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

ABSTRACT: 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.

ORGANISM(S): Solanum tuberosum

PROVIDER: GSE189081 | GEO | 2021/11/20

REPOSITORIES: GEO

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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

Genome-Wide Identification of microRNAs and Their Targets in Cold-Stored Potato Tubers by Deep Sequencing and Degradome Analysis

Project description:Two small RNA libraries and 2 degradome libraries were constructed from potato tubers stored at room temperature or exposed to cold stress for deep sequencing. Through small RNA sequencing, 53 known miRNAs and 59 novel miRNAs were identified. Seventy genes were identified as miRNA targets by degradome sequencing.

2015-12-24 | GSE43237 | GEO

Genome-Wide Identification of microRNAs and Their Targets in Cold-Stored Potato Tubers by Deep Sequencing and Degradome Analysis

2015-12-24 | E-GEOD-43237 | biostudies-arrayexpress

Identification and Comparative Analysis of Cotton miRNA Target Genes using Degradome Sequencing

Project description:To gain insight into the functions of salt-regulated miRNAs, target genes were identified through degradome sequencing approach. Three cotton RNA libraries were constructed and sequenced under normal consideration, osmotic and ionic stress. A total of 73,988,644 reads represented by 3,254,054 unique reads from the 5â ends of uncapped and poly-adenylated RNAs were obtained. The PairFinder software was used to identify the sliced targets for the known miRNAs and novel miRNAs. These sequences were further compared with transcriptome sequencing data of G. arboretum and G. raimondii. We obtained the data from (Cotton Genome Project, http://cgp.genomics.org.cn/page/species/index.jsp).Based on degradome sequencing, 31 target genes were identified for 20 cotton miRNA families. The abundance of transcripts was plotted for each transcript. Conserved miRNAs target conserved homologous genes in diverse plant species. Three cDNA libraries were constructed using total RNA obtained from control samples (CK), the 4 h and 5 d salt-treated samples. A total of 74,351,180 sequence reads were obtained from three libraries. After removing the 3p and 5p adapter sequences and filtering out low quality âânââ sequences, 864,720, 1,217,757 and 1,171,577 clean reads remained in the CK, 4 h and 5 d samples, respectively.

2016-06-11 | E-GEOD-69820 | biostudies-arrayexpress

Small RNA sequencing Analysis of adipose in six month calf Chinese swamp buffalo

Project description:Background: Intramuscular fat (IMF) content is an important index for beef quality. However, the genetics of IMF deposition is complex and still largely unclear, especially in buffalo. To identify miRNAs with potential regulatory role in lipid accumulated in muscle, we performed small RNA sequencing and identified miRNAs expressed in the longissimus dorsi muscle and back fat of Chinese buffalo, which provided vital information for further identification of miRNAs with potential regulatory role in the lipid accumulated in muscle. Results: Three small RNA libraries were constructed. A total of 32762032 raw reads were obtained from adipose groups, respectively. After filtering the adaptor and low quality reads, 32054381 clean reads were retained. In total, 623 miRNAs were identified.

2021-12-31 | GSE171146 | GEO

Integrated RNA-seq and sRNA-seq analysis reveals miRNA effects on secondary metabolism in Solanum tuberosum L [miRNA-seq]

Project description:Light is a major environmental factor that affects metabolic pathways and stimulates the production of secondary metabolites in potato. However, adaptive changes in potato metabolic pathways and physiological functions triggered by light are partly explained by gene expression changes. Regulation of secondary metabolic pathways in potato has been extensively studied at transcriptional level, but little is known about the mechanisms of post-transcriptional regulation by miRNAs. To identify light-responsive miRNAs/mRNAs and construct putative metabolism pathways regulated by the miRNA-mRNA pairs, an integrated omics (sRNAome and transcriptome) analysis was performed to potato under light stimulus. A total of 31 and 48 miRNAs were identified to be differentially expressed in the leaves and tubers, respectively. Among the DEGs, 1353 genes in the leaves and 1841 genes in the tubers were upregulated, while 1595 genes in the leaves and 897 genes in the tubers were downregulated by light. Mapman enrichment analyses showed that genes related to MVA pathway, alkaloids-like, phenlypropanoids, flavonoids, and carotenoids metabolism were significantly upregulated, while genes associated with major CHO metabolism were repressed in the leaves and tubers. Integrated miRNA and mRNA profiles revealed that light-responsive miRNAs are important regulators in alkaloids metabolism, UMP-salvage, lipid biosynthesis, and cellulose catabolism. Moreover, several miRNAs may participate in glycoalkaloids metabolism via JA signaling pathway, UDP-glucose biosynthesis and hydroxylation reaction. This study provides a global view of transcriptome response in potato response to light, our results suggest that miRNAs might play important roles in secondary metabolic pathways, especially in glycoalkaloid biosynthesis. The findings will enlighten us on the genetic regulation of secondary metabolite pathways and pave the way for future application of genetically engineered potato.

2016-09-28 | GSE79984 | GEO

Integrated RNA-seq and sRNA-seq analysis reveals miRNA effects on secondary metabolism in Solanum tuberosum L [RNA-seq]

2016-09-28 | GSE79985 | GEO

degradome sequence data

Project description:To identity the targets of miRNAs, we bundled 12 samples from different developing satages into four mixture samples. These samples were used to cosntruct degradome libraries and preform degradome sequencing on Illumina Hi-seq 2000 analyzer. More than 44.98 millions clean reads were obtained and 33.52 million reads were mapped to the soybean cDNA. The mapped reads were used to identity miRNA targets by CleaveLand4 pipeline.

2017-05-01 | GSE72903 | GEO

Discovery of novel and differentially expressed microRNAs between fetal and six month old skeletal muscle in goat

Project description:MicroRNAs (miRNAs) are small (∼22 nucleotides) noncoding ribonucleic acids (RNAs) that regulate gene expression by binding to their complementary sequences. Recent years, a great deal of miRNAs which highly-enriched in skeletal muscle have been identified, which can influence multiple facets of muscle development and function through their regulation of key genes controlling myogenesis. However, to date no miRNAs have been reported to modulate muscle development in goat. Total RNAs from the xuhuai goats longissimus thoracis at fetal and six month old stages were used to construct small RNA libraries for Solexa SBS technology sequencing. In the small RNA profile, a total of 15,627,457 clean reads were obtained from the fetal goat library and 15,593,721 clean reads from the six month old goat library. There are 471 conserved miRNAs overlapped in both libraries, of which 343 miRNAs were differential expressed. We identified 122 novel miRNAs in the fetal caprine library and 53 novel miRNAs in the six month old-caprine library.

2015-07-19 | GSE49260 | GEO

Gene Expression Changes In potato Tuber Meristems Treated with the Sprout Inhibitor 1,4-dimethylnapthlene

Project description:The suppression of sprout growth is critical for the long-term storage of potato tubers. 1,4-dimethylenapthlene (DMN) is a new class of sprout control agent but the metabolic mode of action for this compound has yet to be elucidated. Changes in transcriptional profiles of meristems isolated from potato tubers treated with the DMN were investigated using an Agilent 44K 60-mer-oligo microarray. RNA was isolated from nondormant Russet Burbank meristems isolated from tubers treated with DMN for three days or activated charcoal as a control. RNA was used to develop probes that were hybridized against a microarray developed by the Potato Oligo Chip Initiative (POCI). Analysis of the array data was conducted in two stages: total array data was examined using a linear model and the software limma and pathway analysis was conducted by linking the potato sequences to the Arabidopsis thaliana. DMN elicited a change in a number of transcripts associated with cold responses, water regulation, salt stress and osmotic adjustment. Additionally, repression of auxin signaling and transport were observed in DMN-treated tubers, and connections between DMN treatment and repression of FT through mi156 regulation were indicated. DMN also resulted in a repression of cyclin or cyclin-like transcripts. DMN also resulted in a 50% decrease in thymidine incorporation suggesting a repression of the S-phase of the cell cycle. QT-PCR analysis demonstrated that DMN increased transcripts for the cell cycle inhibitors KRP1 and KRP2. We conclude the DMN results in alteration of genes associated with cold responses and water regulation and maintenance of a G1/S-phase block possibly through the induction of the cell cycle inhibitors KRP1 andKRP2. Twelve samples, four treatments, three biological replicates

2012-01-01 | GSE31825 | GEO

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