Project description:Cucurbita pepo is high susceptible to Zucchini yellow mosaic virus (ZYMV) and the resistance found in several wild species does not provide complete or broad-spectrum resistance. In this study, a source of tolerance introgressed in C. pepo (381e) from C. moschata, in True French (TF) background, was investigated 12 days after inoculation (DPI) at transcriptomic and genomic levels. A comparative RNA-seq experiment, allowed to evaluate more than 33,000 expressed transcripts and to identify 146 differentially expressed genes (DEGs) in 381e, mainly involved in photosynthesis, transcription, cytoskeleton organization and callose synthesis. By contrast, the susceptible line True French triggered oxidative processes related to response to biotic stimulus and two synaptotagmin (SYTA) genes, key regulators of plant virus intercellular movement. Finally, transcripts mapping allowed the identification of two regions rich in SNPs (Single Nucleotide Polymorphisms) on linkage group 1 and linkage group 8, putatively introgressed from C. moschata, containing a putative disease resistance protein (CNL gene) exclusively expressed in 381e. In conclusion, 381e transcriptome analysis confirmed a globally improved plant fitness by reducing the effect of viral infection and showed the activation of genes putatively involved in tolerance to ZYMV. Our work provides new insight into plant virus recovery process to ZYMV.

2020-10-20 | GSE159530 | GEO

Aromia bungii

Project description:Aromia bungii overview

| PRJNA862236 | ENA

Aromia bungii

Project description:Aromia bungii Genome sequencing

| PRJNA861961 | ENA

tfGorAlbo

Project description:Gordius_albopunctatus, genomic and transcriptomic data

| PRJEB78907 | ENA

Tropheryma whipplei proteome - Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme

Project description:Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme. Testing systematic exchanges of nucleotides over long stretches produces inversed RNA pieces (here named “swinger” RNA) differing from their template DNA. These may explain some trashed data. Here analyses of genomic, transcriptomic and proteomic data of the pathogenic Tropheryma whipplei according to canonical genomic, transcriptomic and translational 'rules' resulted in trashing 58.9% of DNA, 37.7% RNA and about 85% of mass spectra (corresponding to peptides). In the trash, we found numerous DNA/RNA fragments compatible with “swinger” polymerization. Genomic sequences covered by «swinger» DNA and RNA are 3X more frequent than expected by chance and explained 12.4 and 20.8% of the rejected DNA and RNA sequences, respectively. As for peptides, several match with “swinger” RNAs, including some chimera, translated from both regular, and «swinger» transcripts, notably for ribosomal RNAs. Congruence of DNA, RNA and peptides resulting from the same swinging process suggest that systematic nucleotide exchanges increase coding potential, and may add to evolutionary diversification of bacterial populations.

2017-12-18 | PXD006238 | Pride

Cairina moschata

Project description:Cairina moschata Raw sequence reads of Lung TRANSCRIPTOMIC

| PRJNA431971 | ENA

Cairina moschata

Project description:Cairina moschata Raw sequence reads of Liver TRANSCRIPTOMIC

| PRJNA431969 | ENA