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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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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

ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Triticum aestivum

SUBMITTER: Yuxiu Dong

PROVIDER: E-MTAB-6398 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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.

2023-04-24 | GSE198515 | GEO

Increased wheat protein content via introgression of a HMW glutenin selectively reshapes the grain proteome

Project description:Introgression of a high molecular weight glutenin subunit (HMW-GS) gene, 1Ay21*, into commercial wheat cultivars increased overall grain protein content and bread-making quality by unknown mechanisms. As well as increased abundance of 1Ay HMW-GS, 115 differentially expressed proteins (DEPs) were discovered between three cultivars and corresponding introgressed near-isogenic lines (NILs). Functional category analysis showed that the DEPs were predominantly other storage proteins, and proteins involved in protein synthesis, protein folding, protein degradation, stress response and grain development. Nearly half the genes encoding the DEPs showed strong co-expression patterns during grain development. Promoters of these genes are enriched in elements associated with transcription initiation and light response, indicating a potential connection between these cis-elements and grain protein accumulation. A model of how this HMW-GS enhances the abundance of machinery for protein synthesis and maturation during grain filling is proposed. This analysis not only provides insights into how introgression of the 1Ay21* improves grain protein content, but also directs selection of protein candidates for future wheat quality breeding programmes.

2021-05-30 | PXD021706 | Pride

The grain protein turnover atlas of hexaploid wheat Triticum aestivum

Project description:Cellular protein abundance results from the relative rates of protein synthesis and protein degradation. Through combining in vivo stable isotope labelling and in-depth quantitative proteomics, we created a protein turnover atlas of wheat grain proteins during grain development. Our data demonstrate that protein turnover rates for 1447 unique wheat grain protein groups have an apparent spatiotemporal pattern that aids explanation of the 60% of variation in protein abundances that are not attributable to gene expression. Protein synthesis rates of individual proteins vary over 100 fold and degradation rates over 20 fold. Storage proteins have both higher synthesis and degradation rates than the overarching average rates of grain proteins in other functional categories, while those proteins involved in photosynthesis, DNA synthesis and glycolysis, by contrast, are house-keeping proteins that show low synthesis and degradation rates at all times. Approximately 20% of total grain ATP production through respiration is used for grain proteome biogenesis and maintenance, and the grain invests nearly half of this budget in storage protein synthesis alone. Degradation of storage proteins as a class of grain proteins also consumed a significant amount of the total ATP allocated to protein degradation processes. This analysis suggests that 20% of newly synthesized storage proteins are turned over rather than stored suggesting that this process is not energetically optimal. This approach to measure protein turnover rates at the proteome scale shows how different functional categories of grain proteins accumulate, calculates the costs of futile cycling of protein turnover during wheat grain development and identifies the most and the least stable wheat grain proteins.

2021-12-21 | PXD022231 | Pride

SRA of transcriptome of Hevea brasiliensis

Project description:We report here the use of next-generation massively parallel sequencing technologies and de novo transcriptome assembly to gain insight into the wide range of transcriptome of two Hevea brasiliensis clones (RY8-79 and PR107). The output of sequenced data showed that more than 26 million sequence reads with average length of 90nt were generated in both clones. Totally 51829 unigenes (mean size = 640 bp) were assembled through transcriptome de novo assembly, which represent more than 16-fold of all the sequences of Hevea brasiliensis deposited in the GenBank. Assembled sequences were annotated with gene descriptions, gene ontology and clusters of orthologous group terms. Base on limit rule with FDR≤0.001 and |log2 Ratio|≥1, 6726 different expression unigenes (3018 up and 3708 down) were detected as PR107 versus RY8-79. Functional analysis showed mass of categories were reprogrammed between two clones, which relate latex generation and expelling difference between them. As a comparative transcriptome analysis, the results obtained here will greatly expand our understanding of physiological differences among varieties in molecular level and will contribute t The transcriptome of latex in Hevea brasiliensis

2015-03-29 | E-GEOD-59981 | biostudies-arrayexpress

SRA of transcriptome of Hevea brasiliensis

Project description:We first report the use of next-generation massively parallel sequencing technologies and de novo transcriptome assembly to gain insight into the wide range of transcriptome of Hevea brasiliensis. The output of sequenced data showed that more than 12 million sequence reads with average length of 90nt were generated. Totally 48,768 unigenes (mean size = 488 bp) were assembled through transcriptome de novo assembly, which represent more than 3-fold of all the sequences of Hevea brasiliensis deposited in the GenBank. Assembled sequences were annotated with gene descriptions, gene ontology and clusters of orthologous group terms. Total 37,373 unigenes were successfully annotated and more than 10% of unigenes were aligned to known proteins of Euphorbiaceae. The unigenes contain nearly complete collection of known rubber-synthesis-related genes. Our data provides the most comprehensive sequence resource available for study rubber tree and demonstrates the availability of Illumina sequencing and de novo transcriptome assembly in a species lacking genome information. The transcriptome of latex and leaf in Hevea brasiliensis

2011-09-01 | E-GEOD-26514 | biostudies-arrayexpress

Transcriptional analysis of genes expressed during wheat grain development.

Project description:Investigation of genome wide expression level changes during 11 stages of wheat grain development in normal growth conditions (19°C).

2011-12-20 | E-MTAB-690 | biostudies-arrayexpress

RNA-seq of Sitobion avenae body parts and developmental stages

Project description:The English grain aphid, Sitobion avenae, is a major agricultural pest of wheat, barley and oats, and is a major vector of Barley Yellow Dwarf Virus (BYDV) leading to reductions in grain yield. RNA-seq data from a genotype (SA3) was generated from heads and bodies, and from winged and unwinged aphids. The primary goal was to generate evidence for genome annotation, and the secondary goal was to compare expression of genes between head and body, and also between winged and unwinged aphids.

2021-12-01 | E-MTAB-10540 | biostudies-arrayexpress

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.

2022-10-31 | GSE216754 | GEO

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

Project description:Transcriptional comparison of developing grains between two wheat genotypes with contrasting levels of minerals in grain, using Affymetrix GeneChipM-BM-. Wheat Genome Array. Gene expression data of two wheat genotypes with high and low grain mineral concentration at two seed development stages (14, and 28 days after anthesis)

2014-10-31 | E-GEOD-56032 | biostudies-arrayexpress

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