Abstract
Aegilops sharonensis Eig (Sharon goatgrass) is a wild diploid relative of wheat within the Sitopsis section of Aegilops . This species represents an untapped reservoir of genetic diversity for traits of agronomic importance, especially as a source of novel disease resistance. To gain a foothold in this genetic resource, we sequenced the cDNA from leaf tissue of two geographically distinct Ae . sharonensis accessions (1644 and 2232) using the 454 Life Sciences platform. We compared the results of two different assembly programs using different parameter sets to generate 13 distinct assemblies in an attempt to maximize representation of the gene space in de novo transcriptome assembly. The most sensitive assembly (71,029 contigs; N50 674 nts) retrieved 18,684 unique best reciprocal BLAST hits (BRBH) against six previously characterised grass proteomes while the most specific assembly (30,609 contigs; N50 815 nts) retrieved 15,687 BRBH. We combined these two assemblies into a set of 62,243 non-redundant sequences and identified 139 belonging to plant disease resistance genes of the nucleotide binding leucine-rich repeat class. Based on the non-redundant sequences, we predicted 37,743 single nucleotide polymorphisms (SNP), equivalent to one per 1,142 bp. We estimated the level of heterozygosity as 1.6% in accession 1644 and 30.1% in 2232. The Ae . sharonensis leaf transcriptome provides a rich source of sequence and SNPs for this wild wheat relative. These sequences can be used with existing monocot genome sequences and EST sequence collections (e.g. barley, Brachypodium , wheat, rice, maize and Sorghum ) to assist with genetic and physical mapping and candidate gene identification in Ae . sharonensis . These resources provide an initial framework to further build on and characterise the genetic and genomic structure of Ae . sharonensis .
Highlights
Wheat (Triticum spp) is one of the world’s most important cereal crops; it is a major staple across much of the developed and developing world, supplying ~20% of human dietary calories [1]
Two Ae. sharonensis accessions were chosen based on their reaction to Ug99, a highly virulent isolate of Puccinia graminis f. sp. tritici (Pgt), the causal agent of wheat stem rust
We present the de novo assembly, the functional characterisation, and the genetic variability of the leaf transcriptome of two Ae. sharonensis accessions
Summary
Wheat (Triticum spp) is one of the world’s most important cereal crops; it is a major staple across much of the developed and developing world, supplying ~20% of human dietary calories [1]. Ae. sharonensis has received attention as a source of resistance to the Ug99 race of wheat stem rust [6,7], which poses a major threat to global food security [8]. Several attributes make Ae. sharonensis attractive for identifying genes for wheat improvement: (i) it is diploid, (ii), wild accessions collected from its range along the IsraeliLebanon coastline display high genetic diversity [9], and (iii) pure isolines can be readily maintained in the laboratory
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