De novo transcriptome assembly in polyploid species

Juan J. Gutierrez-Gonzalez, David F. Garvin

Research output: Chapter in Book/Report/Conference proceedingChapter

4 Scopus citations

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. Nonreference 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.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages209-221
Number of pages13
DOIs
StatePublished - Jan 1 2017

Publication series

NameMethods in Molecular Biology
Volume1536
ISSN (Print)1064-3745

Keywords

  • De novo transcriptome assembly
  • Homeoallele
  • Homeolog
  • Oats
  • Polyploid
  • RNAseq
  • Transcript assembly

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    Gutierrez-Gonzalez, J. J., & Garvin, D. F. (2017). De novo transcriptome assembly in polyploid species. In Methods in Molecular Biology (pp. 209-221). (Methods in Molecular Biology; Vol. 1536). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-6682-0_15