Malus hupehensis cultivar:MSU_CC4869_01
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ABSTRACT:
PROVIDER: PRJNA267600 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Malus hupehensis Transcriptome or Gene expression
| PRJNA692062 | ENA
Project description:Malus hupehensis Transcriptome or Gene expression
| PRJNA263644 | ENA
Project description:Malus hupehensis Transcriptome or Gene expression
| PRJNA263561 | ENA
Project description:Malus hupehensis cultivar:MSU_CC4869_01 Genome sequencing
| PRJNA267598 | ENA
Project description:Epigenomic regulatory mechanism in vegetative phase transition of Malus hupehensis
| PRJNA623166 | ENA
Project description:Background: A long juvenile period between germination and flowering is a common characteristic among fruit trees, including Malus hupehensis (Pamp.) Rehd., which is an apple rootstock widely used in China. microRNAs (miRNAs) play an important role in the regulation of phase transition and reproductive growth processes. Results: M. hupehensis RNA libraries, one adult and one juvenile phase, were constructed using tree leaves and underwent high-throughput sequencing. We identified 42 known miRNA families and 172 novel miRNAs. We also identified 127 targets for 25 known miRNA families and 168 targets for 35 unique novel miRNAs using degradome sequencing. The identified miRNA targets were categorized into 58 biological processes, and the 123 targets of known miRNAs were associated with phase transition processes. The KEGG analysis revealed that these targets were involved in starch and sucrose metabolism, and plant hormone signal transduction. Expression profiling of miRNAs and their targets indicated multiple regulatory functions in the phase transition. The higher expression level of mdm-miR156 and lower expression level of mdm-miR172 in the juvenile phase leaves implied that these two small miRNAs regulated the phase transition. mdm-miR160 and miRNA393, which regulate genes involved in auxin signal transduction, could also be involved in controlling this process. The identification of known and novel miRNAs and their targets provides new information on this regulatory process in M. hupehensis, which will contribute to the understanding of miRNA functions during growth, phase transition and reproduction in woody fruit trees. Conclusions: A comprehensive study on M. hupehensis miRNAs related to the juvenile to adult phase transition was performed. The combination of sRNA and degradome sequencing can be used to better illustrate the profiling of hormone-regulated miRNAs and miRNA targets involving complex regulatory networks, which will contribute to the understanding of miRNA functions during growth, phase transition and reproductive growth in perennial woody fruit trees.
2015-10-10 | GSE63373 | GEO
Project description:Fritillaria hupehensis isolate:Fritillaria | cultivar:hupehensis Genome sequencing
| PRJNA755878 | ENA
Project description:Genome-wide DNA methylation analysis between long-term in vitro shoot culture and acclimatized apple plants DNA methylation is a process of epigenetic modification that can alter the functionality of a genome. Using whole-genome bisulfite sequencing, this study quantify the level of DNA methylation in the epigenomes of two diploid apple (Malus x domestica) scion cultivars ('McIntosh' and 'Húsvéti rozmaring') derived from three environmental conditions: in vivo mother plants in an orchard, in vitro culture, and acclimatized in vitro plants. The global DNA methylation levels were not dependent on the source of plant material. Significant differences in DNA methylation were identified in 586 out of 45,116 genes, including promoter and coding sequences, and classified as differentially methylated genes (DMGs). Differential methylation was visualised by an MA plot and functional genomic maps were established for biological processes, molecular functions and cellular components. Considering the DMGs, in vitro tissue culture resulted in the highest level of methylation, which decreased after acclimatization and tended to be similar to that in the mother tree. Methylation patterns of the two scions differed, indicating cultivar-specific epigenetic regulation of gene expression during adaptation to various environments. After selecting genes that displayed differences larger than ±10% in CpG and CHG contexts, or larger than ±1.35% in the CHH context from among the DMGs, they were annotated in Blast2GO v5.1.12 for Gene Ontology. These DNA methylation results suggest that epigenetic changes may contribute to the adaptation of apple to environmental changes by modifying gene expression.
2019-07-25 | GSE116995 | GEO
Project description:Malus hybrid cultivar Transcriptome or Gene expression
| PRJNA476432 | ENA