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Global transcriptome analysis in fast-growing Arabidopsis thaliana with elevated level of ATP [shoots]

ABSTRACT: Higher ATP supply in AtPAP2 overexpression line is the driving force for its fast-growth phenotypes, leading to massive changes in its transcriptome and metabolome. The OE lines are previously described in Sun et al., New Phytol. 2012 Apr;194(1):206-19.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE40306 | GEO | 2014/08/25

SECONDARY ACCESSION(S): PRJNA173488

REPOSITORIES: GEO

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Global transcriptome analysis in fast-growing Arabidopsis thaliana with elevated level of ATP [shoots]

Project description:Higher ATP supply in AtPAP2 overexpression line is the driving force for its fast-growth phenotypes, leading to massive changes in its transcriptome and metabolome. The OE lines are previously described in Sun et al., New Phytol. 2012 Apr;194(1):206-19. 20-day-old Arabidopsis seedlings at middle of day under long day growth conditions were collected for RNA extraction and microarray analysis

2014-08-25 | E-GEOD-40306 | biostudies-arrayexpress

Global transcriptome analysis in fast-growing Arabidopsis thaliana with elevated level of ATP [roots]

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Global transcriptome analysis in fast-growing Arabidopsis thaliana with elevated level of ATP [roots]

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Global transcriptome analysis in fast-growing Arabidopsis thaliana with elevated level of ATP

Project description:This SuperSeries is composed of the SubSeries listed below.

2014-08-25 | GSE40307 | GEO

Global transcriptome analysis in fast-growing Arabidopsis thaliana with elevated level of ATP

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

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Global small RNA analysis in fast-growing Arabidposis thaliana with elevated level of ATP and sugars

Project description:The sRNA profiles of the leaf and the root of 20-day-old plants were sequenced and the impacts of high energy status on sRNA expression were analyzed

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Global small RNA analysis in fast-growing Arabidposis thaliana with elevated level of ATP and sugars

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2013-08-07 | E-GEOD-48309 | biostudies-arrayexpress

Global small RNA analysis in fast-growing Arabidopsis thaliana with elevated concentrations of ATP and sugars.

Project description:BackgroundIn higher eukaryotes, small RNAs play a role in regulating gene expression. Overexpression (OE) lines of Arabidopsis thaliana purple acid phosphatase 2 (AtPAP2) were shown to grow faster and exhibit higher ATP and sugar contents. Leaf microarray studies showed that many genes involved in microRNAs (miRNAs) and trans-acting siRNAs (tasiRNAs) biogenesis were significantly changed in the fast-growing lines. In this study, the sRNA profiles of the leaf and the root of 20-day-old plants were sequenced and the impacts of high energy status on sRNA expression were analyzed.Results9-13 million reads from each library were mapped to genome. miRNAs, tasiRNAs and natural antisense transcripts-generated small interfering RNAs (natsiRNAs) were identified and compared between libraries. In the leaf of OE lines, 15 known miRNAs increased in abundance and 9 miRNAs decreased in abundance, whereas in the root of OE lines, 2 known miRNAs increased in abundance and 9 miRNAs decreased in abundance. miRNAs with increased abundance in the leaf and root samples of both OE lines (miR158b and miR172a/b) were predicted to target mRNAs coding for Dof zinc finger protein and Apetala 2 (AP2) proteins, respectively. Furthermore, a significant change in the miR173-tasiRNAs-PPR/TPR network was observed in the leaves of both OE lines.ConclusionIn this study, the impact of high energy content on the sRNA profiles of Arabidopsis is reported. While the abundance of many stress-induced miRNAs is unaltered, the abundance of some miRNAs related to plant growth and development (miR172 and miR319) is elevated in the fast-growing lines. An induction of miR173-tasiRNAs-PPR/TPR network was also observed in the OE lines. In contrast, only few cis- and trans-natsiRNAs are altered in the fast-growing lines.

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Transcriptome sequencing and analysis of the fast growing shoots of moso bamboo (Phyllostachys edulis).

Project description:BackgroundThe moso bamboo, a large woody bamboo with the highest ecological, economic, and cultural value of all bamboos, has one of the highest growth speeds in the world. Genetic research into moso bamboo has been scarce, partly because of the lack of previous genomic resources. In the present study, for the first time, we performed de novo transcriptome sequencing and mapped to the moso bamboo genomic resources (reference genome and genes) to produce a comprehensive dataset for the fast growing shoots of moso bamboo.ResultsThe fast growing shoots mixed with six different heights and culms after leaf expansion of moso bamboo transcriptome were sequenced using the Illumina HiSeq™ 2000 sequencing platform, respectively. More than 80 million reads including 65,045,670 and 68,431,884 clean reads were produced in the two libraries. More than 81% of the reads were matched to the reference genome, and nearly 50% of the reads were matched to the reference genes. The genes with log 2 ratio > 2 or < -2 (P<0.001) were characterized as the most differentially expressed genes. 6,076 up-regulated and 4,613 down-regulated genes were classified into functional categories. Candidate genes which mainly involved transcript factors, plant hormones, cell cycle regulation, cell wall metabolism and cell morphogenesis genes were further analyzed and they may form a network that regulates the fast growth of moso bamboo shoots.ConclusionFirstly, our data provides the most comprehensive transcriptomic resource for moso bamboo to date. Candidate genes have been identified and they are potentially involved in the growth and development of moso bamboo. The results give a better insight into the mechanisms of moso bamboo shoots rapid growth and provide gene resources for improving plant growth.

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Global transcriptome analysis in fast-growing Arabidopsis thaliana with elevated level of ATP

Project description:Global transcriptome analysis in fast-growing Arabidopsis thaliana with elevated level of ATP

| PRJNA173484 | ENA