Abstract
In the absence of a reference genome, the ultimate goal of a de novo transcriptome assembly is to accurately and comprehensively reconstruct the set of messenger RNA transcripts represented in the sample. Non-reference assembly of the transcriptome of polyploid species poses a particular challenge because of the presence of homeologs that are difficult to disentangle at the sequence level. This is especially true for hexaploid oats, which have three highly similar subgenomes, two of which are thought to be nearly identical. Under these circumstances, most software packages and established pipelines encounter difficulties in rendering an accurate transcriptome because they are typically developed, refined, and tested for diploid organisms. We present a protocol for transcriptome assembly in oats that can be extended both to other polyploids and species with highly duplicated genomes.
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Acknowledgments
Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. This work was carried out in part using computing resources at the University of Minnesota Supercomputing Institute. The authors thank the Biomedical Genomics Center, University of Minnesota for the testing of different protocols for library preparation and sequencing reactions.
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Gutierrez-Gonzalez, J.J., Garvin, D.F. (2017). De Novo Transcriptome Assembly in Polyploid Species. In: Gasparis, S. (eds) Oat. Methods in Molecular Biology, vol 1536. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6682-0_15
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DOI: https://doi.org/10.1007/978-1-4939-6682-0_15
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Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-6680-6
Online ISBN: 978-1-4939-6682-0
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