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Updated: May 30, 2026
10:41
Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms
Published on: May 9, 2017
Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database.
Nicolas Blavet1, Delphine Charif, Christine Oger-Desfeux
1Institute of Integrative Biology, ETH Zurich, Switzerland. nicolas.blavet@env.ethz.ch
BMC Genomics
|July 28, 2011
Summary
This study developed a new genomic resource for Silene and Dianthus species using transcriptome sequencing. The SiESTa database provides valuable genetic data to advance plant evolutionary and ecological research.
Area of Science:
- Plant genomics
- Evolutionary biology
- Ecological research
Background:
- The genus Silene is a key model for plant ecology and evolution.
- Limited genomic resources hinder research in Silene.
- Transcriptome sequencing offers a solution for non-model organisms.
Purpose of the Study:
- To characterize the transcriptomes of four Silene species and one Dianthus species.
- To establish a public genomic database for Silene research.
- To develop molecular markers for future studies.
Main Methods:
- Massively parallel cDNA sequencing using Roche GS-FLX 454.
- Analysis of expressed sequence tags (ESTs) and assembly into contigs.
- Annotation of sequences and identification of single-nucleotide polymorphisms (SNPs).
Main Results:
- Generated over 1 million EST reads.
- Assembled and annotated unigenes, with 49% showing similarity to Arabidopsis thaliana.
- Identified thousands of SNPs.
- Established the publicly accessible SiESTa database.
Conclusions:
- The study provides a crucial genomic resource for Silene and Dianthus.
- This resource will facilitate further development of Silene as a model system.
- Comparative transcriptome sequencing is effective for generating genomic resources in non-model plants.
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