GEO DataSets

(Submitter supplied) Ectomycorrhizal (ECM) fungi are crucial for tree nitrogen (N) nutrition, however, mechanisms governing N transfer from fungal tissues to the host plant are not well understood. ECM fungal isolates, even from the same species, vary considerably in their ability to support tree N nutrition resulting in a range of often unpredictable symbiotic outcomes. In this study, we used isotopic labelling to quantify the transfer of N to the plant host by isolates from the ECM genus Pisolithus known to have significant variability in colonisation and transfer of nutrients to a host. more...

Organism:

Eucalyptus grandis; Pisolithus microcarpus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33522 GPL33523 GPL33524

43 Samples

Download data: TXT

(Submitter supplied) Members of the fungal genus Armillaria are necrotrophic pathogens with efficient plant biomass-degrading strategies. Armillaria species are some of the largest terrestrial organisms on Earth that cause tremendous losses in diverse ecosystems. Despite their global importance, how Armillaria evolved pathogenicity in a clade of dominantly non-pathogenic wood-degraders (Agaricales) remains elusive. Here, using new genomic data, we show that Armillaria species, in addition to widespread gene duplications and de novo gene origins, acquired at least 1,025 genes via 124 horizontal gene transfer (HGT) events, primarily from Ascomycota donors. more...

Organism:

Eucalyptus grandis; Armillaria luteobubalina

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33426 GPL20030 GPL33427

28 Samples

Download data: TXT

(Submitter supplied) The plant xylem tissue is responsible for water transportation, mechanical support and lateral growth, and can be utilized as wood. The seed plant xylem has a radial system composed of ray parenchyma cells and an axial system of fusiform cells, including tracheids in gymnosperms and vessel elements and libriform fibers in angiosperms. Little is known about the developmental programs and evolutionary relationships of these xylem cell types. more...

Organism:

Eucalyptus grandis; Liriodendron chinense; Populus trichocarpa; Trochodendron aralioides

Type:

Expression profiling by high throughput sequencing

6 related Platforms

48 Samples

Download data: CSV, H5, TAR, TXT

(Submitter supplied) Several reports have investigated the effects of future climate conditions on photosynthesis and biomass production in woody plants but none combining temperature and atmospheric CO2 concentration. We used grow chambers to expose Eucalyptus grandis and E. globulus seedlings to three temperature regimes (10-12°C - low temperature, 20-22°C - control temperature and 33-35°C - high temperature) combined with two CO2 concentration (390 ppm – normal and 700 ppm - high). more...

Organism:

Eucalyptus globulus; Eucalyptus grandis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29683 GPL20030

36 Samples

Download data: TXT

(Submitter supplied) Illumina HiSeq technology was used to generate mRNA profiles from Pisolithus microcarpus Si9, MW3, R4 or R10 ectomycorrhizal root tips compared to their respective free-living mycelium.

Organism:

Eucalyptus grandis; Pisolithus microcarpus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19282 GPL28947

23 Samples

Download data: TXT

(Submitter supplied) DNA methylation is a chemical modification of DNA that can be faithfully inherited across generations in flowering plant genomes. Failure to properly maintain DNA methylation can lead to epigenetic variation and transposon reactivation. Plant genomes are dynamic, spanning large ranges in size and there is an interplay between the genome and epigenome in shaping one another. To understand the variation in genomic patterning of DNA methylation between species, we compared methylomes of numerous diverse angiosperm species. more...

Organism:

Populus trichocarpa; Erythranthe guttata; Eutrema salsugineum; Beta vulgaris; Panicum hallii; Cannabis sativa; Cucumis sativus; Prunus persica; Manihot esculenta; Panicum virgatum; Fragaria vesca; Eucalyptus grandis; Medicago truncatula; Setaria viridis; Sorghum bicolor; Vitis vinifera; Theobroma cacao; Brassica rapa; Malus domestica; Ricinus communis; Brachypodium distachyon; Lotus japonicus; Citrus x clementina

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

30 related Platforms

34 Samples

Download data: TSV

(Submitter supplied) The study was conducted to identify differentially expressed polyethylene glycol (PEG) induced water stress responsive genes in E. grandis. Forty day old rooted cutting of E. grandis was subjected to -0.225 MPa PEG treatment and total RNA was isolated from leaves of water treated control and PEG treated samples after three hours of treatment. The differential expression of water stress responsive genes was analyzed using microarray technique.

Organism:

Eucalyptus; Eucalyptus grandis

Type:

Expression profiling by array

Platform:

GPL20919

3 Samples

Download data: TXT

(Submitter supplied) Rooting capability is one of the economically traits lost during the juvenile to mature phase change in woody plants. A comprehensive microarray analysis was performed to compare the profiles of gene expression in juvenile and mature cuttings from E. grandis, either auxin treated or untreated on days, 0, 1, 3, 6, 9 and 12 post excision. At the end of the experiment, root primordia were observed only in auxin treated juvenile cuttings. more...

Organism:

Eucalyptus grandis

Type:

Expression profiling by array

Platform:

GPL18659

64 Samples

Download data

(Submitter supplied) Histone modifications play an integral role in plant development, but have been poorly studied in woody plants. Investigating chromatin organization in wood-forming tissue and its role in regulating gene expression allows us to understand the mechanisms underlying cellular differentiation during xylogenesis (wood formation) and identify novel functional regions in plant genomes. However, woody tissue poses unique challenges for using high-throughput chromatin immunoprecipitation (ChIP) techniques for studying genome-wide histone modifications in vivo. more...

Organism:

Eucalyptus grandis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20030

5 Samples

Download data: BEDGRAPH

(Submitter supplied) Background: Eucalyptus species and interspecific hybrids exhibit valuable growth and wood properties that make them a highly desirable commodity. However, these trees are challenged by a wide array of biotic stresses during their lifetimes. The Eucalyptus grandis reference genome sequence provides a resource to study pest and pathogen defence mechanisms in long-lived woody plants. E. grandis trees are generally susceptible to Chrysoporthe austroafricana, a causal agent of stem cankers on eucalypts. more...

Organism:

Eucalyptus grandis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19989

12 Samples

Download data: TXT

(Submitter supplied) Illumina HiSeq technology was used to generate mRNA profiles from in vitro Eucalyptus grandis roots interacting with two different Pisolithus microcarpus strains (SI-9 and SI-12) and under two different CO2 concentrations (400 and 650 ppm) . Control roots or ectomycorrhizal root tips were harvested after 1 month and used for RNA extraction. Paired-end (2X150bp) reads were generated and aligned to Eucalyptus grandis transcripts (http://www.phytozome.net/; primarytranscripts only) using CLC Genomics Workbench 6.

Organism:

Eucalyptus grandis; Pisolithus microcarpus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19282 GPL19281

23 Samples

Download data: TXT

(Submitter supplied) Background: The change from juvenile to mature phase in woody plants is often accompanied by a gradual loss of rooting ability, as well as by reduced microRNA (miR) 156 and increased miR172 expression. Results: We characterized the population of miRNAs of Eucalyptus grandis and compared by Northern blot the gradual reduction in miR156 and increase in miR172 expression during development to the loss of rooting ability. more...

Organism:

Eucalyptus grandis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18777

1 Sample

Download data: TXT

(Submitter supplied) The loss of rooting capability following the transition from the juvenile to the mature phase is a known phenomenon in woody plant development. Eucalyptus grandis was used here as a model system to study the differences in gene expression between juvenile and mature cuttings. RNA was prepared from the base of the two types of cuttings before root induction and hybridized to a DNA microarray of E. grandis. more...

Organism:

Eucalyptus grandis

Type:

Expression profiling by array

Platform:

GPL15313

4 Samples

Download data: TXT

(Submitter supplied) In order to pinpoint the most differentially expressed genes between Eucalyptus grandis leaf blades and vascular (xylem) tissues as well as between E. grandis and Eucalyptus globulus xylem tissues, a total number of nine 50mer-oligoprobes covering the length of each one of 21,432 unique sequences derived from the Genolyptus EST dataset were synthesized “on-chip” in duplicate, randomly distributed in two blocks of each slide. more...

Organism:

Eucalyptus globulus; Eucalyptus grandis; Eucalyptus spp. mixed library

Type:

Expression profiling by array

Platform:

GPL14357

10 Samples

Download data: FTR, TXT

(Submitter supplied) Fast-growing Eucalyptus grandis trees are one of the most efficient producers of wood in South Africa. It is essential to maximize the effectiveness of these plantations by increasing their productivity, the quality and value of their products. We used microarray-based DNA-amplified fragment length polymorphism (AFLP) analysis in combination with expression profiling to develop fingerprints and profile gene expression of wood-forming tissue of seven individual E. more...

Organism:

Eucalyptus grandis

Type:

Expression profiling by array

Platform:

GPL8164

21 Samples

Download data: GPR

(Submitter supplied) The daily cycle of night and day affects the behaviour and physiology of almost all living things. At the molecular level, many genes show daily changes in expression levels. To determine whether changes in transcript abundance occur in wood forming tissues of Eucalyptus trees we used a cDNA microarray to examine gene expression levels at roughly four hour intervals throughout the day.

Organism:

Eucalyptus grandis x Eucalyptus urophylla; Eucalyptus camaldulensis x Eucalyptus grandis; Eucalyptus grandis; Eucalyptus tereticornis

Type:

Expression profiling by array

Platform:

GPL6942

24 Samples

Download data: GPR, TXT

(Submitter supplied) The gene expression profiles of the differentiating xylem of 91 Eucalyptus grandis backcross individuals were characterized following a loop design (Churchill, G.A. Nat Genet. 2002 Dec;32 Suppl:490-5). In this design, RNA from genotype 1666 (labeled with Cy5) was hybridized with RNA from genotype 1667 (labeled with Cy3) on the first slide(GEO accession number GSM7637); the same genotype 1667 (now labeled with Cy5) was compared with genotype 1669 (Cy3) on the second slide (GSM7638), and so on. more...

Organism:

Eucalyptus grandis; Eucalyptus tereticornis

Type:

Expression profiling by array

Platform:

GPL348

91 Samples

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