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ABSTRACT: Populus trichocarpa Genomic Resources

PROVIDER: PRJNA808363 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR23629788_1.fastq.gz	Fastqsanger.gz
	SRR23629788_2.fastq.gz	Fastqsanger.gz
	SRR23629789_1.fastq.gz	Fastqsanger.gz
	SRR23629789_2.fastq.gz	Fastqsanger.gz

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Transcriptome analyses of the Laccaria bicolor-Populus trichocarpa mycorrhiza

Project description:Illumina HiSeq2000 technology was used to generate mRNA profiles from the ectomycorrhizal fungi Laccaria bicolor colonizing roots of Populus trichocarpa. Samples were taken after 3 months of contact in order to identify mycorrhiza-regulated transcripts. 100bp reads were generated and aligned to the Populus trichocarpa (http://www.phytozome.net/poplar.php) reference genome.

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Poplar tissue types 1

Project description:Global gene expression pattern of different poplar tissue types were determined using a Nimblegen microarray based on JGI v1.1 gene models. All tissue except reproductive tissue were obtained from the same clone used for the poplar genome sequencing project (Populus trichocarpa Nisqually-1). Reproductive tissue were from wild Populus trichocarpa trees.

2010-08-01 | GSE21481 | GEO

Identification of Populus small RNAs responsive to mutualistic interactions with mycorrhizal fungi, Laccaria bicolor and Rhizophagus irregularis

Project description: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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Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max

Project description:This SuperSeries is composed of the following subset Series: GSE26195: Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max [Populus] GSE26197: Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max [Arabidopsis] GSE26198: Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max [Soy] Refer to individual Series

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Poplar tissue types 2

Project description:Global gene expression pattern of phloem and xylem tissue were determined using a Nimblegen microarray based on JGI v1.1 gene models. Xylem tissue from both Populus trichocarpa Nisqually-1 and Populus tremula X Populus alba hybrid were used in the study.

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Transcriptome analyses of the Laccaria bicolor-Populus trichocarpa mycorrhiza development

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.

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Project description:A microarray analysis of whole-genome gene expression in leaves was carried out in a (Populus trichocarpa X Populus deltoides) X Populus deltoides pseudo-backcross pedigree. Genetic variation in gene expression was quantified for 55,793 predicted gene models based on a single probe per gene. Resultant data contributed to the analysis of the genetic architecture of gene expression in leaves of Populus.

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Gene expression in whole-roots of a Populus trichocarpa and Populus deltoides pseudo-backcross population

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Gene expression in whole-roots of a Populus trichocarpa and Populus deltoides pseudo-backcross population

Project description:A microarray analysis of whole-genome gene expression in roots was carried out in a (Populus trichocarpa X Populus deltoides) X Populus deltoides pseudo-backcross pedigree. Genetic variation in gene expression was quantified for 55,793 predicted gene models based on a single probe per gene. Resultant data contributed to the analysis of the genetic architecture of gene expression in roots of Populus. Data include one biological replicate of 163 individuals segregating from a pseudo-backcross pedigree of (Populus trichocarpa X Populus deltoides) X Populus deltoides analyzed for gene expression (GE) in roots using one probe per gene for 55793 independent gene models (probes E_POPLARSxxxxxPxxxxx) and single feature sequence polymorphism (SFP) using one probe per gene for 12084 independent gene models (probes G_POPLARSxxxxxPxxxxx). GE and SFP probes were selected from 6-7 probes per gene previously tested in a pilot study of the two parent trees of the cross (Populus deltoides X Populus trichocarpa)

2010-06-24 | E-GEOD-20118 | biostudies-arrayexpress

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