Nutrition metabolism plays an important role in the alternate bearing of the olive tree (Olea europaea L.)
Ontology highlight
ABSTRACT:
ORGANISM(S): Olea europaea
SUBMITTER: mine turktas
PROVIDER: E-GEOD-42950 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We aimed to identify miRNA regulated by alternate bearing in O. europaea. For this purpose, six olive (Olea europaea L. )(Ayvalık variety) small RNA libraries were constructed from fruits (ripe and unripe) and leaves ("on-year" and "off-year" mature -leaven in November and juvenile - leaven in July plants) and sequenced by high-throughput Illumina sequencing. Bioinformatics analyses of 93,526,915 reads identified 135 conserved miRNA, belonging to 22 miRNA families in olive tree. In addition, 38 novel miRNA were discovered in the datasets. Expression of olive tree miRNA varied greatly among the six libraries, indicating contribution of diverse miRNA in balancing between reproductive and vegetative phases. The differential expression of miRNA was evaluated on the basis of the developmental phase of the samples. Sequences of six olive miRNAs (Olea europaea L. )(Ayvalık variety) plants (ripe and unripe fruits, leaves of mature and juvenile plants of both "on-year" and "off-year") were generated by Illumina sequencing
2012-12-18 | E-GEOD-42978 | biostudies-arrayexpress
Project description:We aimed to identify miRNA regulated by alternate bearing in O. europaea. For this purpose, six olive (Olea europaea L. )(Ayvalık variety) small RNA libraries were constructed from fruits (ripe and unripe) and leaves ("on-year" and "off-year" mature -leaven in November and juvenile - leaven in July plants) and sequenced by high-throughput Illumina sequencing. Bioinformatics analyses of 93,526,915 reads identified 135 conserved miRNA, belonging to 22 miRNA families in olive tree. In addition, 38 novel miRNA were discovered in the datasets. Expression of olive tree miRNA varied greatly among the six libraries, indicating contribution of diverse miRNA in balancing between reproductive and vegetative phases. The differential expression of miRNA was evaluated on the basis of the developmental phase of the samples.
2012-12-18 | GSE42978 | GEO
Project description:Vegetative phase change is the developmental transition from the juvenile phase to the adult phase during which a plant becomes competent for sexual reproduction. Gain of ability to flower is often accompanied by changes in patterns of differentiation in newly forming vegetative organs. In maize, juvenile leaves differ from adult leaves in morphology, anatomy, and cell wall composition. Whereas the normal sequence of juvenile followed by adult is repeated with every sexual generation, this sequence can be altered in maize by the isolation and culture of the shoot apex from an adult phase plant; an “adult” meristem so treated reverts to forming juvenile vegetative organs. To investigate the molecular differences between the juvenile and adult phases in maize comparisons among two juvenile samples, leaf 4 and culture-derived leaf 3 or 4, and an adult sample (leaf 9) were made using cDNA microarrays. All samples were leaf primordia at plastochron 6. A gene was scored as “phase specific” if it was up- (or down-) regulated in both juvenile samples compared to the adult sample with at least a twofold-change in gene expression at P-value less than or equal to 0.005. Some 221 ESTs up-regulated in juvenile and 28 ESTs up-regulated in adult were identified. Altered patterns of expression of selected ESTs in the phase change mutants Tp2, d1 and gl15 further confirmed these genes as being phase-specific and allowed us to position these genes in the known genetic hierarchy regulating phase change. Keywords: Transcript profiling among seed-derived juvenile leaf 4 and adult leaf 9 and culture-rejuvenated leaf 3 or 4 in maize
2008-09-01 | GSE9430 | GEO
Project description:Vegetative phase change is the developmental transition from the juvenile phase to the adult phase during which a plant becomes competent for sexual reproduction. Gain of ability to flower is often accompanied by changes in patterns of differentiation in newly forming vegetative organs. In maize, juvenile leaves differ from adult leaves in morphology, anatomy, and cell wall composition. Whereas the normal sequence of juvenile followed by adult is repeated with every sexual generation, this sequence can be altered in maize by the isolation and culture of the shoot apex from an adult phase plant; an âadultâ meristem so treated reverts to forming juvenile vegetative organs. To investigate the molecular differences between the juvenile and adult phases in maize comparisons among two juvenile samples, leaf 4 and culture-derived leaf 3 or 4, and an adult sample (leaf 9) were made using cDNA microarrays. All samples were leaf primordia at plastochron 6. A gene was scored as âphase specificâ if it was up- (or down-) regulated in both juvenile samples compared to the adult sample with at least a twofold-change in gene expression at P-value less than or equal to 0.005. Some 221 ESTs up-regulated in juvenile and 28 ESTs up-regulated in adult were identified. Altered patterns of expression of selected ESTs in the phase change mutants Tp2, d1 and gl15 further confirmed these genes as being phase-specific and allowed us to position these genes in the known genetic hierarchy regulating phase change. Keywords: Transcript profiling among seed-derived juvenile leaf 4 and adult leaf 9 and culture-rejuvenated leaf 3 or 4 in maize To identify juvenile or adult specific ESTs, total RNA from leaf primordia at plastochron 6 (P6) was isolated from leaves 4 (L4) and 9 (L9) from seed-derived plants and leaf 3 or 4 (RL3/4) from culture-derived plants. For each of six biological replications, each of the three pairwise comparisons of P6-staged leaf primordia from L4, L9 and RL3/4 was made on one slide. With six biological replications and three slides per replication (L4 vs. L9, L9 vs. RL3/4, RL3/4 vs. L4), this replicated loop design used a total of 18 slides. To ensure dye balance, each of the 18 target samples was measured once with Cy3 labeling and once with Cy5 labeling.
2010-06-20 | E-GEOD-9430 | biostudies-arrayexpress
Project description:Buds were collected at equivalent branch positions and always at the same time of the day. Samples corresponding to May (MAY), June (JUN), July (JUL), September (SEP), November (NOV), January (JAN), March (MAR) and April (APR) buds were analyzed. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Jose Diaz-Riquelme. The equivalent experiment is VV36 at PLEXdb.]
2012-11-17 | GSE42345 | GEO
Project description:Using a custom microarray platform, we examined expression of 366 genes in leaf, two peel tissues, juice sac, and whole fruit during various developmental stages of Washington Navel orange fruit (Citrus sinensis L. Osbeck). 366 genes were chosen from Citrus EST libraries by in-silico analysis method. Keywords: time course and tissue comparison Study to compare gene expression between peel layers and over time as fruit matured. Samples taken from leaf tissue, whole fruit at 24 and 38 days after full bloom (DAFB), and from albedo and flavedo layers of the peel at 80 and 165 DAFB, and flavedo from mature fruit at 220 DAFB. In all cases except one, there were three technical replicates hybridized for each Sample simultaneously.
2010-05-26 | E-GEOD-10731 | biostudies-arrayexpress
Project description:Autotetraploid carries several phenotypic changes with larger leaves and fruit compared to diploid. To analysis of phenotypic changes in mulberry autotetraploids on the transcriptome, we performed RNA-Seq analyses on mulberry leaf samples of diploid and autotetraploids using Illumina HiSEq 2000.
2017-02-09 | GSE70428 | GEO
Project description:We studied the changes that occur in gene transcription during seasonal senescence in Populus trichocarpa pioneer leaves and fine roots. Plant senescence is a strictly regulated physiological process that allows relocating of valuable nutrients from senescent tissues before death. It might be induced by internal or external factors and among them, phytohormones play an undoubtedly significant role. Senescence was extensively studied in leaves, but the aging of other ephemeral organs, located underground, and its drivers are still poorly understood. We focused on collective results to fill in the knowledge gap about senescence of fine, absorptive roots and leaves in order to check if there are universal mechanisms involved during plant organ senescence. Transcriptional profiling was conducted with the use of microarrays to identify genes involved in developmental PCD. Samples were collected three times during a growth season. The first collection was considered as a control and was collected in early summer (July 7–15) when leaves and the root system were fully developed and functional. The second group of leaf and root samples were harvested in early autumn (October 1–7) when chlorophyll levels in leaves had decreased by approximately 40% and when fine roots had changed in color from white to brown. The third group of samples were harvested in the middle of autumn (November 2–9) when chlorophyll levels in leaves decreased by approximately 65% and fine roots were dark brown or black color. Our results reveal the important role of phytohormones in regulating the senescence of both studied organs. The transcriptomic analyses showed significant changes in gene expression that are associated with phytohormones, especially with ABA and jasmonates. We conclude that phytohormonal regulation of senescence in roots and leaves is organ-specific. In roots, phytohormones are involved indirectly in regulation of senescence by increasing tolerance for cold or resistance for pathogens, whereas such correlation was not observed in leaves.
2020-03-07 | GSE143559 | GEO
Project description:In this study, we have elucidated the DNA methylation patterns in different organs of a cultivated chickpea genotype ICC 4958 (leaf, root, flower and young pod) and leaf of wild chickpea PI 489777 using bisulphite sequencing. Approximately 108 million read pairs were analyzed per sample. The extent of methylation along-with the context and genomic location of methylated Cs was identified. Further processing was performed to identify the differentially methylated regions among samples with leaves of ICC 4958 as the reference sample. The high resolution methylome maps of different organs and differentially methylated regions will serve as reference for understanding the epigenetic regulation in chickpea.
2018-07-15 | GSE103575 | GEO