Project description:The hypersensitive response (HR) system of Chenopodium spp. confers broad-spectrum virus resistance. However, scant knowledge exists at the genomic level for Chenopodium, thus impeding the advanced molecular research of this attractive feature. Hence we took advantage of RNA-seq to survey the foliar transcriptome of C. amaranticolor, one Chenopodium species being widely used as laboratory indicator for pathogenic viruses, in order to facilitate the characterization of the HR-type of virus resistance. In a single run, we obtained 39,868,984 reads with 3,588,208,560 bp, which were assembled into 112,453 unigenes (3,848 clusters and 108,605 singletons). BlastX search against the NCBI NR database identified 62,482 sequences with a cut-off E-value above 10-5. Assembled sequences were annotated with gene descriptions, GO, COG and KEGG terms. A dataset containing 738 resistance gene analogs and sequences represent 6 key signaling proteins within the R proteins-directed signaling pathway was generated. Additionally, using RNA-Seq digital gene expression analysis, we investigated the gene expression profiles over the stage of HR induced by Tobacco mosaic virus and Cucumber mosaic virus in C. amaranticolor leaves, and identified numerous candidate genes specifically or commonly regulated by these two distinct viruses at early and late stages of the HR. Specifically, the dynamic changes of the differently expressed genes enriched in the pathway of plant-pathogen interaction were analyzed. To our knowledge, this is the first study to elucidate the genetic makeup of Chenopodium spp., providing a starting-point for future functional genomics studies on Chenopodium.
Project description:The hypersensitive response (HR) system of Chenopodium spp. confers broad-spectrum virus resistance. However, scant knowledge exists at the genomic level for Chenopodium, thus impeding the advanced molecular research of this attractive feature. Hence we took advantage of RNA-seq to survey the foliar transcriptome of C. amaranticolor, one Chenopodium species being widely used as laboratory indicator for pathogenic viruses, in order to facilitate the characterization of the HR-type of virus resistance. In a single run, we obtained 39,868,984 reads with 3,588,208,560 bp, which were assembled into 112,453 unigenes (3,848 clusters and 108,605 singletons). BlastX search against the NCBI NR database identified 62,482 sequences with a cut-off E-value above 10-5. Assembled sequences were annotated with gene descriptions, GO, COG and KEGG terms. A dataset containing 738 resistance gene analogs and sequences represent 6 key signaling proteins within the R proteins-directed signaling pathway was generated. Additionally, using RNA-Seq digital gene expression analysis, we investigated the gene expression profiles over the stage of HR induced by Tobacco mosaic virus and Cucumber mosaic virus in C. amaranticolor leaves, and identified numerous candidate genes specifically or commonly regulated by these two distinct viruses at early and late stages of the HR. Specifically, the dynamic changes of the differently expressed genes enriched in the pathway of plant-pathogen interaction were analyzed. To our knowledge, this is the first study to elucidate the genetic makeup of Chenopodium spp., providing a starting-point for future functional genomics studies on Chenopodium. Analysis of the differentially expressed genes over the stage of hypersensative response induced by viruses in C. amaranticolor
Project description:We generated 70.9 Gb of high-quality sequencing data (~7.88 Gb per sample) and catalogued the expression profiles of 54,238 annotated Chenopodium quinoa genes in each sample. These genes have known or potential roles in the roots, stems, and leaves of quinoa. Therefore, we are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms.
2022-03-03 | GSE156523 | GEO
Project description:Whole-genome assembly of huauzontle (Chenopodium berlandieri subsp. nuttaliae) and its relationship to Andean quinoa
Project description:Chenopodium quinoa, a pseudo-cereal and facultative halophyte, is a species of great economic potential. When exposed to saline soil, this salt-tolerant crop takes up sodium and chloride ions and sequesters large NaCl quantities in epidermal bladders cells (EBC). We have analyzed the Quinoa EBC transcriptome by RNA sequencing and elucidated the molecular identity and function of key ion transporters. Thereby we analyzed transcripts differentially expressed between EBCs and total leaves under control conditions.
Project description:Lipomyces genome scale model based on the Lipomyces starkeyi NRRL-11557 genome.
Published in:
Genome-Scale Model Development and Genomic Sequencing of the Oleaginous Clade Lipomyces
Frontiers in Bioengineering and Biotechnology
Industrial Biotechnology
Volume 12 - 2024 | doi: 10.3389/fbioe.2024.1356551
Project description:Analysis od the transcriptome changes of Vitis riparia x Vitis berlandieri culture cells in response to the modified beta-cyclodextrin, DIMEB, a resveratrol inducer. <br>Cell cultures were treated for 6 hours with 50 mM DIMEB (and without, as reference) and then used for Affymetrix Vitis GeneChip v1.0 hybridization. The experiment has been performed in biological triplicates.