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RNA-seq

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...

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Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Published on: March 8, 2018

Transcriptome sequencing and simple sequence repeat marker development for three Macaronesian endemic plant species.

Oliver W White¹, Bethany Doo², Mark A Carine³

¹Plants Division, Natural History Museum, London SW7 5BD, United Kingdom; Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom.

Applications in Plant Sciences

|September 10, 2016

Summary

This study developed hundreds of simple sequence repeat (SSR) markers from transcriptome data for three Macaronesian endemic plants. These SSR markers are valuable genomic resources for studying island plant evolution and adaptation.

Keywords:

Argyranthemum broussonetii Descurainia bourgaeana Echium wildpretii Macaronesia marker development simple sequence repeats (SSRs)transcriptomics

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Last Updated: Mar 15, 2026

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Published on: January 25, 2019

Area of Science:

Evolutionary biology
Genomics
Island biogeography

Background:

Oceanic islands are crucial for studying adaptation and speciation.
Genomic resources for island endemic species are scarce.
Macaronesian endemic plants represent key evolutionary lineages.

Purpose of the Study:

To provide transcriptome sequences for three Macaronesian endemic plant species.
To demonstrate the utility of transcriptome data for developing genetic markers.
To facilitate evolutionary studies on island plant lineages.

Main Methods:

Sequencing, assembly, and annotation of transcriptomes from three endemic species.
Identification of simple sequence repeats (SSRs) within the assembled transcriptomes.
Design and testing of SSR primers for marker development.

Main Results:

Transcriptomes were successfully sequenced and annotated for Argyranthemum broussonetii, Descurainia bourgaeana, and Echium wildpretii.
Hundreds of SSRs were identified per species (1972–2282).
Twelve SSR primers amplified successfully across species, with eight showing polymorphism.

Conclusions:

A single transcriptome sequence is sufficient for identifying numerous polymorphic SSR markers.
Developed SSR markers are applicable to diverse evolutionary research questions concerning island lineages.