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Title: De novo transciptome assembly in polyploid species

item GUTIERREZ-GONZALEZ, J - University Of Minnesota
item Garvin, David

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 4/29/2016
Publication Date: 1/29/2017
Citation: Gutierrez-Gonzalez, J.J., Garvin, D.F. 2017. De novo transciptome assembly in polyploid species. In: Gasparis, S., editor. Oat. Methods and Protocals. Vol 1536. New York, NY: Springer. p.209-221.

Interpretive Summary:

Technical 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.