Characterisation and analysis of the Aegilops sharonensis transcriptome, a wild relative of wheat in the Sitopsis section.
Characterisation and analysis of the Aegilops sharonensis transcriptome, a wild relative of wheat in the Sitopsis section.
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DOI：
10.1371/journal.pone.0072782
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Wulff BB
中科院分区：
文献类型：
--
作者：
Bouyioukos C;Moscou MJ;Champouret N;Hernández-Pinzón I;Ward ER;Wulff BB
沙毛山羊草(Aegilopps Sharonensis Eig)是山羊草属Sitopsis组小麦的野生二倍体近缘种。本种代表了一个尚未开发的遗传多样性储藏库，具有重要的农艺性状，特别是作为一种新的抗病来源。为了在这一遗传资源中站稳脚跟，我们从两个地理位置不同的Ae.使用454生命科学平台的沙龙种质(1644和2232)。我们比较了使用不同参数设置的两个不同汇编程序的结果，以生成13个不同的汇编，试图最大化地表示从头转录组组装中的基因空间。最敏感的组合(71,029个重叠群；N50 674个核苷酸)检索到针对六个先前特征的GRASS蛋白质组的18,684个唯一的最佳相互冲击(BRBH)，而最特异的组合(30,609个重叠群；N50 815个核苷酸)检索到15,687个BRBH。我们将这两个组合组合成一组62,243个非冗余序列，并鉴定出139个属于富含亮氨酸的核苷酸结合重复类的植物抗病基因。基于非冗余序列，我们预测了37,743个单核苷酸多态(SNP)，相当于每1,142个碱基中有一个。我们估计1644和2232的杂合度水平分别为1.6%和30.1%。Ae.Sharonensis叶片转录组为这一野生小麦近亲提供了丰富的序列和SNPs来源。这些序列可以与现有的单子叶植物基因组序列和EST序列集合(例如大麦、短穗麦、小麦、水稻、玉米和高粱)结合使用，以帮助进行遗传和物理定位以及鉴定Ae.沙龙。这些资源为进一步建立和描述Ae的遗传和基因组结构提供了一个初步的框架。沙龙。
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 .
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