Separating homeologs by phasing in the tetraploid wheat transcriptome

• Autores: Krasileva, Ksenia V.; Buffalo, Vince; Bailey, Paul; Pearce, Stephen; Ayling, Sarah; Tabbita, Facundo; Soria, Marcelo Abel; Wang, Shichen; Akhunov, Eduard; Uauy, Cristobal; Dubcovsky, Jorge
• Año de publicación: 2013
• Idioma: inglés
• Tipo de recurso: artículo
• Fuente: Genome Biology; Vol.14, no.6; 14:R66; http://genomebiology.com/
• Materia: GENE PREDICTION; PHASING; POLYPLOID; PSEUDOGENES; TRANSCRIPTOME ASSEMBLY; TRITICUM TURGIDUM; TRITICUM URARTU; WHEAT; CONTIG; PROTEOME; TRANSCRIPTOME; CONTROLLED STUDY; DIPLOIDY; GENE SEQUENCE; GENOME; GENOMICS; HETEROZYGOTE; HOMEOLOG; NONHUMAN; OPEN READING FRAME; PLANT GENOME; SINGLE NUCLEOTIDE POLYMORPHISM; TETRAPLOIDY; TRITICUM AESTIVUM; MULTIPLE K-MER ASSEMBLY; PHASING; COMPLEMENTARY DNA
• Institución: Universidad de Buenos Aires. Facultad de Agronomía

Fil: Krasileva, Ksenia V. University of California. Dept. Plant Sciences. Davis, CA 9561, USA.
Fil: Buffalo, Vince. University of California. Dept. Plant Sciences. Davis, CA 9561, USA.
Fil: Bailey, Paul. The Genome Analysis Centre. Norwich Research Park. Norwich NR4 7UH, UK.
Fil: Pearce, Stephen. University of California. Dept. Plant Sciences. Davis, CA 9561, USA.
Fil: Ayling, Sarah. The Genome Analysis Centre. Norwich Research Park. Norwich NR4 7UH, UK.
Fil: Tabbita, Facundo. University of California. Dept. Plant Sciences. Davis, CA 9561, USA.
Fil: Soria, Marcelo Abel. University of California. Dept. Plant Sciences. Davis, CA 9561, USA.
Fil: Soria, Marcelo Abel. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Biología Aplicada y Alimentos. Cátedra de Microbiología Agrícola. Buenos Aires, Argentina.
Fil: Soria, Marcelo Abel. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA). Buenos Aires, Argentina.
Fil: Soria, Marcelo Abel. CONICET – Universidad de Buenos Aires. Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA). Buenos Aires, Argentina.
Fil: Wang, Shichen. Kansas State University. Department of Plant Pathology. Manhattan, KS 66506, USA.
Fil: Akhunov, Eduard. Kansas State University. Department of Plant Pathology. Manhattan, KS 66506, USA.
Fil: Uauy, Cristobal. John Innes Centre. Norwich Research Park. Norwich NR4 7UH, UK.
Fil: Dubcovsky, Jorge. University of California. Dept. Plant Sciences. Davis, CA 9561, USA.
Fil: Dubcovsky, Jorge. Howard Hughes Medical Institute. Chevy Chase, MD 20815, USA.
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 percent 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 percent 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 percent 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.