Pyrus ussuriensis strain:Nanguo
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA257551 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1537288_1.fastq.gz | Fastqsanger.gz | |||
| SRR1537288_2.fastq.gz | Fastqsanger.gz | |||
| SRR1537289_1.fastq.gz | Fastqsanger.gz | |||
| SRR1537289_2.fastq.gz | Fastqsanger.gz |
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Project description:Although pear is an important edible fruit species, the current available genomic information is limited. Combining the Solexa/ Illumina RNA-seq high-throughput sequencing approach with Digital Gene Expression (DGE) analysis results in a powerful transcriptomic study. This publication reports the transcriptome profiling analysis of Pyrus bretschneideri Rehd. using RNA-seq and DGE in order to better understand the molecular mechanisms underlying biological aspects of pear, especially fruit development and maturation.Using high-throughput Illumina RNA-seq combined with a tag-based Digital Gene Expression (DGE) system, de novo transcriptome assembly and gene expression analysis of P. bretschneideri were performed at an unprecedented depth (5.47 gigabase pairs). Approximately 60.77 million reads were obtained, trimmed, and assembled into 90,227 unigenes. The unigenes comprised 17,619 contig clusters and 72,608 singletons and were an average length of 508 bp and had an N50 of 635 bp. Sequence similarity analyses against six public databases (Uniprot, NR and COGs at NCBI, Pfam, InterPro and KEGG) found 61,636 unigenes that could be annotated with gene descriptions, conserved protein domains, or gene ontology terms. 34.6% of the unigenes (31,215) were annotated against KEGG into 121 known metabolic or signaling pathways. DGE libraries of five different developmental fruit stages were constructed and analyzed, and the gene expression variations between two consecutive stages were compared. Thousands of genes showed significantly different expression levels based on the various comparisons. Extensive transcriptome and DGE profiling data have been obtained from the deep sequencing of the Chinese white pear, which can serve as an important public information platform for gene expression, genomic, and functional genomic studies in P. bretschneideri and which provides comprehensive gene expression information at the transcriptional level that could facilitate understanding of the molecular mechanisms in fruit development and maturation.
2015-09-30 | GSE33388 | GEO
Project description:Transcriptional profiling of pear tree comparing a resistant/tolerant cultivar with a susceptible cultivar to the Stemphylium vesicarium fungus Rocha' pear is an economically important portuguese Pyrus communis L. cultivar very susceptible to the Stemphylium vesicarium pathogenic fungus, the brown spot agent, causing huge decrease on fruit quality and yield production. Field control of brown spot disease is based in systemic application of antifungal chemicals with high economic costs and dramatic consequences to public health and environmental pollution. Plant-pathogen interactions involve a series of events encompassing constitutive and induced plant defence responses whose dissection has been a research target for control many crop diseases. The biosynthesis of cell wall polymers and antifungal compounds appear to be an efficient physical and chemical barrier to infection.To understand the molecular responses behind defence mechanisms of resistant/tolerant and susceptible cultivars of Pyrus communis L. to the S. vesicarium fungus, cDNA microarray technology was used to identify the genes differentially expressed along a time course leaf inoculation between 'Rocha' pear cultivar (a high susceptible cultivar) and 'Ercolini' pear cultivar (a resistant/tolerant pear cultivar). This study aims to contribute with information on the molecular mechanisms involved in host-pathogen interactions responsible for pear tree brown spot disease and resistance to Stemphylium vesicarium. Experimental condition: 'Ercolini' vs 'Rocha' (each experiment including 5 plants from each cultivar). 3 time-points: water-inoculation (T0h), 6 hours after inoculation with S. vesicarium (T6h) and 24 hours after inoculation with S. vesicarium. Biological replicates: 3 in each time-point. One replicate per array.
2011-07-02 | E-GEOD-30353 | biostudies-arrayexpress
Project description:Purpose: The goals of this study was to obtain transcriptome data from five developmental stages of adventitious roots of Pyrus ussuriensis Maxim using transcriptome analysis (RNA-Seq) and qRT-PCR analysis. Mathods: The mRNA profiles of the adventitious root development of Pyrus ussuriensis on day 0, day 3, day 6, day 9, and day 12 were examined by deep sequencing, in triplicate, using Illumina HiSeq 2000. Ultra™ RNA LibraryPrep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and indexcodes were added to attribute sequences to each sample. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: The transcriptome regulation analysis of the Pyrus ussuriensis adventitious root formation was performed on this study. And a total of 19,470 DEGs (Differentially Expressed Gene), which were mainly enriched in hormone synthesis and signaling pathways, energy metabolism, synthesis and metabolism of secondary products, were detected. the key regulatory genes of adventitious root formation were screened, mainly including the gene family WOX, LBD and SRS. Auxin, plays a key role in the induction and development of root primordium, its signal transduction pathway-related genes were up-regulated during the induction period of root primordium, and down-regulated during the development of root primordia. Carotenoids is the precursor substance of abscisic acid synthetize. And for the reasons that the genes of carotenoid synthesis and signal transduction pathway of abscisic acid were down-regulated during the period of stable development and the root primordium induction, and up-regulated during the period of root primordium development of adventitious root, it was supposed that abscisic acid was a control substance, that regulated the metabolic network of development of adventitious roots. Conclusions: Our results provide a comprehensive high-resolution characterization of gene expression profiles during the pear root transition process.A number of DEGs were detected from the root primordium to adventitious root growth stages, and these belonged to hormone metabolism pathways.These results provide a valuable resource for studies in other closely related species with similar agricultural and productive value. The differentially expressed genes dataset will also provide useful candidate genes for functional analysis of pear rooting.
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Project description:Transcriptional profiling of pear tree comparing a resistant/tolerant cultivar with a susceptible cultivar to the Stemphylium vesicarium fungus Rocha' pear is an economically important portuguese Pyrus communis L. cultivar very susceptible to the Stemphylium vesicarium pathogenic fungus, the brown spot agent, causing huge decrease on fruit quality and yield production. Field control of brown spot disease is based in systemic application of antifungal chemicals with high economic costs and dramatic consequences to public health and environmental pollution. Plant-pathogen interactions involve a series of events encompassing constitutive and induced plant defence responses whose dissection has been a research target for control many crop diseases. The biosynthesis of cell wall polymers and antifungal compounds appear to be an efficient physical and chemical barrier to infection.To understand the molecular responses behind defence mechanisms of resistant/tolerant and susceptible cultivars of Pyrus communis L. to the S. vesicarium fungus, cDNA microarray technology was used to identify the genes differentially expressed along a time course leaf inoculation between 'Rocha' pear cultivar (a high susceptible cultivar) and 'Ercolini' pear cultivar (a resistant/tolerant pear cultivar). This study aims to contribute with information on the molecular mechanisms involved in host-pathogen interactions responsible for pear tree brown spot disease and resistance to Stemphylium vesicarium.
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Project description:We carried out the transcriptome analysis to identify the key genes involved in pear fruit semi-russet formation, by comparing the CK (russet) and bagging treated (green) ‘Cuiguan’ pear fruit skin 95 DAFB.
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Project description:Watercore is a physiological disorder develops in the Japanese pear fruit showing a watery translucent area in the flesh while on the tree and lead to the loss of commercial value. The sustainability to watercore is one of the most important characterization to be studied it the breeding of the Japanese pear. However, even in susceptible cultivars like ‘Hosui’, the degree of watercore development is significantly different from year to year, this makes it difficult to analyze the characteristic phenomena prior to watercore development. We’d obtained two reproducible sib strains, that is, susceptible strains developed severe watercore in all of the fruit every year while no watercore was found in the non-sustainable ones even when they were overmatured. They are originated from ‘Hosui’ x ‘Hogetsu’ and ‘Akiakari’ x ‘Taihaku’. In order to search the genes related to watercore, we used these susceptible and non-susceptible F1 sib strain pairs. By using pear custom microarray, the genes that differed in expression level prior to watercore development were extracted. The sugar-metabolism, hormone, and cell wall related genes were identified in the 105 differentially expressed genes. Some of them showed different expression levels only in the immature stages prior to watercore development.
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