Transcriptome analysis of avocado embryogenic cultures selected for resistance to Rosellinia necatrix exudates
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ABSTRACT:
ORGANISM(S): Persea americana
PROVIDER: GSE228295 | GEO | 2023/09/01
REPOSITORIES: GEO
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Project description:Transcriptome analysis of avocado embryogenic cultures selected for resistance to Rosellinia necatrix exudates
| PRJNA949214 | ENA
Project description:To understand the molecular foundation of the SE induction and development in avocado, we compared by proteomics approach, the embryogenic (EC) and non-embryogenic (NEC) cultures of two avocado varieties. Although Criollo and Hass EC exhibits particularities in the proteome and metabolome profile, in general, we observed a more active phenylpropanoid pathway in EC than NEC. Our proteomic pipeline consisted of a peptide labeled with TMT6plex and synchronous precursor selection (SPS) MS3
2020-08-14 | PXD019705 | Pride
Project description:White root rot disease caused by Rosellinia necatrix is one of the most important pathogens affecting avocado productivity in temperate, tropical and subtropical climates. Control of this disease is complex and nowadays, lies in the use of physical and chemical methods, although none have proven to be fully effective. Detailed understanding of the molecular mechanisms underlying white root rot disease has the potential of aiding future developments in disease resistance and management. In this regard, this study used RNAseq technology to compare the transcriptomic profiles of R. necatrix during infection of susceptible avocado `Dusa´ roots with that obtained from the fungus cultured in rich medium. The transcriptomes from three biological replicates of R. necatrix colonizing avocado roots (RC) and R. necatrix growing on potato dextrose agar media (PDA) were obtained using Illumina sequencing. A total of 12,104 transcripts were obtained, among which 1937 were differentially expressed genes (DEG), 137 exclusively expressed in RC and 160 and PDA. Interestingly genes involved in the production of fungal toxins, detoxification of toxic compounds, hormone biosynthesis, gene silencing and plant cell wall degradation were overexpressed during the infection process. In addition, 23 out of the 137 contigs, only expressed during R. necatrix growth on avocado roots, were predicted as candidate effector proteins (CEP) by the CSIRO tool with a probability above 60%. The PHI (Pathogen Host Interaction) database revealed that 11 R. necatrix CEP were previously annotated as effectors genes proven experimentally via pathogen-host interaction.
2020-01-08 | GSE134243 | GEO
Project description:Background: Rosellinia necatrix is the causal agent of avocado white root rot (WRR). Control of this soil-borne disease is difficult and tolerant rootstocks may represent an effective method to lessen its impact. To date, no studies on molecular mechanisms regulating the avocado plant response towards this pathogen have been undertaken. To shed light onto the mechanisms underpinning disease susceptibility and tolerance, molecular analysis of the gene's response of two contrasting-disease-reaction avocado rootstocks was assessed. Results: Gene expression profiles against R. necatrix were assessed in the susceptible 'Dusa' and the tolerant selection BG83 avocado genotypes by micro-array analysis. In 'Dusa', the early response is mainly related to redox processes and cell-wall degradation activities, all becoming more remarkable after disease progression affected photosynthetic capacity; whereas, tolerance to R. necatrix in BG83 relies on the induction of protease inhibitors and their negative regulators, as well as salt and osmotic stress related genes besides oxido-reduction processes. We identified three protease inhibitors, glu protease, trypsin and endopeptidase inhibitors, highly overexpressed in the tolerant genotype, when compared to susceptible 'Dusa', after infection with R. necatrix, reaching fold change values of 44, 34 and 16 respectively. Conclusions: The contrasting results between 'Dusa' and BG83 give new insights into the different mechanisms involved in the avocado tolerance to P. cinnamomi and R. necatrix, which are consistent with their biotrophic and necrotrophic lifestyles, respectively. The differential induction of genes involved in salt and osmotic stress in BG83 could indicate that R. necatrix penetration into the roots is associated with osmotic effects suggesting that BG83's tolerance to R. necatrix is related to the ability to withstand osmotic imbalance. In addition, the high expression of protease inhibitors in tolerant BG83 compared to susceptible 'Dusa' after infection with the pathogen, suggests the important role that these proteins could play in the defence of avocado rootstocks against R. necatrix.
2019-02-26 | GSE119140 | GEO
Project description:The aim of this study was to evaluate the physiological response and the expression analysis of `Dusa´ avocado rootstocks subjected to two different levels of water stress, and their subsequent recovery. At the beginning of the experiment, avocado plants were divided in Control plants (watered to field capacity (Fc) throughout the experiment) and stressed plants that were subjected to controlled substrate drying-up until they reached 50% of Fc (mild-WS) and 25% of Fc (severe-WS), respectively. Afterwards, plants were fully irrigated to assess drought recovery response. A set of physiological measurement were taken at leaf and whole-plant levels to assess avocado response to each level of water stress and rewatering. Root samples were collected in mild-WS and severe-WS and gene expression analysis was carried out using a targeted cDNA avocado stress microarray containing transcripts from de novo sequencing of 'Dusa' in response to biotic and abiotic stress. Avocado gene expression profiles under different levels of water stress are discussed in order to shed light on the molecular mechanisms associated with water deprivation in Dusa avocado rootstocks.
2021-11-03 | GSE151051 | GEO
Project description:First report of Avocado sunblotch viroid (ASBVd) naturally infecting avocado (Persea americana) in Greece
| PRJEB23838 | ENA
Project description:Objectives: to characterize and to better understand differences at a protein level in embryonic and non-embryogenic tissues of embryonal masses in Douglas-fir. In Europe, Douglas-fir is a major species for reforestation with increasing demand for its wood. Harvested stems provide timber of outstanding wood quality, mechanical properties and durability. Commercial Douglas-fir plantations in France are limited by the ability to produce seed from the latest breeding developments. Somatic embryogenesis is considered a promising biotechnology for large-scale clonal propagation of forest trees, due to the high multiplication rates it can provide. Moreover, embryogenic cultures are amenable to both cryogenic storage for long-term preservation of genetic resources and genetic engineering (including genome editing) for functional characterization of genes expressed during embryogenesis. In conifers, embryogenic cultures take the form of embryonal mass made up of early differentiated cells forming immature somatic embryos that proliferate via cleavage polyembryony. In Douglas-fir embryogenic lines consisting in embryonal mass have been compared to non-embryogenic callus during their proliferation. Comparison of proteomes (free-gel proteomics) of embryonal mass vs non-embryogenic callus were performed.
2019-05-17 | PXD011176 | Pride
Project description:Somatic variation is a valuable source of trait diversity in clonally propagated crops. In grapevine, which has been clonally propagated worldwide for centuries, important phenotypes such as white berry colour are the result of genetic changes caused by transposable elements. Additionally, epiallele formation may play a role in determining geo-specific (‘terroir’) differences in grapes and thus ultimately in wine. This genomic plasticity might be co-opted for crop improvement via somatic embryogenesis, but that depends on a species-specific understanding of the epigenetic regulation of transposable element (TE) expression and silencing in these cultures. For this reason, we used whole-genome bisulphite sequencing, mRNA sequencing and small RNA sequencing to study the epigenetic status and expression of TEs in embryogenic callus, in comparison with leaf tissue.
2021-08-27 | GSE164586 | GEO
Project description:A new avocado reference genome provides insight into genome evolution and the genetic basis of important traits
| PRJNA758103 | ENA