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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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K-Mer-Based Genome Size Estimation in Theory and Practice.

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Establishing MinION Sequencing and Genome Assembly Procedures for the Analysis of the Rooibos (<i>Aspalathus linearis</i>) Genome.

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Transcriptomics of the Rooibos (<i>Aspalathus linearis</i>) Species Complex.

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Rooibos (<i>Aspalathus linearis</i>) Genome Size Estimation Using Flow Cytometry and K-Mer Analyses.

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Visualization of Aspalathin in Rooibos (<i>Aspalathus linearis</i>) Plant and Herbal Tea Extracts Using Thin-Layer Chromatography.

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Updated: Jun 13, 2026

A Stepwise Guide to the Isolation and Analysis of Leaf Surface and Apoplastic RNA Using Arabidopsis Rosettes
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A Stepwise Guide to the Isolation and Analysis of Leaf Surface and Apoplastic RNA Using Arabidopsis Rosettes

Published on: August 8, 2025

Transcriptome Profiling of Leaves and Roots from Rooibos (Aspalathus linearis) Using Oxford Nanopore Sequencing.

Tanweer Beckett1, Uljana Hesse1,2

  • 1Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville 7535, South Africa.

Plants (Basel, Switzerland)
|June 12, 2026
PubMed
Summary

Long-read sequencing of rooibos (Aspalathus linearis) provides a comprehensive transcriptome resource. This data aids in identifying molecular markers for improved stress tolerance, crucial for enhancing rooibos breeding programs and plant longevity.

Keywords:
Aspalathus linearisOxford NanoporeRNA-seqdifferential gene expressionlong readrooibostranscriptome

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Published on: May 14, 2020

Area of Science:

  • Plant science
  • Genomics
  • Bioinformatics

Background:

  • Rooibos (Aspalathus linearis) is an economically important South African endemic plant, primarily used as herbal tea.
  • Declining commercial rooibos longevity, due to low stress tolerance, threatens its production.
  • Short-read sequencing has limitations in assembling full-length rooibos transcripts for breeding.

Purpose of the Study:

  • To establish long-read transcriptome analysis for rooibos leaf and root samples.
  • To identify potential pitfalls in transcriptome data pre-processing and assembly.
  • To generate a high-quality transcriptome resource for identifying molecular markers for stress tolerance.

Main Methods:

  • Oxford Nanopore long-read sequencing of rooibos leaf and root transcriptomes.
  • Evaluation of PolyA tail trimming and rRNA removal pre-processing steps.
  • Comparison of assemblers (RATTLE, RNA-Bloom2) and clustering algorithms (VSEARCH, CD-HIT).

Main Results:

  • The optimal assembly (RNA-Bloom2 with CD-HIT) yielded 169,122 transcripts, with 33% novel proteins compared to short-read data.
  • The novel sequences included full-length transcripts from various biosynthesis pathways.
  • Comparative transcriptomics revealed overexpressed transcripts in leaves (photosynthesis, carbon fixation) and roots (growth regulation, secondary metabolites).

Conclusions:

  • Long-read sequencing provides a more comprehensive rooibos transcriptome, revealing novel gene sequences.
  • The generated transcriptome is a valuable resource for data mining and identifying breeding targets.
  • Overexpressed transcripts in leaves and roots are potential targets for developing molecular markers to improve rooibos stress tolerance.