The transcriptome of four tissues/organs (shoots and roots at the seedling stage, reproductive organs and developing grains) was assembled de novo, yielding 180,108 contigs, with a N50 length of 1121 bp and mean contig length of 883 bp. Alignment against the transcriptome of nine plant species identified 43% of transcripts with homology to at least one reference transcriptome. The functional annotation was completed by means of a combination of complementary software. The presence of differential expression between the A- and B-homoeolog copies of the durum wheat tetraploid genome was ascertained by phase reconstruction of polymorphic sites based on the T. urartu transcripts and inferring homoeolog-specific sequences. We observed greater expression divergence between A and B homoeologs in grains rather than in leaves and roots. The transcriptomes of 13 durum wheat cultivars spanning the breeding period from 1969 to 2005 were analysed for SNP diversity, leading to 95,358 non-rare, hemi-SNPs shared among two or more cultivars and 33,747 locus-specific (diploid inheritance) SNPs. Our study updates and expands the de novo transcriptome reference assembly available for durum wheat. Out of 180,108 assembled transcripts, 13,636 were specific to the Svevo cultivar as compared to the only other reference transcriptome available for durum, thus contributing to the identification of the tetraploid wheat pan-transcriptome. Additionally, the analysis of 13 historically relevant hallmark varieties produced a SNP dataset that could successfully validate the genotyping in tetraploid wheat and provide a valuable resource for genomics-assisted breeding of both tetraploid and hexaploid wheats.ĭurum wheat ( Triticum turgidum L. Husnot) is a naked, free-threshing domesticated tetraploid wheat derived from a natural intergeneric hybridisation and polyploidisation event involving the A and B genomes of Triticum urartu and an unknown species related to Aegilops speltoides. It is believed that the diploid progenitors of wheat diverged from a common ancestor about 2.5–4.5 million years ago, which would explain the relatively high sequence identity of coding regions among the different wheat homoeologs. dicoccoides Körn) was domesticated as emmer wheat ( Triticum turgidum ssp. dicoccum Schrank) approximately 10,000 years ago and subsequently as durum wheat, hence undergoing successive reductions in population size and genetic diversity. Compared to diploid wheats (einkorn), tetraploid wheats were more attractive for domestication due to a larger ear and seed size.Īssembling tetraploid wheat sequences poses significant challenges owing to the large genome size and its high redundancy as well as the high level of chromosomal rearrangements. Therefore, the conservation of gene content and expression patterns across species is unknown. Moreover, particularly important is the correct identification, hence separation, of the homoeolog sequences.Ī remarkable advancement in high-throughput sequencing of transcriptomes in polyploid species was achieved by adopting a multiple k-mer assembly strategy that allowed Krasileva et al.įor the above reasons, de novo assembly of the transcriptome is essential for the identification of candidate genes, the development of SNP markers and genomic analyses. to obtain a high-quality transcriptome assembly of the durum wheat cultivar Kronos. The same authors separated homoeolog sequences as reported also in previous work along with the development of a specific tool to disentangle homoeolog contigs in durum wheat genes. The final transcriptome resulted in 140,118 contigs of T. turgidum and 66,633 predicted ORFs that were functionally annotated using a comparative genomics approach. An evaluation of the assembly showed that 96% of a benchmark full-length cDNA dataset is assembled in a single contig.
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