Transcriptome analysis of adductor muscle with VPS29 RNAi in QN Orange scallops
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ABSTRACT:
PROVIDER: PRJNA576474 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10246889_1.fastq.gz | Fastqsanger.gz | |||
| SRR10246889_2.fastq.gz | Fastqsanger.gz | |||
| SRR10246890_1.fastq.gz | Fastqsanger.gz | |||
| SRR10246890_2.fastq.gz | Fastqsanger.gz | |||
| SRR10246891_1.fastq.gz | Fastqsanger.gz |
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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.
2019-10-09 | GSE138590 | GEO
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: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: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.
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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:Transcriptome analysis of adductor muscle color in Boihai Red Scallop
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Project description:miRNA analyses of genetic factors and the role of carotenoid accumulation in adductor muscles of QN Orange scallops
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2012-06-22 | E-GEOD-22505 | biostudies-arrayexpress
Project description:• To dissect how the genes are dynamically and differentially expressed during fruit development in sweet orange, a comprehensive transcriptomic study was performed in a pleiotropic mutant (MT) and its wild type (WT). • The detection of the fruit transcriptomic changes was conducted at five stages of fruit development by deep sequencing; the obtained millions of reliable tags were mapped on orange unigenes and subjected to cluster analysis and functional categorization. Sugar and organic acid contents were determined based on the prediction of differential biological processes. • The global clustering analysis revealed a total of 14 expression patterns for the genes involved in fruit development of sweet orange. More than 94% of the genes showed differential expression during fruit development. Comparative transcripts profiling between WT and MT revealed that between 410 and 634 genes were significantly differentially expressed at the five stages. Functional categorization indicated that TCA cycle, carotenoid biosynthesis, and pentose phosphate pathway (OPP) were among the most regulated pathways. • This study provided a dynamic-view of the transcriptome changes during fruit ripening in sweet orange; the results highlighted a set of molecular processes involved in the formation of the mutation trait in the orange fruits.
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