De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum.
De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum.
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DOI：
10.1371/journal.pone.0096855
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Jaiswal P
中科院分区：
文献类型：
--
作者：
Fox SE;Geniza M;Hanumappa M;Naithani S;Sullivan C;Preece J;Tiwari VK;Elser J;Leonard JM;Sage A;Gresham C;Kerhornou A;Bolser D;McCarthy F;Kersey P;Lazo GR;Jaiswal P
单粒小麦（Triticum monococcum, 2n）是栽培六倍体小麦a基因组祖先T. urartu的近亲，因此是研究二倍体小麦光形态发生调控成分的一个有用模型。为了为这一研究开发遗传和基因组资源，我们构建了两个小麦亚种、野生冬小麦T. monococum ssp的全基因组转录组。春小麦（品种G3116）和驯化春小麦。通过生成来自黄化和绿色幼苗的RNA-Seq数据的从头组装。DV92和G3116的从头转录组组装分别代表120,911和117,969个转录本。我们成功地将这些转录本中的90%定位到大麦中，并将95%的转录本定位到T. urartu基因组中。然而，只有约77%的转录本映射到注释的大麦基因，约85%的转录本映射到注释的T. urartu基因。差异基因表达分析显示，与DV92相比，G3116转录组中的光上调转录多22%，光下调转录多35%。DV92和G3116 mRNA序列与参考大麦基因组比对，鉴定出约500,000个单核苷酸多态性（SNP）和约22,000个简单序列重复（SSR）位点。小麦单粒小麦（T. monococum）两个二倍体材料的从头转录组组装为改进小麦基因组注释提供了新的经验转录组参考，并为光形态发生过程中的转录编程提供了新的见解。在我们的分析中发现的SNP和SSR位点为分子标记的开发提供了额外的资源。
Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes of two Triticum monococcum subspecies, the wild winter wheat T. monococcum ssp. aegilopoides (accession G3116) and the domesticated spring wheat T. monococcum ssp. monococcum (accession DV92) by generating de novo assemblies of RNA-Seq data derived from both etiolated and green seedlings. The de novo transcriptome assemblies of DV92 and G3116 represent 120,911 and 117,969 transcripts, respectively. We successfully mapped ∼90% of these transcripts from each accession to barley and ∼95% of the transcripts to T. urartu genomes. However, only ∼77% transcripts mapped to the annotated barley genes and ∼85% transcripts mapped to the annotated T. urartu genes. Differential gene expression analyses revealed 22% more light up-regulated and 35% more light down-regulated transcripts in the G3116 transcriptome compared to DV92. The DV92 and G3116 mRNA sequence reads aligned against the reference barley genome led to the identification of ∼500,000 single nucleotide polymorphism (SNP) and ∼22,000 simple sequence repeat (SSR) sites. De novo transcriptome assemblies of two accessions of the diploid wheat T. monococcum provide new empirical transcriptome references for improving Triticeae genome annotations, and insights into transcriptional programming during photomorphogenesis. The SNP and SSR sites identified in our analysis provide additional resources for the development of molecular markers.
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DOI：
10.1186/1939-8433-6-14
发表时间：
2013-05-29
期刊：
Rice (New York, N.Y.)
影响因子：
--
作者：
Hanumappa M;Preece J;Elser J;Nemeth D;Bono G;Wu K;Jaiswal P
通讯作者：
Jaiswal P
影响因子：
3.7
作者：
Fu N;Wang Q;Shen HL
通讯作者：
Shen HL
影响因子：
3.7
作者：
Cumbie JS;Kimbrel JA;Di Y;Schafer DW;Wilhelm LJ;Fox SE;Sullivan CM;Curzon AD;Carrington JC;Mockler TC;Chang JH
通讯作者：
Chang JH
agriGO：农业界的 GO 分析工具包
影响因子：
14.9
作者：
Du Z;Zhou X;Ling Y;Zhang Z;Su Z
通讯作者：
Su Z
DOI：
10.1073/pnas.2435133100
发表时间：
2003-12-09
影响因子：
11.1
作者：
Feuillet, C;Travella, S;Keller, B
通讯作者：
Keller, B