Rice
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ABSTRACT:
PROVIDER: PRJNA1232397 | ENA |
REPOSITORIES: ENA
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Project description:Transcriptome analysis is an important approach to associate genotype with phenotype. The content and dynamics of eukaryotic transcriptome are far more complex than previously anticipated. Here we integrated high-throughput RNA-seq and paired-end method to conduct an unprecedentedly deep survey of transcription profile for cultivated rice, one of the oldest domesticated crops species and has since spread worldwide to become one of the major staple foods. Analysis of reads mapping revealed 4,244 previously uncharacterized transcripts, including a mass of protein-coding genes and putative functional non-coding RNA genes. Alignment of junction reads indicated over 42% of rice multiple-exon genes produce two or more distinct splicing isoforms. It’s intriguing that we identified 1,356 putative gene fusion events, indicating the 234 fusion gene produced by trans-splicing vastly increases the complexity of rice transcriptome, together with the pervasive alternative splicing events. Digital gene expression profiling revealed most rice duplicate genes were maintained by the selection constraint on gene dosages, which would increase the genetic robustness of rice to counteract deleterious mutations Keywords: Expression profiling by high throughput sequencing
2010-03-01 | GSE16631 | GEO
Project description:Transcriptome analysis is an important approach to associate genotype with phenotype. The content and dynamics of eukaryotic transcriptome are far more complex than previously anticipated. Here we integrated high-throughput RNA-seq and paired-end method to conduct an unprecedentedly deep survey of transcription profile for cultivated rice, one of the oldest domesticated crops species and has since spread worldwide to become one of the major staple foods. Analysis of reads mapping revealed 4,244 previously uncharacterized transcripts, including a mass of protein-coding genes and putative functional non-coding RNA genes. Alignment of junction reads indicated over 42% of rice multiple-exon genes produce two or more distinct splicing isoforms. It’s intriguing that we identified 1,356 putative gene fusion events, indicating the 234 fusion gene produced by trans-splicing vastly increases the complexity of rice transcriptome, together with the pervasive alternative splicing events. Digital gene expression profiling revealed most rice duplicate genes were maintained by the selection constraint on gene dosages, which would increase the genetic robustness of rice to counteract deleterious mutations
2010-03-01 | GSE16507 | GEO
Project description:Transcriptome analysis is an important approach to associate genotype with phenotype. The content and dynamics of eukaryotic transcriptome are far more complex than previously anticipated. Here we integrated high-throughput RNA-seq and paired-end method to conduct an unprecedentedly deep survey of transcription profile for cultivated rice, one of the oldest domesticated crops species and has since spread worldwide to become one of the major staple foods. Analysis of reads mapping revealed 4,244 previously uncharacterized transcripts, including a mass of protein-coding genes and putative functional non-coding RNA genes. Alignment of junction reads indicated over 42% of rice multiple-exon genes produce two or more distinct splicing isoforms. It’s intriguing that we identified 1,356 putative gene fusion events, indicating the 234 fusion gene produced by trans-splicing vastly increases the complexity of rice transcriptome, together with the pervasive alternative splicing events. Digital gene expression profiling revealed most rice duplicate genes were maintained by the selection constraint on gene dosages, which would increase the genetic robustness of rice to counteract deleterious mutations Keywords: Expression profiling by high throughput sequencing mRNA expression of 8 independent rice tissues was determined by method of RNA-Seq using short reads from high throughput sequencing technology. Meanwhile small RNA populations from mixture solution pooled from total RNA of each 8 tissues were also sequenced.
2010-03-01 | E-GEOD-16631 | biostudies-arrayexpress
Project description:Yellow stem borer (YSB), Scirpophaga incertulas (Walker) (Lepidoptera: Crambidae), is a major pest of rice in India, that can lead to 20-60% loss in rice production. Effective management of YSB infestation is challenged by the non-availability of adequate source of resistance and poor understanding of resistance mechanisms, thus necessitating studies for generating resources to breed YSB resistant rice and to understand rice-YSB interaction. Here we performed transcritpomics profiling of rice lines with contrasting response to YSB. RNA-sequencing of the susceptible (SM) and tolerant (SM92 lines revealed multiple genes to be differentially regulated upon YSB infestation. Comparative transcriptome analysis revealed a putative candidate gene that was predicted to encode an alpha-amylase inhibitor. Analysis of the transcriptome and metabolite profiles further revealed a possible link between phenylpropanoid metabolism and YSB tolerance.
2023-10-15 | GSE245213 | GEO
Project description:Rice-Xanthomonas oryzae is an economically important pathosystem owing to the loss caused by bacterial blight disease. Understanding the moleulcar dynbamics that occur during rice-Xoo interaction is crucial for understanding disaease susceptible and resistance mechanisms. SM210, harbors the resistance alleles xa5, xa13, and Xa21 and is resistant against Xoo. Transcriptome analysis of Xoo-treated. SM210 and SM, its parent variety, indicated different pathways that are altered in these varieties after Xoo treatment.
2025-04-30 | GSE292776 | GEO
Project description:Post-transcriptional mechanisms, including alternative splicing (AS) and alternative translation initiation (ATI), have been used to explain the protein diversity involved in plant developmental processes and stress responses. Rice germination under hypoxia conditions is a classical model system for the study of low oxygen stress. It is known that there is transcriptional regulation during rice hypoxic germination, but the potential roles of AS and ATI in this process are not well understood. In this study, a proteogenomic approach was used to integrate the data from RNA sequencing, qualitative and quantitative proteomics to discover new players or pathways in the response to hypoxia stress. The improved analytical pipeline of proteogenomics led to the identification of 10,253 intron-containing genes, 1,729 of which were not present in the current annotation. Approximately 1,741 differentially expressed AS (DAS) events from 811 genes were identified in hypoxia-treated seeds in comparison to controls. Over 95% of these were not present in the list of differentially expressed genes (DEG). In particular, regulatory pathways such as spliceosome, ribosome, ER protein processing and export, proteasome, phagosome, oxidative phosphorylation and mRNA surveillance showed substantial AS changes under hypoxia, suggesting that AS responses are largely independent of traditional transcriptional regulation. Massive AS changes were identified, including the preference usage of certain non-conventional splice sites and enrichment of splicing factors in the DAS datasets. In addition, using self-constructed protein libraries by 6-frame translation, thousands of novel proteins/peptides contributed by ATI were identified. In summary, these results provide deeper insights towards understanding the underlying mechanisms of AS and ATI during rice hypoxic germination.
2019-11-12 | PXD010923 | Pride
Project description:Although Sm-like proteins (LSMs) form the core of U6 RNPs and function in pre-mRNA splicing, little is known regarding their regulatory role in selection of splice sites, alternative splicing (AS) and splicing efficiency in eukaryotes. The Arabidopsis SAD1 locus encodes the LSM5 protein and was defined in a genetic screen for components that regulate the expression of stress-responsive gene. To further investigate regulatory role of the protein SAD1 in pre-mRNA splicing, we performed RNA sequencing (RNA-seq) to examine the changes of the global alternative splicing (AS) among the wildtype Arabidopsis plant (C24), the mutant plant (sad1) and the sad1-overexpressed plant (SAD1-OE). Our work not only provided novel insights into the regulatory role of SAD1 or LSM proteins in splicing, but also provided new cues to improving splicing efficiency and optimizing biological functions and screening the stress-resistant plant.
2013-11-01 | E-MTAB-4336 | biostudies-arrayexpress
Project description:Differentiated Vascular Smooth Muscle Cells (VSMCs) express a unique network of splice isoforms (smooth muscle specific alternative splicing - SM-AS) in functionally critical genes including those comprising the contractile machinery. We previously described RNA Binding Protein Multiple Splicing (RBPMS) as a potent driver of contractile, aortic tissue like SM-AS in VSMCs using rodent models. What is unknown is how RBPMS affects VSMC phenotype and behaviour. Here, we use human embryonic stem cell-derived VSMCs (hES-VSMCs) to dissect the role of RBPMS in SM-AS in human cells and determine the impact on VSMC phenotypic properties. hES-VSMCs are inherently immature and display only partially differentiated SM-AS patterns while RBPMS levels are undetectable endogenously. Hence, we used an over-expression system and found that RBPMS induces SM-AS patterns in hES-VSMCs akin to the contractile tissue VSMC splicing patterns in multiple events. We present in silico and experimental findings that support RBPMS’ splicing activity as mediated through direct binding and via functional cooperativity with splicing factor RBFOX2 on a significant subset of targets. Finally, we demonstrate that RBPMS can alter the motility and the proliferative properties of hES-VSMCs to mimic a more differentiated state. Overall, this study emphasizes a critical splicing regulatory role for RBPMS in human VSMCs and provides evidence of phenotypic modulation by RBPMS.
2024-12-19 | GSE242826 | GEO
Project description:RNA splicing is a molecular mechanism to increase protein diversities acquired through the evolution while the underlieing driving forces for the phenomenon are unknown especially in terms of gene expression. Rice alternatively spliced transcript detecting microarray (ASDM) was designed and applied to differentiate the transcriptome of 4 representative organs of Oryza sativa L. cv. Ilmi including leaves, roots, panicles at 1 cm stage and young seeds at 20 days after pollination. The comparison of the data between the microarray and RNA-seq shows a ‘bell shape distribution’ and a strong co-lineation for highly expressed genes. The transcripts are classified according to the degree of organ enrichment using coefficient value (CV, the ratio of standard deviation to the mean values); highly variable (CVI), variable (CVII), and constitutive (CVIII) groups. The genes of highly variable group show the characteristics of the organs. The index of the portion of loci with alternatively spliced transcripts in a group (IAS) is designated for these CV groups and showed the higher value in the constitutive group. In addition, within a locus, a transcript with longer cds tends to be higher expressed and the spliced_intron is the most commonly found type of alternative splicing for the extended cds. Thus, constitutively expressed genes might be under evolutionary pressure toward alternative splicing that might have a longer cds. These data show that less resource consuming and better designed microarray might be a niche technology to test the transcriptome analysis including alternatively spliced transcripts in plants.
2017-01-01 | GSE87536 | GEO
Project description:Rice (Oryza sativa) is one of the world's major rations. The widely planted hybrid rice in Jiangxi Province is seriously affected by Magnaporthe oryzae, which seriously restricts the rice yield in Jiangxi Province. In recent years, studies have found that alternative polyadenylation (APA) is an important post-transcriptional regulation in eukaryotes. The genetic law and function of APA in the occurrence of hybrid rice blast in Jiangxi are not clear. In this study, Wufengyou T025 (WFY) and its parents (male parent Changhui T025(CH), and female parent Wufeng B(WFB)) were used as the research objects. Transcriptome and metabolome sequencing, combined with a variety of bioinformatics analysis methods and modern molecular biology experimental techniques, revealed the APA expression profile during the occurrence of Jiangxi hybrid rice blast. To explore the regulatory mechanism of APA core factors during the occurrence of rice blast. This study not only provides a new understanding of the occurrence of Jiangxi hybrid rice blast, but also provides more abundant resources for molecular breeding.
2024-07-17 | GSE272164 | GEO