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Related Concept Videos

RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

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Related Experiment Video

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Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
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Deep RNA-Seq uncovers the peach transcriptome landscape.

Lu Wang1, Shuang Zhao, Chao Gu

  • 1Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China, wanglu@wbgcas.cn.

Plant Molecular Biology
|June 21, 2013
PubMed
Summary

This study mapped peach RNA-Seq reads to the draft genome, identifying transcription factors, novel transcribed regions, and genetic variations like SNPs and SSRs. These findings illuminate peach transcriptome complexity for future horticultural trait research.

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Area of Science:

  • Plant genomics
  • Transcriptomics
  • Fruit tree research

Background:

  • Peach (Prunus persica) is a globally significant deciduous fruit tree.
  • Understanding its genetic makeup is crucial for improving horticultural traits.

Purpose of the Study:

  • To characterize the peach transcriptome through RNA-Seq.
  • To identify genes and regulatory elements controlling key peach traits.

Main Methods:

  • Generated 133 million pair-end RNA-Seq reads from peach leaf, flower, and fruit tissues.
  • Mapped reads to the peach draft genome, assembled transcripts, and identified single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs).
  • Analyzed alternative splicing (AS) events and transcribed regions.

Main Results:

  • Successfully mapped 90% of RNA-Seq reads.
  • Identified 1,162 transcription factors and 2,140 novel transcribed regions (NTRs), including protein-coding and non-coding RNAs.
  • Discovered 9,587 SNPs and characterized SSRs, noting higher SNP density on chromosome 2.
  • Exon-skipping was the predominant alternative splicing event (43%).

Conclusions:

  • This research provides the first comprehensive view of the peach transcriptome complexity.
  • The identified genetic resources will significantly aid functional genomics and breeding efforts in peach.
  • The data offers valuable insights into gene expression and regulation in peach development.