Project description:To investigate which genes are affected by MiSSP7, a secreted effector protein of Laccaria bicolor, we analyzed the transcriptomes of poplar roots incubated with MiSSP7 protein.
Project description:To investigate which genes are affected by MiSSP7, a secreted effector protein of Laccaria bicolor, we analyzed the transcriptomes of poplar roots incubated with MiSSP7 protein. The Populus trichocarpa custom-exon expression array (12x135K) manufactured by Roche NimbleGen Systems Limited (Madison, WI) (http://www.nimblegen.com/products/exp/index.html) contained three independent, nonidentical, 60-mer probes per gene model coding sequence. Included in the oligoarray were 43,929 annotated gene models (Populus trichocarpa genome v2 ; Phytozome 5.0), 5,859 random 60-mer control probes and labelling controls. We performed six hybridizations, three biological replicates from poplar roots inoculated with MiSSP7 peptide for one hour and three biological replicates from control roots.
Project description:Illumina technology was used to generate mRNA profiles of Populus tremula x alba 717-1B4 control roots and Laccaria bicolor S238N ectomycorrhiza. Total RNA was extracted, TruSeq mRNA Stranded libraries were constructed and and sequenced (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 Populus trichocarpa v4.1 primary transcripts available at Phytozome (https://phytozome-next.jgi.doe.gov/info/Ptrichocarpa_v4_1l) using CLC Genomics Workbench v24.
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: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
Project description:Plants transition through juvenile and adult phases of vegetative development in a process known as vegetative phase change (VPC). In poplars (genus Populus) the differences between these stages are subtle, making it difficult to determine when this transition occurs. Previous studies of VPC in poplars have relied on plants propagated in vitro, leaving the natural progression of this process unknown. We examined developmental morphology of seed-grown and in vitro derived Populus tremula × alba (clone 717-1B4), and compared the phenotype of these to transgenics with manipulated miR156 expression, the master regulator of VPC. In seed-grown plants, most traits changed from node-to-node during the first 3 months of development but remained constant after node 25. Many traits remained unchanged in clones over-expressing miR156, or were enhanced when miR156 was lowered, demonstrating their natural progression is regulated by the miR156/SPL pathway. The characteristic leaf fluttering of Populus is one of these miR156-regulated traits. Vegetative development in plants grown from culture mirrored that of seed-grown plants, allowing direct comparison between plants often used in research and those found in nature. These results provide a foundation for further research on the role of VPC in the ecology and evolution of this economically important genus.
