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Assembly, Assessment, and Availability of De novo Generated Eukaryotic Transcriptomes

Moreton, Joanna; Izquierdo, Abril; Emes, Richard D.

Authors

Joanna Moreton

Abril Izquierdo

RICHARD EMES richard.emes@nottingham.ac.uk
Professor of Bioinformatics



Abstract

De novo assembly of a complete transcriptome without the need for a guiding reference genome is attractive, particularly where the cost and complexity of generating a eukaryote genome is prohibitive. The transcriptome should not however be seen as just a quick and cheap alternative to building a complete genome. Transcriptomics allows the understanding and comparison of spatial and temporal samples within an organism and allows surveying of multiple individuals or closely related species. De novo assembly in theory allows the building of a complete transcriptome without any prior knowledge of the genome it also allows the discovery of alternate splice forms of coding RNAs and also non-coding RNAs, which are often missed by proteomic approaches or are incompletely annotated in genome studies. The limitations of the method are that generation of a truly complete assembly is unlikely and so we require some method for assessment of the quality and appropriateness of a generated transcriptome. Whilst no single consensus pipeline or tools is agreed as optimal, various algorithms and easy to use software do exist making transcriptome generation a more common approach. With this expansion of data, questions still exist relating to how do we make these datasets fully discoverable, comparable and most useful to understand complex biological systems?

Citation

Moreton, J., Izquierdo, A., & Emes, R. D. (2016). Assembly, Assessment, and Availability of De novo Generated Eukaryotic Transcriptomes. Frontiers in Genetics, 6, https://doi.org/10.3389/fgene.2015.00361

Journal Article Type Article
Acceptance Date Dec 19, 2015
Online Publication Date Jan 11, 2016
Publication Date Jan 11, 2016
Deposit Date Jan 26, 2017
Publicly Available Date Jan 26, 2017
Journal Frontiers in Genetics
Electronic ISSN 1664-8021
Publisher Frontiers Media
Peer Reviewed Peer Reviewed
Volume 6
Article Number 361
DOI https://doi.org/10.3389/fgene.2015.00361
Keywords de novo transcriptome assembly, high-throughput sequencing, assessment, availability, annotation
Public URL http://eprints.nottingham.ac.uk/id/eprint/40091
Publisher URL http://journal.frontiersin.org/article/10.3389/fgene.2015.00361/full
Copyright Statement Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by/4.0

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fgene-06-00361.pdf (1.3 Mb)
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Publisher Licence URL
http://creativecommons.org/licenses/by/4.0/

Copyright Statement
Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by/4.0





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