscle of scallops. The present findings highlight the functional roles of muscle contractile proteins, calcium signaling pathways, membrane and extracellular matrix proteins, and glycogen metabolism involved in the different contractile and metabolic properties between fast and slow muscles. The present findings will help better understand the molecular basis underlying muscle contraction and its physiological regulation in invertebrates.
2018-10-26 | PXD005166 | Pride
Project description:Expression data from citrus embryogenic calli with engineered carotenoid accumulation
| PRJNA261719 | ENA
Project description:Boihai Red is new strains of inter-specific hybridizing the bay scallop (Argopecten irradians irradians) with the Peruvian scallop (Argopecten purpuratus). Orange color variant of adductor muscle have been developed through successive selective breeding in this strain. In the present study, transcriptomic was conducted on orange and white adductor muscle tissues. Transcriptomic analysis showeds 416 differentially expressed genes (DEGs) were identified between white and orange adductor muscle tissues in Boihai Red Scallop, with 216 up regulated and 200 down. In DEGs, apolipophorin, CYP450 and tyrosinase were expressed highly in orange adductor muscle tissues, which related to carotenoids or melanin. It is probable that not only carotenoids, but also melanin act on orange color of adductor muscle. This study provides valuable genetic resources for understanding underlying mechanisms and pathways of adductor muscle color.
2019-04-15 | GSE122451 | GEO
Project description:Background: Anthocyanins are the most important compounds for nutritional quality and economic values of blood orange. However, there are few reports on the pre-harvest treatment accelerate the accumulation of anthocyanins in postharvest blood orange fruit. Here, we performed a comparative Transcriptome and metabolomics analysis to elucidate the underlying mechanism involved in seasonal drought (SD) treatment during fruit expansion stage on anthocyanin accumulation in postharvest ‘Tarocco’ blood orange fruit. Results: Our results showed that SD treatment slowed down the fruit enlargement and increased the sugar accumulation during fruit development and matured period. Obviously, under SD treatment, the accumulation of anthocyanin in blood orange fruit during postharvest storage was significantly accelerated and markedly higher than that in CK. Meanwhile, the total flavonoids and phenols contents and antioxidant activity in SD treatment fruit were also sensibly increased during postharvest storage. Based on metabolome, we found that substrates required for anthocyanin biosynthesis, such as amino acids and their derivatives, and phenolic acids, have significantly accumulated and higher in SD treated mature fruit compared with that of CK. Further according to the results of transcriptome data and weighted gene coexpression correlation network analysis (WGCNA) analysis, phenylalanine ammonia-lyase (PAL3) was considered key structural gene. qRT-PCR analysis verified that the PAL3 was highly expressed in SD treated postharvest stored fruit and was significantly positively correlated with the anthocyanin content. Moreover, we found that other structural genes in anthocyanin biosynthesis pathway were also upregulated under SD treatment through transcriptome data and qRT-PCR analysis. Conclusions: The findings suggest that SD treatment promotes the accumulation of substrates necessary for anthocyanin biosynthesis during fruit ripening process, and activates the expression of anthocyanin biosynthesis pathway genes during postharvest storage period, especially PAL3, co-contributed to the rapid accumulation of anthocyanin. The present study provides a theoretical basis for postharvest quality control and water-saving utilization of blood orange fruit.
2024-03-06 | GSE253283 | GEO