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Transcriptome analysis of lateral buds from Phyllostachys edulis rhizome during germination and early shoot stages

ABSTRACT: Transcriptome analysis of lateral buds from Phyllostachys edulis rhizome during germination and early shoot stages

PROVIDER: PRJNA595601 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10691684.fastq.gz	Fastqsanger.gz
	SRR10691685.fastq.gz	Fastqsanger.gz

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Transcriptome analysis of lateral buds from Phyllostachys edulis rhizome during germination and early shoot stages

Project description:We adopted the high-throughput sequencing technology and compared the transcriptomes of Moso bamboo rhizome buds in germination stage and late development stage. We found that the development of Moso bamboo rhizome lateral buds was coordinated by multiple pathways, including meristem development, sugar metabolism and phytohormone signaling. Phytohormones have fundamental impacts on the plant development. We found the evidence of several major hormones participating in the development of Moso bamboo rhizome lateral bud. Furthermore, we showed direct evidence that Gibberellic Acids (GA) signaling participated in the Moso bamboo stem elongation.

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Transcriptome analysis of lateral buds from Phyllostachys edulis rhizome during germination and early shoot stages.

Project description:BackgroundThe vegetative growth is an important stage for plants when they conduct photosynthesis, accumulate and collect all resources needed and prepare for reproduction stage. Bamboo is one of the fastest growing plant species. The rapid growth of Phyllostachys edulis results from the expansion of intercalary meristem at the basal part of nodes, which are differentiated from the apical meristem of rhizome lateral buds. However, little is known about the major signaling pathways and players involved during this rapid development stage of bamboo. To study this question, we adopted the high-throughput sequencing technology and compared the transcriptomes of Moso bamboo rhizome buds in germination stage and late development stage.ResultsWe found that the development of Moso bamboo rhizome lateral buds was coordinated by multiple pathways, including meristem development, sugar metabolism and phytohormone signaling. Phytohormones have fundamental impacts on the plant development. We found the evidence of several major hormones participating in the development of Moso bamboo rhizome lateral bud. Furthermore, we showed direct evidence that Gibberellic Acids (GA) signaling participated in the Moso bamboo stem elongation.ConclusionSignificant changes occur in various signaling pathways during the development of rhizome lateral buds. It is crucial to understand how these changes are translated to Phyllostachys edulis fast growth. These results expand our knowledge on the Moso bamboo internodes fast growth and provide research basis for further study.

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Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation reveals in moso bamboo (Phyllostachys edulis)

Project description:Moso bamboo (Phyllostachys edulis) represents one of the fastest-spreading plants in the world, due in part to their well-developed rhizomes system. However, the post-transcriptional regulation mechanism has not been comprehensively studied for the development of rhizome system in bamboo. We therefore used single-molecule long-read sequencing technology to re-annotate the bamboo genome, and genome-wide identify alternative splicing (AS) and alternative polyadenylation (APA) in the rhizomes system. In total, 145,522 mapped full-length non-chimeric (FLNC) reads were analyzed, resulting in the correction of 2,241 mis-annotated genes and identification of 8,091 previously unannotated loci. Markedly, more than 42,280 contiguous exon connectivity were derived from full-length splicing isoforms, including a large number of AS events that associated with rhizome systems. In addition, we characterized 25,069 polyadenylation sites from 11,450 genes, 6,311 of which have APA sites. Further analysis of intronic polyadenylation revealed that LTR/Gypsy and LTR/Copia were two major transposable elements (TEs) within the intronic polyadenylation region. Furthermore, this study provided a quantitative altas of poly(A) usage and identified several hundreds of differential poly(A) sites in rhizome-root system using a combination of polyadenylation site sequencing (PAS-seq) and PacBio reads. Taken together, these results suggest that posttranscriptional regulation may potentially play vital role in the underground rhizome-root system.

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