|
| Status |
Public on Oct 27, 2023 |
| Title |
E. grandis Root (1/2 MMN) GA-28 |
| Sample type |
SRA |
| |
|
| Source name |
Root tissue (axenic control)
|
| Organism |
Eucalyptus grandis |
| Characteristics |
tissue: Root tissue (axenic control)
cell type: Root
treatment: Axenic Control
|
| Treatment protocol |
Once the E. grandis seedlings were two months old and the fungal cultures had grown for 2 weeks, the plants and fungi were separated into one of two treatment categories: (1) fungal-free controls whereby the seedlings were transferred onto new half-strength MMN medium; (2) ‘physical contact’ seedlings were transferred onto new half-strength MMN medium and then placed into direct contact with the active growing edge of a fungal colony and then samples were harvested at 2 week post-contact. These plates were then closed using micropore tape to allow for gas exchange with the external environment.
|
| Growth protocol |
Plants and fungus were grown on half-strength MMN medium ((pH 5.5; 0.1 g l−1 glucose) at 22–30°C night/day temperature with a 16 h light cycle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spectrum Plant Total RNA (Sigma-Aldrich
Poly-A RNA libraries were prepared and sequenced using Illumina HiSeq platform with a 150bp paired-end configuration
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Biological Replicate 1
|
| Data processing |
Raw reads were trimmed and mapped to either the P. microcarpus (Plett et al., 2023) or E. grandis (Myberg et al., 2014) genomes in CLC Workbench (v22).
Normalisation of raw count data and analysis of differential gene regulation was performed using the DESeq2 package in R (version 1.30.1; Love et al., 2014).
Genes having less than an average of 5 counts per sample for all conditions were considered to be unexpressed and removed prior to the analysis. Genes were considered to be significantly differentially expressed when the padj < 0.05 (calculated from DESeq2 based on a Benjamini-Hochberg method) and the log2(fold change) was above 1 (over-expressed) or below 1 (under-expressed) for fungal genes or above 2.23 (over-expressed) or below 2.23 (under-expressed) for plant genes (equivalent to 2x and 5x differentially expressed, respectively).
Assembly: https://phytozome-next.jgi.doe.gov/info/Egrandis_v2_0; https://mycocosm.jgi.doe.gov/Pismi2/Pismi2.home.html
Supplementary files format and content: Raw read counts of all genes across all samples for E. grandis
Supplementary files format and content: Raw read counts of all genes across all samples for Pisolithus microcarpus
|
| |
|
| Submission date |
Jun 23, 2023 |
| Last update date |
Oct 27, 2023 |
| Contact name |
Jonathan Michael Plett |
| E-mail(s) |
j.plett@westernsydney.edu.au
|
| Organization name |
Western Sydney University
|
| Department |
Hawkesbury Institute for the Environment
|
| Street address |
Bourke St. Entrance, Building L9
|
| City |
Richmond |
| State/province |
NSW |
| ZIP/Postal code |
2753 |
| Country |
Australia |
| |
|
| Platform ID |
GPL33524 |
| Series (1) |
| GSE235669 |
Fungal metabolism and free amino acid content may predict nitrogen transfer to the host plant in the ectomycorrhizal relationship between Pisolithus spp. and Eucalyptus grandis |
|
| Relations |
| BioSample |
SAMN35880178 |
| SRA |
SRX20762529 |
