Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1166699 | ENA |
REPOSITORIES: ENA
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Project description:Protein kinases (PKs) are involved in plant growth and stress responses, and constitute one of the largest superfamilies due to numerous gene duplications. However, limited PKs have been functionally described in pecan, an economically important nut tree. Here, the comprehensive identification, annotation and classification of the entire pecan kinome was reported. A total of 967 PK genes were identified from pecan genome, and further classified into 20 different groups and 121 subfamilies using the kinase domain sequences, which were verified by the phylogenetic analysis. The receptor-like kinase (RLK) group contained 565 members, which constituted the largest group. Gene duplication contributed to the expansion of pecan kinome, 169 duplication events including 285 PK genes were found, and Ka/Ks ratio revealed they experienced strong negative selection. GO functional analysis indicated majority PKs involved in molecular functions and biological processes. The RNA-Seq data of PK genes in pecan were further analyzed at subfamily level, and different PK subfamilies performed various expression patterns across different conditions or treatments, suggesting PK genes in pecan involved in multiple biological functions and stress responses. Taken together, this study provided insight into the expansion, evolution and function of pecan PKs. Our findings regarding expansion, expression and co-expression analyses could lay a good foundation for future research to understand the roles of pecan PKs, and find the key candidate genes more efficiently.
2021-07-05 | GSE179336 | GEO
Project description:Background Many environmental and lifestyle factors have been implicated in the decline of sperm quality, with diet being one of the most plausible factors identified in recent years. Moreover, several studies have reported a close association between the alteration of specific sperm DNA methylation signatures and semen quality. Objectives To evaluate the effect of tree nuts consumption on sperm DNA methylation patterns in healthy individuals reporting eating a Western‐style diet. Material and Methods This is a post‐hoc analysis conducted in a subset of participants (healthy, non‐smoking, and young) from the FERTINUTS 14‐wk randomized‐controlled, parallel‐trial, recruited between December 2015 and February 2017. The participants included in the current study (n=72) were randomly selected in a proportion 2:1 from the original FERTINUTS trial between the 98 participants that completed the entire dietary intervention (nut group, n=48; control group, n=24). Sperm DNA methylation patterns were examined at baseline and after 14 weeks in 48 individuals consuming 60 g/d of mixed nuts (nuts group) and in 24 individuals following the usual Western‐style diet avoiding consumption of nuts (control group). Results Over the course of the trial, no significant changes in global methylation were observed between groups. However, in the nuts group, we identified 36 genomic regions that were significantly differentially methylated between the baseline and the end of the trial and 97.2% of the regions displayed hypermethylation. We identified no such change in the control group over the same period of time. We also utilized the recently developed germ line age calculator to determine if nut consumption resulted in alterations to the epigenetic age of cells and no significant differences were found. Discussion and Conclusion Adding nuts to a regular Western‐style diet subtly impacts sperm DNA methylation in specific regions, demonstrating that there are some sperm epigenome regions that could respond to diet.
2020-09-24 | GSE140004 | GEO
Project description:To investigate the mechanisms of cell competition, we analysed the molecular differences between wild type and mild CncC (Nrf2) over-expressing causing the loser phenotype in Drosophila wing discs. We then compared the genes differentially expressed in these conditions to our previously identified ‘loser signature’ which reveal a significant overlap. From this later comparison, we raised a list of 121 up-regulated genes to conduct a cell competition screen using PECAn (Pipeline for Enhanced Clonal Analysis) for automating analysis of mosaic experiment.
2023-04-06 | GSE181165 | GEO
Project description:Genome wide DNA methylation from peripheral white blood cells (PWBCs) from individuals enrolled in PREDIMED trial. The objective was to analyse whether an intervention with two Mediterranean diets, one rich in extra-virgin olive oil (MedDiet+EVOO) and the other one in nuts (MedDiet+nuts), was influencing the methylation status of PWBC genes. A group with a low-fat diet was considered as control. The Illumina Infinium 420k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in these samples. Samples included 12 MedDiet+EVOO, 12 MedDiet+nuts and 12 low-fat control group, at baseline (n=36) and after five years of intervention (n=36).
2017-11-23 | GSE107205 | GEO