Transcriptome analyses of variegated leaf development in ornamental kale
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ABSTRACT:
PROVIDER: PRJNA447962 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6914840_1.fastq.gz | Fastqsanger.gz | |||
| SRR6914840_2.fastq.gz | Fastqsanger.gz | |||
| SRR6914841_1.fastq.gz | Fastqsanger.gz | |||
| SRR6914841_2.fastq.gz | Fastqsanger.gz | |||
| SRR6914842_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of leaf color at different development stages. The goals of this study are to compare chlorophyll metabolism and chloroplast organization transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: leaf mRNA profiles of 12 RNA sequencing libraries (S1, S2, S3_S, and S3_C) were generated by deep sequencing, in triplicate, using an Illumina HiSeq 4000 system. After removing reads of low quality, those that remained were mapped to the reference genome (ftp://ftp.ensemblgenomes.org/pub/release-38/plants/genbank/brassica_oleracea/) using the HISAT package, allowing for a maximum of two mismatches and multiple alignments per read (up to 20 by default). qRT–PCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow, we mapped about 571.74 million sequence reads per sample to the the reference genome (ftp://ftp.ensemblgenomes.org/pub/release-38/plants/genbank/brassica_oleracea/) and identified 1028, 4323, 428, and 1033 DEGs were detected in pairwise comparison (S2 vs. S1, S3_S vs. S2, S3_S vs. S2, and S3_S vs. S3_C, respectively). The DEGs were associated with ‘photosynthesis’, ‘carbon fixation in photosynthetic organisms’, ‘porphyrin and chlorophyll metabolism’ and other pathways in the Kyoto Encyclopedia of Genes and Genomes database; DEGs related to chloroplast organization were identified in the Gene Ontology analysis. The DEGs identified by RNA sequencing were confirmed by qRT-PCR analysis, indicating that the data were reliable. These findings provide information that can be useful for investigating the molecular basis for leaf variegation in ornamental kale and other plants. Conclusions: The results presented here reveal changes in the transcriptome profile of a variegated leaf kale. DEGs related to chlorophyll metabolism and chloroplast organization were detected. These results demonstrate that leaf color at different stages of development is influenced by chloroplast and pigment metabolism, providing a foundation for investigating the molecular basis for leaf variegation in ornamental kale and other plants.
2021-03-27 | GSE112493 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of leaf color at different development stages. The goals of this study are to compare anthocyanin biosynthesis, chlorophyll metabolism and chloroplast organization transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: Leaf mRNA profiles of 12 RNA sequencing libraries (S1, S2, S3_S, and S3_C) were generated by deep sequencing, in triplicate, using an Illumina HiSeq 4000 system. After removing reads of low quality, those that remained were mapped to the reference genome (ftp://ftp.ensemblgenomes.org/pub/release-38/plants/genbank/brassica_oleracea/) using the HISAT package, allowing for a maximum of two mismatches and multiple alignments per read (up to 20 by default). qRT–PCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow, we mapped about 571.74 million sequence reads per sample to the the reference genome (ftp://ftp.ensemblgenomes.org/pub/release-38/plants/genbank/brassica_oleracea/) and identified 99, 391, 74, and 543 DEGs were detected in pairwise comparison (S2 vs. S1, S3_S vs. S2, S3_C vs. S2, and S3_S vs. S3_C, respectively). The DEGs were associated with ‘photosynthesis’and other pathways in the Kyoto Encyclopedia of Genes and Genomes database; DEGs related to chloroplast organization were identified in the Gene Ontology analysis. The DEGs identified by RNA sequencing were confirmed by qRT-PCR analysis, indicating that the data were reliable. These findings provide information that can be useful for investigating the molecular basis for leaf variegation in ornamental kale and other plants. Conclusions: The results presented here reveal changes in the transcriptome profile of a bicolor leaf kale. DEGs related to anthocyanin biosynthesis, chlorophyll metabolism and chloroplast organization were detected. These results demonstrate that leaf color at different stages of development is influenced by anthocyanin biosynthesis, chloroplast and pigment metabolism, providing a foundation for investigating the molecular basis for bicolor leaf in ornamental kale and other plants.
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Project description:Transcriptome analyses of bicolor leaf development in ornamental kale
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Project description:Morphotypes of Brassica oleracea are the result of a dynamic interaction between the genes that regulate the transition between vegetative and reproductive stages and those that regulate leaf morphology and plant architecture. In kales ornate leaf patterns, flowering delaying and nutrient quality are some of the characters were potentially selected by humans during domestication. Understanding candidate genes responsible for kale domestication is of importance to ultimately improve crop production. We aim to identify candidate genes that are responsible for kale leaf shape diversity and the evolution of domestic kale. Here we look at the global pattern of expressed genes during one single phase of development in kale, cabbage and TO1000 to gain an understanding of the genome-wide differences among some of the vegetative B. oleracea phenotypes. We identified gene expression patterns that are shared among the phenotypes and estimate the contribution of morphotype-specific gene expression patterns that set each of them apart. Differentially expressed developmental genes that regulate the vegetative to reproductive transition were abundant and present in all comparisons.
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Project description:To unveil the role of posttranslational modification in the variegated phenotype, we conducted global quantitative phosphoproteomic analysis on different leaf color sectors of Maiyuanjinqiu and the corresponding of Catalpa fargesii using Ti4+-IMAC phosphopeptide enrichment. 3778 phosphorylated sites assigned to 1646 phosphoproteins were identified, and 3221 in 1434 proteins were quantified. Differential phosphoproteins (above 1.5 or below 1/1.5) in various leaf color sectors were selected for functional enrichment analyses. GO enrichment revealed that processes of photosynthesis, regulation of the generation of precursor metabolites, response to stress, homeostasis, amino acid metabolism, transport–related processes and most of the energy metabolisms might contribute to leaf color. KEGG pathway enrichment analysis was performed based on differential phosphoproteins (DPs) in different organelles. The result showed that most enriched pathways were located in the chloroplasts and cytosol. The phosphorylation levels of glycometabolism enzymes might greatly affect leaf variegation.
2019-11-12 | PXD013065 | Pride
Project description:Brassica oleracea and Brassica napus are comprised of diverse cultivars that collectively constitute an important global food source. Of those, the Brassica oleracea convar. acephala cultivar group containing var. sabellica and var. palmifolia and Brassica napus var. pabularia, collectively known as kale, are nutritious leafy greens consumed for their abundance of vitamins and micronutrients. Typified by their curly, serrated or wavy leaves, kale varieties have been primarily defined based on their leaf morphology and geographic origin, despite maintaining complex genetic backgrounds. With changes in the diel molecular environment directly tied to multiple agronomic traits across the food production landscape (e.g. time-of-day nutritional content) and kale representing a candidate crop for vertical farming, we selected nine diverse kale varieties encompassing a wide swath of consumer kale varieties for growth under LED lights using precise real-world dawn/dusk growth conditions followed by quantitative GC-MS metabolomic and LC-MS proteomic analyses. With plant growth and development driven by the day-to-day molecular activities of plants, we harvested kale leaf tissue at end-of-day (ED) and end-of-night (EN) time-points for all metabolomic and proteomic analyses. Our results reveal that kale forms 2 distinct groups, defined by their diel metabolome and proteome signatures primarily involving amino acids and sugars along, with proteome changes in carbon and nitrogen metabolism, mRNA splicing, protein translation and light harvesting. Together, our analysis have derived robust quantitative insights into the diel growth and development landscape of kale, significantly advancing our fundamental understanding of this nutritious leafy green for next-generation breeding and biotechnology.
2023-07-26 | PXD031780 | Pride
Project description:This dataset contains information on genetic variation of an F1DH population of ornamental kale which was developed in our research laboratory by mircospore culture. The dataset includes information on individual plants, including their genotype at various SNP loci. We believe that this dataset will be useful for other researchers who are studying the genetics of ornamental kale.
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Project description:Phalaenopsis aprodite subsp. formosana is one of the most important species for Phalaenopsis breeding. A mutant line with variegated leaf is found in this species. The green leaves bear unstable yellow sectors. In order to investigate the molecular mechanism of the variegated mutant line, we sequenced the transcriptome of variegated mutant by Illumina's Solexa sequencing technology. The sequence analysis results showed 22,598 unigenes by de novo assembly method, and the average unigene length was 1,286 bp. The bioinformatics tools were used to screen the differential expression between green and yellow sectors of leaves. There were 389 differentially expressed unigenes were identified. In addition, Gene ontology (GO) and KEGG pathway analyses revealed diverse biological functions and processes from differentially expressed genes. In transcriptome analysis, seven differential expression gene between the green and yellow sectors of leaves can be identified as CHLM, CRD1, POR, CLH, SGR, psbA and Lhcb6 by RNA deep sequencing. The expression of candidate genes was confirmed using semi-quantitative reverse transcription (RT) PCR and real-time RT PCR. The result showed that the significantly differential expression of CLH and SGR between green and yellow sectors was confirmed. It is suggested that the overexpressed SGR gene promotes the function of chlorophyllase, leading to the rapid degradation of chlorophyll in yellow sector. It causes the chlorophyll to not accumulate in the yellow sector, as a result, the variegated leaves are shown.
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