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Identification and characterization of potato anthocyanin synthesis and regulatory genes based on comparative transcriptome [mRNA-seq]

ABSTRACT: Identification and characterization of potato anthocyanin synthesis and regulatory genes based on comparative transcriptome [mRNA-seq]

PROVIDER: PRJNA781498 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16975054_1.fastq.gz	Fastqsanger.gz
	SRR16975054_2.fastq.gz	Fastqsanger.gz
	SRR16975055_1.fastq.gz	Fastqsanger.gz
	SRR16975055_2.fastq.gz	Fastqsanger.gz
	SRR16975056_1.fastq.gz	Fastqsanger.gz

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Identification and characterization of potato anthocyanin synthesis and regulatory genes based on comparative transcriptome [mRNA-seq]

Project description:The anthocyanin glycosides in potato tubers not only provide the plant with bright color and high nutritional value, but also have pharmacological effects such as antioxidant, hypotensive, lipid-lowering and immunity-boosting. However, the regulatory mechanism of anthocyanin in potato tubers is still unclear. In this study, the content of anthocyanin was measured in four potato varieties (B, R, Y and W) and genes regulating anthocyanin synthesis in different potato varieties were identified by comparing transcriptomic approaches. The results showed that 82.6G of filtered data were obtained in 12 sequencing libraries, of which 82.23-87.66% of clean fragments were covered to the reference genome. In total, 42,793 genes were found in the twelve libraries of which 3765 were new genes. Finally, 3638 (B), 4295 (R) and 3594 (Y) DEGs were obtained in the three groups by the strict threshold screening (FDR<0.05 and |log2FC|>1), respectively. GO analysis showed that DEGs were mainly enriched in entries such as cell (GO:0005623), metabolic process (GO:0008152), catalytic activity (GO:0003824), etc. KEGG analysis revealed that metabolic pathways (ko01100), phenylalanine metabolism (ko00360), photosynthesis (ko00195) were significantly enriched. In addition, some genes related to anthocyanin synthesis (e.g. CHS, bHLH and MYB) were highly induced or repressed in different varieties. In conclusion, the results of this study provide insight into the genes regulating anthocyanin formation in potato and provide a scientific reference for breeding better quality potato varieties.

2021-11-20 | GSE189082 | GEO

Identification and characterization of potato anthocyanin synthesis and regulatory miRNA based on comparative transcriptome [miRNA-seq]

Project description:The anthocyanin glycosides in potato tubers not only provide the plant with bright color and high nutritional value, but also have pharmacological effects such as antioxidant, hypotensive, lipid-lowering and immunity-boosting. However, the regulatory mechanism of anthocyanin in potato tubers is still unclear. In this study, twelve miRNA libraries, three of which are from the Red beauty (R-1, R-2 and R-3), three of which are from the Black kingkong (B-1, B-2 and B-3), three of which are from the Longshu No.7 (Y-1, Y-2 and Y-3) and three of which are from the LK77 (W-1, W-2 and W-3), were constructed and analyzed by high-throughput sequencing. A total of 167.3 M of clean reads were obtained. After the raw reads were subjected to quality control and filtering, 151,010,820 clean tags were obtained from the twelve libraries. The filtered reads were subsequently compared with the updated potato reference genome, and the vast majority of effective reads were successfully mapped. The mapped reads from the twelve libraries covered 77.10-84.48% of the potato genome, therefore, the analysis based on the genome was considered reliable. The lengths of the obtained miRNAs were further analysed to find that 64% of the miRNAs were concentrated at 21bp in length, followed by a higher number of miRNAs at 22bp and 24bp in length.

2021-11-20 | GSE189081 | GEO

Identification and characterization of potato anthocyanin synthesis and regulatory miRNA based on comparative transcriptome

Project description:Identification and characterization of potato anthocyanin synthesis and regulatory miRNA based on comparative transcriptome

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Identification and characterization of potato anthocyanin synthesis and regulatory miRNA based on comparative transcriptome [miRNA-seq]

Project description:Identification and characterization of potato anthocyanin synthesis and regulatory miRNA based on comparative transcriptome [miRNA-seq]

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Identification and characterization of potato anthocyanin synthesis and regulatory miRNA based on comparative transcriptome

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-11-20 | GSE189083 | GEO

The function of the GIGANTEA gene StGI.04 in potato: Uncovering a new function affecting the anthocyanin content of tuber skin

Project description:GIGANTEA (GI) is a plant-specific, circadian clock-regulated, nuclear protein with pleiotropic functions studied in many plant species. It is involved in flowering, circadian clock control, chloroplast biogenesis, carbohydrate metabolism, stress responses and synthesis of volatiles. In potato (Solanum tuberosum L.), however, only its role in tuber initiation is reported. Based on the findings in other plant species we hypothesized that the function of GI is not restricted to tuberization in potato. To test this hypothesis we repressed the expression of a GI gene, StGI.04 in the commercial potato cultivar ‘Désirée’ and investigated the effect of repression at morphological and transcriptome level. We found that, like GI in other plant species, StGI.04 influences the expression of the key genes of circadian clock, flowering, starch synthesis and stress responses. Furthermore, we detected a novel function of a GI gene in influencing the anthocyanin synthesis and skin colour of potato tubers.

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Project description:We report the application of high-throughput analysis of genes related to anthocyanin synthesis in red and green walnuts based on transcriptome sequencing technology. By obtaining a sequence of more than 3 billion bases from mRNA, we found genes that are differentially expressed with anthocyanin synthesis in 4 leaf growth stages and 3 peel growth stages of red and green walnuts.

2021-01-05 | GSE162007 | GEO

Identification and characterization of potato long noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection [Time-course RNAseq]

Project description:Long noncoding RNAs (lncRNAs) represent a class of RNA molecules that are implicated in regulation of gene expression, both in mammals and plants. While much progress has been made in determining the biological functions of lncRNAs in mammals, the functional roles of lncRNAs in plants are still poorly understood. Specifically, the roles of lncRNAs in plant defense responses are yet to be fully explored. Here, we used strand-specific RNA sequencing to identify 1649 lncRNAs in potato (Solanum tuberosum) from stem tissues. The lncRNAs are expressed from all 12 potato chromosomes and generally smaller in size compared to protein-coding genes. Like in other plants, most potato lncRNAs (86%) are transcribed from intergenic regions and possess single exons. A time-course RNA-seq analysis between a tolerant and susceptible potato cultivar challenged with Pectobacterium carotovorum subsp. brasilience revealed that 227 of these lncRNAs could be associated with response to this pathogen. These results suggest that lncRNAs have potential functional roles in potato defense responses. This work provides the foundation for further functional studies in understanding potato defense mechanisms.

2016-12-31 | GSE74870 | GEO

Transcriptome analysis reveals candidate genes related to anthocyanin biosynthesis in different carrot genotypes and tissues

Project description:Taproots of different carrot genotypes were used to identify the candidate genes related to anthocyanin synthesis with particular focus on R2R3MYB, bHLH transcription factors, and glutathione S-transferase gene (GST). The RNA-sequencing analysis (RNA-Seq) showed that DcMYB6 and DcMYB7 had genotypic dependent expressed and they are likely involved in the regulation of anthocyanin biosynthesis. They were specifically upregulated in solid black taproots, including both black phloem and xylem. DcbHLH3 (LOC108204485) was upregulated in all black samples compared with the orange ones. We also found that GST1 (LOC108205254) might be an important anthocyanin transporter, and its upregulated expression resulted in the increasing of vacuolar anthocyanin accumulation in black samples.

2020-03-06 | GSE146419 | GEO

Identification and characterization of potato long noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection [Strand-specific RNA-seq]

2016-11-23 | GSE74869 | GEO