Genome distribution of differential homoeologue contributions to leaf gene expression in bread wheat.
Genome distribution of differential homoeologue contributions to leaf gene expression in bread wheat.
复制标题
差异同源物对面包小麦中叶基因表达的差异贡献的基因组分布。
DOI：
10.1111/pbi.12486
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发表时间：
2016-05
影响因子：
13.8
通讯作者：
Bancroft I
中科院分区：
文献类型：
--
作者：
Harper AL;Trick M;He Z;Clissold L;Fellgett A;Griffiths S;Bancroft I
使用从头转录组组装，新开发的9495标记转录组SNP遗传连锁图谱和比较基因组学方法的组合，我们开发了六倍体小麦每个亚基因组的有序非冗余转录本集：A（47 160 unigenes），B（59 663 unigenes）和D（40 588 unigenes）。我们使用这些作为参考序列，对照其映射来自幼叶组织的Illumina mRNA-Seq读数。对每个单基因的转录物丰度进行定量。使用三向相互BLAST方法，鉴定了15527个同源物的三联体集（每个基因组一个）。鉴定了5248个单基因的差异表达（P < 0.05），其中2906个单基因的丰度高于其两个同源物，2342个单基因的丰度低于其两个同源物。基因本体论术语的分析显示，同源之间没有偏见。没有证据表明存在全基因组显性效应，相反，转录水平更高的单个基因分布在所有三个基因组中。转录组显示瓦片图，一种基于CMYK颜色空间的可视化方法，被开发并用于评估基因组中偏斜同源物转录丰度的区域。广泛的条纹显示，指示许多小区域的基因组优势（转录同源物从一个基因组比其他更丰富）和许多较大的区域的基因组抑制（转录同源物从一个基因组比其他更少丰富）。
Using a combination of de novo transcriptome assembly, a newly developed 9495‐marker transcriptome SNP genetic linkage map and comparative genomics approaches, we developed an ordered set of nonredundant transcripts for each of the subgenomes of hexaploid wheat: A (47 160 unigenes), B (59 663 unigenes) and D (40 588 unigenes). We used these as reference sequences against which to map Illumina mRNA‐Seq reads derived from young leaf tissue. Transcript abundance was quantified for each unigene. Using a three‐way reciprocal BLAST approach, 15 527 triplet sets of homoeologues (one from each genome) were identified. Differential expression (P < 0.05) was identified for 5248 unigenes, with 2906 represented at greater abundance than their two homoeologues and 2342 represented at lower abundance than their two homoeologues. Analysis of gene ontology terms revealed no biases between homoeologues. There was no evidence of genomewide dominance effects, rather the more highly transcribed individual genes were distributed throughout all three genomes. Transcriptome display tile plot, a visualization approach based on CMYK colour space, was developed and used to assess the genome for regions of skewed homoeologue transcript abundance. Extensive striation was revealed, indicative of many small regions of genome dominance (transcripts of homoeologues from one genome more abundant than the others) and many larger regions of genome repression (transcripts of homoeologues from one genome less abundant than the others).