Next generation sequencing and de novo transcriptomics to study gene evolution

Plant Methods

Joshua S Mylne³  James Whelan¹  Oliver Berkowitz²  Kalia Bernath-Levin³  David Secco³  Achala S Jayasena³ 

[1] La Trobe University, Department of Botany, School of Life Sciences & ARC Centre of Excellence in Plant Energy Biology, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Melbourne, Bundoora Victoria 3086, Australia;The University of Western Australia, School of Plant Biology, 35 Stirling Highway, Crawley, Perth 6009, Australia;The University of Western Australia, School of Chemistry and Biochemistry & ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley, Perth 6009, Australia

关键词: Cyclic peptides;    PawS1;    Gene evolution;    De novo transcriptomics;   

Others  :  1151514
DOI  :  10.1186/1746-4811-10-34

 received in 2014-07-30, accepted in 2014-10-08,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Jayasena et al.; licensee BioMed Central Ltd.

【 图 表 】

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