Project description:Illumina technology was used to generate mRNA profiles of a time course of Laccaria bicolor S238N and Populus tremula x alba 717-1B4 in vitro ectomycorrhizal development. Total RNA was extracted, TruSeq mRNA Stranded libraries were constructed and and sequenced in triplicates (2 x 150 bp Illumina HiSeq3000) at the Genotoul sequencing facilities (Toulouse, France). Raw reads were trimmed for low quality (quality score 0.05), Illumina adapters and sequences shorter than 15 nucleotides and aligned to the L. bicolor v2 reference transcripts available at the JGI database https://mycocosm.jgi.doe.gov/Lacbi2/Lacbi2.home.html using CLC Genomics Workbench v8.
Project description:The early phase of the interaction between tree roots and ectomycorrhizal (ECM) fungi, prior to symbiosis establishment, is accompanied by a stimulation of lateral root (LR) development. We set out to identify gene networks that regulate LR development during the early signal exchanges between Populus tremula x Populus alba (hereafter called poplar) and the ECM fungus Laccaria bicolor. A sandwich culture system was developed in order to bring plant and fungus into an indirect contact, which permits signal molecule exchange and LR stimulation (emergence after 4-5 days of contact) but prohibits root colonization. A NimbleGen full genome poplar oligo-array was used to investigate transcript profiles at three days of indirect poplar/L. bicolor contact, referring to the time point of LR initiation in response to the fungus.
Project description:To obtain genes expression in different parts of 84k poplar stems, transcriptome sequencing was performed using Illumina Novaseq 6000 second-generation sequencing platform from Shanghai BIOZERON Co. Ltd (www.biozeron.com). Selecte three stem segments of plants REPEAT 1, 2 and 3 with good and similar growth to use: 2nd-3rd internodes (poplar stem top: PST1, PST2, PST3); 9th-10th internodes (poplar stem middle: PSM1, PSM2, PSM3); 14th-15th internodes (poplar stem bottom: PSB1, PSB2, PSB3). [Or the three repeating organisms are also called poplar A, B, C. From top to bottom, the three parts of the stem are also called stem 1, 2, 3.]
Project description:Here we applied a novel approach to isolate nuclei from complex plant tissues (https://doi.org/10.1371/journal.pone.0251149), to dissect the transcriptome profiling of the hybrid poplar (Populus tremula × alba) vegetative shoot apex at single-cell resolution.
Project description:Illumina HiSeq technology was used to generate mRNA profiles from Cenococcum geophilum ectomycorrhizal poplar roots compared to free-living mycelium . Ectomycorrhizal poplar roots and control mycelium were harvested after 60 days and used for RNA extraction. Reads of 150bp were generated and aligned to the C. geophilum reference genome (https://genome.jgi.doe.gov/Cenge3/Cenge3.home.html).
Project description:This study characterizes the transcriptomic alterations of P. trichocarpa during interaction with the ectomycorrhizal fungus Laccaria bicolor S238N. Four time-points were analyzed, two weeks, four weeks , six weeks and twelve weeks after inoculation. We performed 32 hybridizations (NimbleGen) with samples derived from Populus trichocarpa control roots and P.trichocarpa mycorrhizal root tips. Samples were taken after 2,4,6 and 12 weeks of interaction (four biological replicates). All samples were labeled with Cy3.
Project description:This study characterizes the transcriptomic alterations of P. tremula x P. alba at three weeks after inoculation with the ectomycorrhizal fungus Laccaria bicolor. We performed 6 hybridizations (NimbleGen) with samples derived from Populus tremula x P. alba control roots and mycorrhizal root tips. Samples were taken after 3 weeks of interaction (three biological replicates). All samples were labeled with Cy3.
Project description:Illumina GAIIx technology was used to generate mRNA profiles from the ectomycorrhizal fungi Laccaria bicolor colonizing roots of Populus trichocarpa. Samples were taken after two, four and 12 weeks of contact in order to identify mycorrhiza-regulated transcripts. 37bp reads were generated and aligned to the Populus trichocarpa (http://www.phytozome.net/poplar.php) and the Laccaria bicolor (http://genome.jgi-psf.org/Lacbi2/Lacbi2.home.html) reference genomes using CLC Genomics Workbench 6.
Project description:The Poplar transcriptome was analyzed in mycorrhizal root tips in contact with Laccaria bicolor for 2 weeks. During mycorrhization the roots were treated with either 250µm ACC, 10nM JA or 500µM SA and compared to untreated mycorrhiza or control roots without contact to L. bicolor. In addition the poplar mutants 35S::PttACO1 and 35S::Atetr1 were used
