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Series GSE117158 Query DataSets for GSE117158
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.
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)
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
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)
GSM3272528 PDA_rep1
GSM3272532 PDA_rep2
GSM3272533 PDA_rep3
BioProject PRJNA481323
SRA SRP153905

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

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
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Processed data are available on Series record

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