Ontology highlight
ABSTRACT:
PROVIDER: PRJEB23106 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The vast majority of traditional almond varieties are self-incompatible and the level of variability of the species is very high, resulting in a highly heterozygosity genome. Therefore, information on the different haplotypes is particularly relevant to understand the genetic basis of trait variability in this species. However, although reference genomes for several almond varieties exist, none of them is phased and has genome information at the haplotype level. Here we present a phased assembly of genome of the almond cv. Texas. Our analysis shows that the “Texas” genome has a high degree of heterozygosity, both as SNPs, short indels, and structural variants (SV) level. Many of the SVs are due to heterozygous Transposable Element (TE) insertions, and in many cases they also contain genic sequences. In addition to the direct consequences of this genic variability on the presence/absence of genes, our results show that variants located close to genes tend to be associated with allele-specific gene expression (ASE), which highlights the importance of heterozygous SVs in almond.
2024-03-18 | GSE254853 | GEO
Project description:The cultivated almond exhibits self-incompatibility of the gametophytic type regulated by the S-locus, and expressed in pistil (S-RNase) and in pollen (SFB protein). The aim of this study is to clarify the transcription pattern of these 2 S-genes and to identify additional components of the gametophytic self-incompatibility system in almond. With this aim, A2-198 (self compatible) and ITAP-1 (self incompatible) almond selections were used: RNA-seq of pistils of these two accessions both un-pollinated and pollinated with A2-198 pollen were carried out.
2019-06-01 | E-MTAB-6164 | biostudies-arrayexpress
Project description:Plum pox virus (PPV) causes the serious sharka disease in Prunus trees. Peach [P. persica (L.) Batsch] trees are severely affected by PPV and no definitive source of genetic resistance has been identified at this moment. Previous results showed, however, that PPV-resistant ‘Garrigues’ almond [P. dulcis (Mill.) D.A. Webb] was able to transfer its resistance to ‘GF305’ peach through grafting, preventing these trees from PPV infection and reducing symptomatology and viral load in PPV-infected plants. A recent study tried to identify genes responsible for this effect by studying mRNA expression through RNAseq data in peach and almond plants, before and after grafting, and before and after PPV infection. In this work, we used the same peach and almond samples, but focused the high-throughput analyses on small RNAs (sRNAs) expression. We studied massive sequencing data and found an interesting pattern of sRNAs overexpression linked to antiviral defense genes that suggested activation of these genes followed by downregulation to basal levels. We also discovered that ‘Garrigues’ almond plants were infected by different plant viruses that were transferred to peach plants. The large amounts of viral sRNAs found in grafted peaches indicated a strong RNA silencing antiviral response and led us to postulate that these plant viruses could be collaborating by cross-protection in the observed ‘Garrigues’ effect.
2022-11-02 | GSE188935 | GEO
Project description:Almond is one of the most featured nut crops owing to its high nutritional value. However, due to three different waves of flower and fruitlet drop, fruit drop is a major concern for growers. In this study, we carried out a time-course transcriptome analysis to investigate gene expression difference between normal and abnormal fruitlet development. By de novo assembly analysis, we identified 33,577 unigenes and provided their functional annotations. In total, we identified 8,676 differentially expressed genes and observed the most apparent difference between normal and abnormal fruits at 12 and 17 day after flowering. Their biological functions were enriched in carbon metabolism, carbon fixation in photosynthetic organisms and plant hormone signal transduction. RT-qPCR validated the expression pattern of 15 representative genes, including glycosyltransferase like family 2, MYB39, IAA13, gibberellin-regulated protein 11-like and POD44, which confirmed the reliability of our transcriptome data. This study provides an insight into the association between abnormal fruit development and carbohydrate signaling from the early developmental stages and could be served as useful information for understanding the regulatory mechanism related to almond fruit drop.
2021-02-16 | GSE138034 | GEO
Project description:The application of sensors in viticulture is a fast and efficient method to monitor grapevine vegetative, yield, and quality parameters and determine spatial intra-vineyard variability. Molecular analysis at the gene expression level can further contribute to the understanding of the observed variability by elucidating how pathways contributing to different grape quality traits behave in zones diverging on any of these parameters. The intra-vineyard variability of a Cabernet Sauvignon vineyard was evaluated through a Normalized Difference Vegetation Index (NDVI) map calculated from a multispectral image and detailed ground-truthing (e.g., vegetative, yield, and berry ripening compositional parameters). The relationships between NDVI and ground measurements were explored by correlation analysis. Moreover, berries were investigated by microarray gene expression analysis performed at five time points from fruit set to full ripening. Comparison between the transcriptomes of samples taken from locations with the highest and lowest NDVI values identified 968 differentially expressed genes. Spatial variability maps of the expression level of key berry ripening genes showed consistent patterns aligned with the vineyard vigor map. These insights indicate that berries from different vigor zones present distinct molecular maturation programs and suggest that transcriptome analysis may be a valuable tool for the management of vineyard variability.
2024-02-27 | GSE254304 | GEO
Project description:Molecular variability of patient-derived colon tumor xenografts
| PRJNA449541 | ENA
Project description:Gametophytic self-incompatibility is the primary cause of low fruit set in almond. The mechanism of recognition that determines whether the gametophyte is successfully fertilized between pollen tube SCF (F-box-SSK1-Cul1-Rbx1) protein and pistil S-RNase protein during fertilization is unclear. In this study, the pistils of two almond cultivars 'Wanfeng' and 'Nonpareil' were used as the experimental materials after selfing- and nonselfing/cross-pollination, and pistils from the stamen-removed flowers were used as controls. We used fluorescence microscopy to observe the development of pollen tubes after pollination and 4-dimensional label-free quantitation (4D-LFQ) to detect the protein expression profiles of 'Wanfeng' and 'Nonpareil' pistils and in controls. The results showed that it took 24-36 h for the development of the pollen tube to 1/3 of the pistil, and a total of 7684 differentially accumulated proteins (DAPs) were identified in the pistil after pollinating 36 h, of which 7022 were quantifiable. The up- and down-regulation of the 12 differential protein expressions identified by parallel reaction monitoring (PRM) was the same as that identified by 4D-LFQ, with an average fold-change difference of 14.34%, a maximum of 31.37% and a minimum of 3.68%. Bioinformatics analysis based on the function of the differential proteins, including classification, enrichment, and clustering, identified RNA polymerases (4 DAPs), autophagy (3 DAPs), oxidative phosphorylation (3 DAPs), and homologous recombination (2 DAPs) pathways associated with the self-incompatibility process. The interaction between the serine/threonine kinase (MARK2) protein E3 ubiquitin ligase and the microtubule protein component microtubule-associated protein tau (MAPT/ACT) was found using the STRING database, which demonstrated the involvement of the MARK2 protein in the reaction of pollen tube recognition the nonself- and the self-S-RNase protein. It provides a new way to reveal the mechanism by which almond pollen tubes recognize the self and nonself S-RNase enzyme protein.
2022-02-10 | PXD029128 | Pride
Project description:Plant-based diets could be a key source of microRNAs in animals. Plant microRNAs are cross-kingdom gene expression regulators that could modulate mammalian gene expression, influencing their physiology. Therefore, it is important to identify the microRNA expression profile of plant foods in order to identify potential target genes and biological functions in the mammalian host. Next-generation sequencing was applied to identify microRNAs in RNA samples derived from nuts (walnut and almond), vegetables (spinach) and fruits (orange, apple, olive, pear, and tomato). Our data revealed that edible plant contain a large number and diverse type of microRNAs.
2023-09-05 | GSE234786 | GEO