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

PROVIDER: PRJNA517295 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12676675_1.fastq.gz	Fastqsanger.gz
	SRR12822922_1.fastq.gz	Fastqsanger.gz
	SRR12822923_1.fastq.gz	Fastqsanger.gz
	SRR12881185_1.fastq.gz	Fastqsanger.gz
	SRR8491764_1.fastq.gz	Fastqsanger.gz

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

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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.

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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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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.

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Screen of oligonucleotides for microarray transcriptome analysis of Populus deltoides and P. trichocarpa

Project description:The purpose of this study was to evaluate a set of 6-7 long oligonucleotide probes developed based on the sequence of the Populus trichocarpa genome, that are optimal for gene expression analysis of P. deltoides and a hybrid of P. deltoides and P. trichocarpa. To evaluate these probes, multiple tissues (differentiating xyle, leaf and whole-root) of a pure P. deltoides and a hybrid (P. deltoides X P. trichocarpa) were transcript profiled for identification of one or more probes that are not biased towards one or the other genotype.

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