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ABSTRACT: Systematic studies of anthocyanin biosynthesis in the developing grain of purple wheat

PROVIDER: PRJNA749499 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15249505_1.fastq.gz	Fastqsanger.gz
	SRR15249505_2.fastq.gz	Fastqsanger.gz
	SRR15249506_1.fastq.gz	Fastqsanger.gz
	SRR15249506_2.fastq.gz	Fastqsanger.gz
	SRR15249507_1.fastq.gz	Fastqsanger.gz

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RNA-seq of pericarp of purple-grain wheat Luozhen No.1 of 20 days (D20) shading treatment after pollination, against 20 DAP untreated controls

Project description:Purple-grain wheat are caused by anthocyanin accumulation in the seed coat. The anthocyanin biosynthesis and accumulation were affected by light in purple-grain wheat. The spikes of purple-grain wheat Luozhen No.1 were bagged with four-layer Kraft paper bags after pollination. To identify genes involved in the anthocyanin biosynthesis, we sequenced two pericarp cDNA libraries, D20 (20 DAP) of shading treatment, and L20 (20 DAP) of untreated control using an Illumina HiSeqTM 2000.

2018-03-30 | E-MTAB-6398 | biostudies-arrayexpress

RNA-seq of pericarp of purple-grain wheat Luozhen No.1 of 15 days (D15) and 20 days (D20) shading treatment after pollination, against 15 DAP, 20 DAP untreated controls. The purple-grain wheat were grown under natural field conditions at Shandong Agricultural University Experimental Station (36169 N, 117169 E), Taian, China during Octubor, 2015 to June, 2016.

Project description:Purple-grain wheat are caused by anthocyanin accumulation in the seed coat. But little is known about molecular mechanism of anthocyanin biosynthesis. The anthocyanin biosynthesis and accumulation were affected by light in purple-grain wheat. The spikes of purple-grain wheat Luozhen No.1 were bagged with four-layer Kraft paper bags after pollination. To identify genes involved in the anthocyanin biosynthesis, we sequenced four pericarp cDNA libraries, D15 (15 DAP), D20 (20 DAP) of shading treatment, and L15 (15 DAP), L20 (20 DAP) of untreated control using an Illumina HiSeqTM 2000. After quality control, raw reads are filtered into clean reads which will be aligned to the reference sequences. The alignment data is utilized to calculate distribution of reads on reference genes and mapping ratio, and proceed with downstream analysis including gene and isoform expression, deep analysis based on gene expression (PCA/correlation/screening differentially expressed genes and so on),exon expression, gene structure refinement, alternative splicing, novel transcript prediction and annotation, SNP detection, Indel detection. Further, we also perform deep analysis based on different expression genes, including Gene Ontology (GO) enrichment analysis, Pathway enrichment analysis, cluster analysis, and finding transcriptor factor.

2018-03-26 | E-MTAB-5975 | biostudies-arrayexpress

Integrated Transcriptome and Metabolome Identified Novel Candidate Genes Regulating Anthocyanin Biosynthesis in Colored-Grain Wheat (Triticum aestivum L.)

Project description:Purpose: The present study aimed to investigate the anthocyanin components and identify relevant regulatory genes in purple wheat grain by carrying out transcriptome analyses. Methods: The seeds of purple grain wheat and white grain wheat were collected 30 days after flowering, and three biological replicates were set. Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000. Then synthesizing the fragmented RNA into cDNA through the action of reverse transcriptase, and finally obtaining acDNA library. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol. Results: A total of 10440 diferentially expressed genes were signifcantly enriched by RNA sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed signifcantly enriched flavonoid biosynthesis and anthocyanin biosynthesis in CW_S versus W_S. And the ANS and UFGT genes were predicted as core genes in anthocyanin biosynthesis. Conclusions: Our study represents the detailed analysis of wheat grain transcriptomes, with biologic replicates, generated by RNA-seq technology. Through this study, we speculated that ANS and UFGT genes are the core genes of anthocyanin biosynthesis.The significant differences of these genes affect the synthesis of anthocyanins in wheat grains, and thus affect the grain color of wheat.

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Transcriptome and metabolome analysis reveals anthocyanin biosynthesis pathway associated with poplar (Populus deltoids) leaf color formation

Project description:Colored-leaf plants are increasingly popular and have been attracting more and more attentions. However, studies about the anthocyanin components and molecular mechanisms of anthocyanin biosynthesis in QHP and ZSY was still unclear. In present study, an integrated metabolite and transcriptome profiling analysis was performed to explore the anthocyanin compositions and the specific regulatory network of anthocyanin biosynthesis in purple leaves of QHP and ZSY. A total of 39 anthocyanin compounds were detected based on the LC-MS/MS analysis. Of these, 12 cyanidins, 7 pelargonidins, 5 delphindins, and 5 procyanidins are the major anthocyanin compounds, which were significantly differentially accumulated in purple leaves of QHP and ZSY. The major genes associated with anthocyanin biosynthesis, including structural genes and TFs, were differentially expressed in the purple leaves of QHP and ZSY through RNA-seq data analysis, some of which were further assessed by qRT-PCR. Correlation between RNA-seq analysis and metabolite profiling showed that the expression pattern of some differentially expressed genes in anthocyanin biosynthes pathway were closely correlated with the differential accumulation of anthocyanins. In addition, one member of SG5 subgroup of R2R3-MYB TFs, Podel.04G021100, shows a similar expression pattern to some structure genes and closely correlates with sixteen anthocyanin compounds, indicating that the MBY TF (Podel.04G021100) may be involved in the regulation of anthocyanin biosynthesis. The above results not only make us systematic and comprehensive understand the anthocyanin components and corresponding molecular mechanisms of anthocyanin biosynthesis in purple leaves of QHP and ZSY, but also contribute to the promotion and application of anthocyanins in colored-leaf poplars.

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Characterization of development wheat grain in morphological stage by RNA-seq

Project description:Wheat yield is correlated significantly with grain size which is established during morphological stage. In present study, morphological stage of developing wheat grain were analyzed by RNA-seq.This research will help us to understand the mechnism underlying of grain development. This is the first study on gene expression profiling of morphological stage of developing wheat grain and the results may aid the identification of pathways and genes associated with seed development in wheat.

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Comparative transcriptional profiling of developing wheat grains with contrasting levels of minerals

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Production of Red Flower Rapeseed by Ectopic Expression of OvPAP2 Identified in Brassica napus-Orychophragmus violaceus Addition Line by Comparative Transcriptome Analysis

Project description:Oilseed rape is both an important oleaginous crop and agriculture sightseeing crop whereas has relatively scanty flower color. As natural ﬂavonoids, Anthocyanin are responsible for the attractive red, purple, and blue colors of various tissues in higher plants, especially for the ornamental plants flower. One Brassica napus-Orychophragmus violaceus disomic addition line (M4) obtained previously exhibits red petals whichresult from anthocyanin biosynthesis. Transcriptome analysis of M4, B. napus (H3), natural individuals of O. violaceus with purple petals (OvP) and white petals (OvW) revealed that most of structural genes for the anthocyanin synthesis were up-regulated in both M4 and OvP, especially key gene ANS in the last step. Reads assembling and sequence alignment showed that the regulatory DEG PAP2 in M4 was from the transcript of O. violaceus. OvPAP2 was transformed into Arabidopsis thaliana and B. napus driven by the CaMV35S promoter and the rape petal-specific prompter XY355. Transgenic A. thaliana plants showed different levels of purple pigments in most of the organs, including the petals, and transgenic B. napus flowers exhibited restricted accumulation of anthocyanins in stamens when driven by CaMV35S promoter, but generated both red petals and anthers driven by the XY355 promoter. These results provided a platform for expounding the anthocyanin biosynthesis pathway in B. napus petals and give a successful case for flower color modification of the agriculture sightseeing rape.

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