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ABSTRACT: Nanopore Direct-RNA Sequence of stem-differentiating xylem in Populus trichocarpa during drought stress

PROVIDER: PRJNA672182 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12904202_1.fastq.gz	Fastqsanger.gz
	SRR12904624_1.fastq.gz	Fastqsanger.gz
	SRR12904635_1.fastq.gz	Fastqsanger.gz
	SRR12904551_1.fastq.gz	Fastqsanger.gz
	SRR13336716_1.fastq.gz	Fastqsanger.gz

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Project description:Nanopore Direct-RNA Sequence of stem-differentiating xylem in Populus trichocarpa

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Poplar tissue types 2

2010-08-01 | GSE21485 | GEO

RNAseq of transfected protoplasts of Populus trichocarpa

Project description:PtrHSFB3-1 and PtrMYB092 are xylem specific genes in xylem of P. trichocarpa, and their expression levels are down regulated most significantly in tension wood. These two transcription factors were transiently overexpressed in stem differentiating xylem (SDX) of P. trichocarpa , and transcriptomic sequencing was performed to identify the regulatory effects of the two transcription factors on wood formation related genes.

2020-07-11 | GSE154167 | GEO

High resolution survey of drought, high salinity, heat and cold stress-induced transcriptome of bioenergy feedstock model plant western poplar (Populus trichocarpa) accession Nisqually-1

Project description:Abiotic stress is a major factor affecting the growth, development, yield and quality in plants including the important biomass yield such as in a bioenergy feedstock crops. In a first of its kind, RNA-seq based high resolution survey of abiotic stress-induced transcriptome of bioenergy feedstock model plant western poplar (Populus trichocarpa accesion Nisqually-1) was carried out by way of 81 libraries made from total RNA isolated from three tissues, mature vascular leaf, stem xylem and root sampled from plants subjected to untreated control and treated with four individual stress treatments cold, heat, drought and high salinity. For every tissue and treatment type including controls, three individual plants were used per treatment as biological replicates. This research project is supported by the DOE Office of Science, Office of Biological and Environmental Research (BER), USA, grant no. DE-SC0008570

2018-02-23 | E-MTAB-5540 | biostudies-arrayexpress

Differential gene expression analysis of drought responsive sense and antisense genes in Populus

Project description:In this study we employ a strand-specific RNA-seq appoach and stranded gene expression analysis tools to identify drought responsive antisense gene loci and sense-antisense gene pairs in Populus. we generated and sequenced 28 strand-specific cDNA libraries derived from either leaf or root tissues of Populus trichocarpa plants associaed with both short-term drought (24 hours of water stress of 40% of field capacity) and long-term drought ( 25 days of water stress of 40% of field capacity) . We mapped over 71 billion nucleotides to Populus genome. Our data demonstrates that with the current sequence depth ~ 19 % of Populus genome undergoes antisense transcription subjected to drought regulation. All in all we have identified that in root tissues 524 differentially expressed antisense genes and 247 drought-responsive SA gene pairs which are significantly regulated by drought (padj <0.05). Taken all data from both drought treatments, we have identified 1185 unique drought-responsive antisense gene loci and 606 drought-responsive SA gene pairs (padj <0.05).

2019-01-06 | GSE97463 | GEO

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. Xylem tissue: Three biological replicates were hybridized to three arrays Phloem tissue: Two biological replicates were hybridized to two arrays

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A COMPASS histone H3K4 trimethyltransferase pentamer transactivates drought tolerance and growth/biomass production in Populus trichocarpa

Project description:ChIP-seq was carried out with H3K4me3 antibody using Stem differentiating xylem from wild-type plants under drought conditions

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Single-cell transcriptomics unveils xylem cell development and evolution

Project description:The plant xylem tissue is responsible for water transportation, mechanical support and lateral growth, and can be utilized as wood. The seed plant xylem has a radial system composed of ray parenchyma cells and an axial system of fusiform cells, including tracheids in gymnosperms and vessel elements and libriform fibers in angiosperms. Little is known about the developmental programs and evolutionary relationships of these xylem cell types. Here we show that the radial and axial systems of stem-differentiating xylem are differentially conserved across four divergent woody angiosperms. Through transcriptomic profiling of single cells and cell-type regions isolated by laser capture microdissection, we identified cell types corresponding to single-cell clusters in Populus trichocarpa. Cross-species analyses of single-cell trajectories demonstrated highly conserved development in ray lineages across angiosperms. While the core eudicots P. trichocarpa and Eucalyptus grandis share nearly identical fusiform cell lineages, the tracheids in the basal eudicot Trochodendron aralioides, an evolutionarily reversed character, exhibited an expression pattern highly similar to that of vessel elements. It suggests that water transportation, instead of mechanical support, is the dominant feature of tracheary elements. Furthermore, we found that the more basal angiosperm Liriodendron chinense has a distinct fusiform lineage. This evo-developmental framework of xylem cell lineages provides a comprehensive understanding of the formation of the most abundant tissue on Earth.

2022-12-25 | GSE180121 | GEO

Project description:Degradome-Seq of stem-differentiating xylem in Populus trichocarpa

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Project description:MAZTER-seq of stem-differentiating xylem in Populus trichocarpa

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