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Separating homeologs by phasing in the tetraploid wheat transcriptome

Ksenia V Krasileva1, Vince Buffalo1, Paul Bailey2, Stephen Pearce1, Sarah Ayling2, Facundo Tabbita1, Marcelo Soria13, Shichen Wang4, IWGS Consortium5, Eduard Akhunov4, Cristobal Uauy6 and Jorge Dubcovsky17*

Author affiliations

1 Dept. Plant Sciences, University of California, Davis, CA 9561, USA

2 The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK

3 Microbiology, University of Buenos Aires, INBA-CONICET, Buenos Aires, Argentina

4 Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA

5 International Wheat Genome Sequencing Consortium

6 John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK

7 Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA

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Citation and License

Genome Biology 2013, 14:R66  doi:10.1186/gb-2013-14-6-r66

Published: 25 June 2013

Abstract

Background

The high level of identity among duplicated homoeologous genomes in tetraploid pasta wheat presents substantial challenges for de novo transcriptome assembly. To solve this problem, we develop a specialized bioinformatics workflow that optimizes transcriptome assembly and separation of merged homoeologs. To evaluate our strategy, we sequence and assemble the transcriptome of one of the diploid ancestors of pasta wheat, and compare both assemblies with a benchmark set of 13,472 full-length, non-redundant bread wheat cDNAs.

Results

A total of 489 million 100 bp paired-end reads from tetraploid wheat assemble in 140,118 contigs, including 96% of the benchmark cDNAs. We used a comparative genomics approach to annotate 66,633 open reading frames. The multiple k-mer assembly strategy increases the proportion of cDNAs assembled full-length in a single contig by 22% relative to the best single k-mer size. Homoeologs are separated using a post-assembly pipeline that includes polymorphism identification, phasing of SNPs, read sorting, and re-assembly of phased reads. Using a reference set of genes, we determine that 98.7% of SNPs analyzed are correctly separated by phasing.

Conclusions

Our study shows that de novo transcriptome assembly of tetraploid wheat benefit from multiple k-mer assembly strategies more than diploid wheat. Our results also demonstrate that phasing approaches originally designed for heterozygous diploid organisms can be used to separate the close homoeologous genomes of tetraploid wheat. The predicted tetraploid wheat proteome and gene models provide a valuable tool for the wheat research community and for those interested in comparative genomic studies.

Keywords:
Transcriptome assembly; multiple k-mer assembly; wheat; polyploid; Triticum urartu; Triticum turgidum; pseudogenes; phasing; gene prediction