Next generation sequencing and de novo transcriptomics to study gene evolution

A.S. Jayasena, David Secco, Kalia Bernath-Levin, Oliver Berkowitz, James Whelan, Josh Mylne

Research output: Contribution to journalArticle

14 Citations (Scopus)

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.
Original languageEnglish
Pages (from-to)1-14
Number of pages14
JournalPlant Methods
Volume10
Issue number1
DOIs
Publication statusPublished - 20 Oct 2014

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transcriptomics
Genes
genes
Seeds
peptides
Costs and Cost Analysis
Peptides
Computational Biology
seeds
Transcriptome
bioinformatics
transcriptome
Software
Genome
Polymerase Chain Reaction
genome
Proteins

Cite this

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title = "Next generation sequencing and de novo transcriptomics to study gene evolution",
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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Next generation sequencing and de novo transcriptomics to study gene evolution. / Jayasena, A.S.; Secco, David; Bernath-Levin, Kalia; Berkowitz, Oliver; Whelan, James; Mylne, Josh.

In: Plant Methods, Vol. 10, No. 1, 20.10.2014, p. 1-14.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Next generation sequencing and de novo transcriptomics to study gene evolution

AU - Jayasena, A.S.

AU - Secco, David

AU - Bernath-Levin, Kalia

AU - Berkowitz, Oliver

AU - Whelan, James

AU - Mylne, Josh

PY - 2014/10/20

Y1 - 2014/10/20

N2 - 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.

AB - 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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DO - 10.1186/1746-4811-10-34

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