Next generation sequencing and de novo transcriptomics to study gene evolution

Jayasena, Achala S., Secco, David, Bernath-Levin, Kalia, Berkowitz, Oliver, Whelan, James and Mylne, Joshua S. (2014) Next generation sequencing and de novo transcriptomics to study gene evolution. Plant Methods, 10 34: 1-14. doi:10.1186/1746-4811-10-34


Author Jayasena, Achala S.
Secco, David
Bernath-Levin, Kalia
Berkowitz, Oliver
Whelan, James
Mylne, Joshua S.
Title Next generation sequencing and de novo transcriptomics to study gene evolution
Formatted title
Next generation sequencing and de novo transcriptomics to study gene evolution
Journal name Plant Methods   Check publisher's open access policy
ISSN 1746-4811
Publication date 2014-10-20
Year available 2014
Sub-type Article (original research)
DOI 10.1186/1746-4811-10-34
Open Access Status DOI
Volume 10
Issue 34
Start page 1
End page 14
Total pages 14
Place of publication London, United Kingdom
Publisher BioMed Central
Collection year 2015
Language eng
Formatted abstract
Background

Studying gene evolution in non-model species by PCR-based approaches is limited to highly conserved genes. The plummeting cost of next generation sequencing enables the application of de novo transcriptomics to any species.

Results

Here we describe how to apply de novo transcriptomics to pursue the evolution of a single gene of interest. We follow a rapidly evolving seed protein that encodes small, stable peptides. We use software that needs limited bioinformatics background and assemble four de novo seed transcriptomes. To demonstrate the quality of the assemblies, we confirm the predicted genes at the peptide level on one species which has over ten copies of our gene of interest. We explain strategies that favour assembly of low abundance genes, what assembly parameters help capture the maximum number of transcripts, how to develop a suite of control genes to test assembly quality and we compare several sequence depths to optimise cost and data volume.

Conclusions

De novo transcriptomics is an effective approach for studying gene evolution in species for which genome support is lacking.
Keyword De novo transcriptomics
Gene evolution
PawS1
Cyclic peptides
RNA-seq Data
Cyclic peptides
Messenger RNA
Seed protein
Genome
Sunflower
Identification
Biosynthesis
Arabidopsis
Features
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Non HERDC
Institute for Molecular Bioscience - Publications
 
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