ArticlePlant methods2014
Next generation sequencing and de novo transcriptomics to study gene evolution.
Article in Plant methods, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Plant peptides - redefining an area of ribosomally synthesized and post-translationally modified peptides.Natural product reports · 2024Review
- Solution NMR and racemic crystallography provide insights into a novel structural class of cyclic plant peptides.RSC chemical biology · 2021Article
- Plant derived cyclic peptides.Biochemical Society transactions · 2021Review
- A chameleonic macrocyclic peptide with drug delivery applications.Chemical science · 2021Article
- Parallel analysis of global garlic gene expression and alliin content following leaf wounding.BMC plant biology · 2021Article
- Integrated Analysis of the Transcriptome and Metabolome ofInternational journal of molecular sciences · 2020Article
- Impact of arbuscular mycorrhizal fungi (AMF) on gene expression of some cell wall and membrane elements of wheat (Physiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
- Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos.BMC plant biology · 2018Article
- A family of small, cyclic peptides buried in preproalbumin since the Eocene epoch.Plant direct · 2018Article
- Evidence for Ancient Origins of Bowman-Birk Inhibitors fromThe Plant cell · 2017Article
- A tripartite approach identifies the major sunflower seed albumins.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2016Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundStudying 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.
resultsHere 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.
conclusionsDe novo transcriptomics is an effective approach for studying gene evolution in species for which genome support is lacking.
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