Transcriptome analysis of a chlorosis mutant of Pakchoi
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ABSTRACT:
ORGANISM(S): Brassica rapa subsp. chinensis
PROVIDER: GSE112255 | GEO | 2019/03/23
REPOSITORIES: GEO
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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 gene expression profiles of cucumber under short-term chilling stress. The goals of this study are to transcriptome analysis of cucumber leaves under chilling stress. Methods: mRNA profiles of seedlings exposed to an air temperature of 6°C in the absence of light at 0, 2, 6, and 12 h were generated by deep sequencing, in triplicate, using Illumina Hiseq platform. The reference genome and gene model annotation files were downloaded from the genome website （http://cucurbitgenomics.org/）. An index of the reference genome was built using Bowtie v.2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v.2.0.12. qRT–PCR validation was performed using SYBR Green assays. Results: A total of 55.7 million clean reads was generated. Based on the threshold values of absolute value of log2 ratio ≥ 1 and FDR ≤ 0.05, a total of 2113 DEGs was identified at three time points (2, 6, and 12 h). A total of 30 genes was detected at all time points. The number of DEGs increased with time. In total, 100 TFs from 22 families in three subsets were detected. And 19 kinase families were identified in three subsets. 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 mechanisms underlying the response to chilling stress in cucumber and other plants. Conclusions: The results presented here reveal changes in the transcriptome profile of cucumber in response to chilling stress. Exposure to a low temperature induced genes involved in hormone regulation, lipid metabolism, and photosynthesis, including NAC, WRKY, AP2/ERF, ERD, MYB as well as zinc finger TFs and protein kinases such as receptor-like protein kinase, MAPK, and CDK. Most TFs were upregulated whereas CDKs were downregulated. These findings provide information that can be useful for investigating the molecular mechanisms underlying the response to chilling stress in cucumber and other plants.
2018-08-20 | GSE111998 | 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.
2021-03-27 | GSE115279 | GEO
Project description:The leaf of Chinese cabbage is the major place of photosynthesis, the mutation of leaf may directly affect the rate of plant growth and development and the formation of leafy head, and ultimately influence the yield and quality of Chinese cabbage. We identified a developmentally retarded mutant (drm) exhibiting stable inheritance, which was derived from Chinese cabbage DH line âFTâ using a combination of isolated microspore culture and radiation treatment (60Co γ-rays). The drm exhibited slow growth and development at the seedling and heading stages, leading to the production of a tiny, leafy head, as well as chlorophyll-deficient leaves, especially in seedlings. Genetic analysis indicated that the phenotype of drm was controlled by a single recessive nuclear gene. Compared with wild-type line âFTâ, the drmâs chlorophyll content was significantly reduced and its chloroplast structure was abnormal. Moreover, the photosynthetic efficiency and chlorophyll fluorescence parameters were significantly decreased. The changes in leaf color, combined with these altered physiological characters may influence the growth and development of plant, ultimately resulting in the developmentally retarded phenotype of drm. To further understand the molecular regulatory mechanisms of phenotypic differences between âFTâ and drm, comparative transcriptome analysis were performed using RNA-Seq, a total of 338 differentially expressed genes (DEGs) were detected between âFTâ and drm. According to GO and KEGG pathway analysis, a number of DEGs which involved in the chlorophyll degradation and photosynthesis were identified, such as chlorophyllase and ribulose-1,5-bisphosphate carboxylase/oxygenase. In addition, the expression patterns of 12 DEGs, including three chlorophyll degradation- and photosynthesis-related genes and nine randomly selected genes, were confirmed by qRT-PCR. Numerous single nucleotide polymorphisms were also identified, providing a valuable resource for research and molecular marker-assistant breeding in Chinese cabbage. These results contribute to our understanding of the molecular regulatory mechanisms underlying growth and development and lay the foundation for future genetic and functional genomics studies in Chinese cabbage. The RNA from the third true leaves (day 15 to day 24 after the appearance of the third true leaves) of a developmentally retarded mutant (drm) and its wild type âFTâ in Chinese cabbage were sequenced by RNA-Seq, in triplicate.
2016-03-01 | E-GEOD-75464 | biostudies-arrayexpress
Project description:The leaf of Chinese cabbage is the major place of photosynthesis, the mutation of leaf may directly affect the rate of plant growth and development and the formation of leafy head, and ultimately influence the yield and quality of Chinese cabbage. We identified a developmentally retarded mutant (drm) exhibiting stable inheritance, which was derived from Chinese cabbage DH line ‘FT’ using a combination of isolated microspore culture and radiation treatment (60Co γ-rays). The drm exhibited slow growth and development at the seedling and heading stages, leading to the production of a tiny, leafy head, as well as chlorophyll-deficient leaves, especially in seedlings. Genetic analysis indicated that the phenotype of drm was controlled by a single recessive nuclear gene. Compared with wild-type line ‘FT’, the drm’s chlorophyll content was significantly reduced and its chloroplast structure was abnormal. Moreover, the photosynthetic efficiency and chlorophyll fluorescence parameters were significantly decreased. The changes in leaf color, combined with these altered physiological characters may influence the growth and development of plant, ultimately resulting in the developmentally retarded phenotype of drm. To further understand the molecular regulatory mechanisms of phenotypic differences between ‘FT’ and drm, comparative transcriptome analysis were performed using RNA-Seq, a total of 338 differentially expressed genes (DEGs) were detected between ‘FT’ and drm. According to GO and KEGG pathway analysis, a number of DEGs which involved in the chlorophyll degradation and photosynthesis were identified, such as chlorophyllase and ribulose-1,5-bisphosphate carboxylase/oxygenase. In addition, the expression patterns of 12 DEGs, including three chlorophyll degradation- and photosynthesis-related genes and nine randomly selected genes, were confirmed by qRT-PCR. Numerous single nucleotide polymorphisms were also identified, providing a valuable resource for research and molecular marker-assistant breeding in Chinese cabbage. These results contribute to our understanding of the molecular regulatory mechanisms underlying growth and development and lay the foundation for future genetic and functional genomics studies in Chinese cabbage.
2016-03-01 | GSE75464 | GEO
Project description:Ananas comosus var. bracteatus has high ornamental value and widespread application because of its chimeric leaves. However, little is known about the molecular mechanism regulating this characteristic. Here, comparative transcriptomic and proteomic analyses of the white parts (Whs) and green parts (Grs) of the chimeric leaves were performed to identify differentially expressed genes (DEGs) and differentially expressed proteins (DEPs). In total, 1,685 DEGs, including 712 up- and 973 down-regulated ones, and 5,428 DEPs, including 1,018 up- and 795 down-regulated ones, were identified between the Whs and Grs. Comparisons with the GO and KEGG annotations revealed that the DEGs were involved mostly in carbon fixation, porphyrin and chlorophyll metabolism and oxidative phosphorylation. The DEPs were mainly involved in ribosomes, photosynthesis, photosynthesis antennas, and porphyrin and chlorophyll metabolism. Combined analysis showed that nine proteins related to chlorophyll biosynthesis, photosynthetic pigments, and photosynthesis were unchanged at mRNA level but suppressed at protein level. These results indicated that the albino phenotype of the Whs was caused by the proteomic-level suppression of key enzymes involved in the chlorophyll biosynthesis pathway and that translational and post-translational regulation may play important roles in both the biosynthesis of photosynthetic pigments and photosynthesis. Biological significance: Leaves of Ananas comosus var. bracteatus serve as the best materials for the study of albino mechanism. Because the chemic trait of A. comosus var. bracteatus is unstable and the molecular mechanism of the albino cells was poorly understood, we performed comparative analyses both at the transcriptome and proteome levels. This work revealed suppressed proteomic-level and translational and post-translational regulation contribute to the albino phenotype formation. Our results provide better information concerning the molecular mechanism within the chimeric leaves of A. comosus var. bracteatus.
2019-06-10 | PXD010375 | Pride
Project description:Arabidopsis bHLH transcription factor PIF1 has been shown function as a negative regulator of Chlorophyll biosynthesis. Pif1-2 mutant accumulate more protochlorophylide during prolonged dark growth condations, therefore the comparation between Wt and pif1-2 mutant will help us find the PIF1 target genes in Chlorophyll biosynthesis pathway at genome wide level under the dark grown conditions. We used microarrays to detail the global gene expression under the regulation of PIF1. Keywords: Genotype comparison
2008-05-30 | GSE11594 | GEO
Project description:Hybrid chlorosis, one of the hybrid incompatibilities, has frequently been reported in inter- and intraspecific crosses of allopolyploid wheat. In our previous study, hybrid chlorosis was observed in the wheat triploids between a tetraploid wheat cultivar Langdon and four Ae. tauschii accessions and in their derived synthetic hexaploids. However, the molecular mechanisms underlying hybrid chlorosis are not well understood. Here, we performed cytological and comparative gene expression analyses in leaves to characterize the abnormal growth in wheat synthetics showing mild and severe chlorosis symptom. In addition, disease resistance was comparatively assessed. A number of carbohydrate metabolism- and defense-related genes were markedly up-regulated in the hybrid chlorosis lines, and abnormal chloroplasts were formed in the mesophyll cells before the leaves turned to be yellowish. The mild chlorosis plants showed increased resistance to a wheat blast fungus, although little significant differences of agricultural traits were found between the wild-type and mild chlorosis-showing plants. These observations suggest that the senescence processes might be accelerated in the hybrid chlorosis lines of wheat synthetics. Moreover, the negative effects on biomass can be minimized and the substantial fitness may be obtained under pathogen-polluted conditions in the mild chlorosis-showing wheat synthetics. Expression patterns were compared between a wild-type synthetic wheat line (as a reference) and two hybrid chlorosis-showing hybrid chlorosis lines. Total RNA samples were isolated from the 3-week-old leaf tissues. Two independent experiments were conducted in each line.
2014-08-12 | E-GEOD-59640 | biostudies-arrayexpress
Project description:Purpose: Genome-wide expression analysis for introgression line 9L136 and indica variety 93-11 under salt reatment and control to identify specifically differentially expressed in 9L136 under salt stress. Methods: Roots of two-half leaf seedlings of 9L136 and 93-11 were sequenced using an Illumina HiSeq2500 Sequencer; high-quality paired-end reads were mapped to the Nipponbare reference genome (MSU Rice Genome Annotation Project Release 7) using the spliced read mapper TopHat version 2.0.12, and Significant differentially expressed genes (DEGs) were determined based on a threshold of 2-fold expression change and false discovery rate (FDR) < 0.05 using Cuffdiff, one module of Cufflinks. qRT-PCR analysis were performed using SYBR Green Master Mix on CFX96 Real Time System. Results: 1388 genes which specifically differentilly expressed in 9L136 under salt stress were identified, and expression profile of 18 genes randomely selected was confirmed by qRT-PCR.
2017-07-22 | GSE101734 | GEO