MiRNA analyses of genetic factors and the role of carotenoid accumulation in adductor muscles of QN Orange scallops
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ABSTRACT:
PROVIDER: PRJNA1044795 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26942074.fastq.gz | Fastqsanger.gz | |||
| SRR26942075.fastq.gz | Fastqsanger.gz | |||
| SRR26942076.fastq.gz | Fastqsanger.gz | |||
| SRR26942077.fastq.gz | Fastqsanger.gz | |||
| SRR26942078.fastq.gz | Fastqsanger.gz |
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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.
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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.
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Project description:Transcriptome analysis of adductor muscle with VPS29 RNAi in QN Orange scallops
| PRJNA576474 | ENA
Project description:BackgroundQN Orange scallops are interspecific hybrids with orange adductor muscles that are rich in carotenoids. In this study, analysis of miRNA expression profiles was performed to explore possible regulatory patterns involved in carotenoid accumulation in adductor muscles of QN Orange scallops.ResultsA total of 91 differentially expressed miRNA between the white and orange adductor muscles were identified. GO and KEGG analysis of target genes of differentially expressed miRNAs revealed enrichments in the transmembrane transporter activity-related pathways, kinase activity-related pathways, signal transduction-related pathways, ATP binding cassette transporters (ABC transporters), retinol metabolism, lipid-related metabolism, and calcium signaling pathway. In particular, miRNA Contig1462_36180, which was shown to negatively regulate the activity of methyltransferase 3 (METTL3) by dual-luciferase reporter assay, may play a pivotal role in the accumulation of carotenoids. Furthermore, METTL3 interference seemed to reduce the pectenoxanthin content and m6A level.ConclusionIt is thus speculated that Contig1462_36180 may regulate m6A methylation by regulating METTL3, which in turn affects pectenoxanthin accumulation in QN Orange scallops.
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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.
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Project description:Carotenoids have been demonstrated to be indispensable plant secondary metabolites that are involved in photosynthesis, antioxidation, and phytohormone biosynthesis. Carotenoids are likely involved in other biological functions that have yet to be discovered. In this study, we utilized genomic expression investigation to gain a deep insight into the carotenoid-related biological processes in the citrus calli overexpressing CrtB.
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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: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.
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