Open AccessCharacterisation and Analysis of the Aegilops sharonensis Transcriptome, a Wild Relative of Wheat in the Sitopsis Section
Author(s) -
Costas Bouyioukos,
Matthew J. Moscou,
Nicolas Champouret,
Inmaculada Hernández-Pinzón,
Eric Ward,
Brande B. H. Wulff
Publication year - 2013
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0072782
Subject(s) - brachypodium distachyon , biology , aegilops tauschii , brachypodium , contig , genetics , genome , common wheat , single nucleotide polymorphism , plant disease resistance , sequence assembly , transcriptome , gene , ploidy , selfing , pyrosequencing , chromosome , population , gene expression , demography , sociology , genotype
AegilopssharonensisEig (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 distinctAe. sharonensisaccessions (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. TheAe. sharonensisleaf 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 inAe. sharonensis . These resources provide an initial framework to further build on and characterise the genetic and genomic structure ofAe. sharonensis .