|
| Status |
Public on Apr 09, 2019 |
| Title |
Identification of Populus small RNAs responsive to mutualistic interactions with mycorrhizal fungi, Laccaria bicolor and Rhizophagus irregularis |
| Organisms |
Populus trichocarpa; Populus deltoides |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Ecto- and endo-mycorrhizal colonization of Populus roots have a positive impact on the overall tree health and growth. A complete molecular understanding of these interactions will have important implications for increasing agricultural or forestry sustainability using plant:microbe-based strategies. These beneficial associations entail extensive morphological changes orchestrated by the genetic reprogramming in both organisms. In this study, we performed a comparative analysis of two Populus species (Populus deltoides and P. trichocarpa) that were colonized by either an arbuscular mycorrhizal fungus (AmF), Rhizophagus irregularis or an ectomycorrhizal fungus (EmF), Laccaria bicolor, to describe the small RNA (sRNA) landscape including small open reading frames (sORFs) and micro RNAs (miRNAs) involved in these mutualistic interactions. We identified differential expression of sRNAs that were, to a large extent, 1) within the genomic regions lacking annotated genes in the Populus genome and 2) distinct for each fungal interaction. These sRNAs may be a source of novel sORFs within a genome, and in this regard, we identified potential sORFs encoded by the sRNAs. We predicted a higher number of differentially-expressed miRNAs in P. trichocarpa (4 times more) than in P. deltoides (conserved and novel). In addition, 44 miRNAs were common in P. trichocarpa between the EmF and AmF treatments, and only 4 miRNAs were common in P. deltoides between the treatments.
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| Overall design |
Examination of two Populus species (P. deltoides and P. trichocarpa) in response to either an arbuscular mycorrhizal fungus (Rhizophagus irregularis) or an ectomycorrhizal fungus (Laccaria bicolor)
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| Contributor(s) |
Mewalal R, Yin H, Hu R, Jawdy S, Vion P, Tuskan GA, Le Tacon F, Labbé JL, Yang X |
| Citation(s) |
30936859 |
| |
| Submission date |
Jul 16, 2018 |
| Last update date |
Apr 09, 2019 |
| Contact name |
Xiaohan Yang |
| E-mail(s) |
yangx@ornl.gov
|
| Phone |
865-241-6895
|
| Organization name |
Oak Ridge National Laboratory
|
| Department |
Biosciences Division
|
| Street address |
1 Bethel Valley Road
|
| City |
Oak Ridge |
| State/province |
TN |
| ZIP/Postal code |
37831-6407 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL25333 |
Illumina MiSeq (Populus deltoides) |
| GPL25334 |
Illumina MiSeq (Populus trichocarpa) |
|
| Samples (18)
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| Relations |
| BioProject |
PRJNA481323 |
| SRA |
SRP153905 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE117158_isoform_exp_diff_sig_PD.txt.gz |
2.5 Kb |
(ftp)(http) |
TXT |
| GSE117158_isoform_exp_diff_sig_PT.txt.gz |
1.9 Kb |
(ftp)(http) |
TXT |
| GSE117158_isoform_exp_diff_sig_transcript_PD.fa.gz |
7.9 Kb |
(ftp)(http) |
FA |
| GSE117158_isoform_exp_diff_sig_transcript_PT.fa.gz |
4.4 Kb |
(ftp)(http) |
FA |
| GSE117158_miRNA_EXP_diff_sig_PD.fa.gz |
1.9 Kb |
(ftp)(http) |
FA |
| GSE117158_miRNA_EXP_diff_sig_PD.txt.gz |
1.6 Kb |
(ftp)(http) |
TXT |
| GSE117158_miRNA_EXP_diff_sig_PT.fa.gz |
2.3 Kb |
(ftp)(http) |
FA |
| GSE117158_miRNA_EXP_diff_sig_PT.txt.gz |
1.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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