Use of mRNA-seq to discriminate contributions to the transcriptome from the constituent genomes of the polyploid crop species Brassica napus.
Use of mRNA-seq to discriminate contributions to the transcriptome from the constituent genomes of the polyploid crop species Brassica napus.
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DOI：
10.1186/1471-2164-13-247
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发表时间：
2012-06-15
期刊：
影响因子：
4.4
通讯作者：
Bancroft I
中科院分区：
文献类型：
--
作者：
Higgins J;Magusin A;Trick M;Fraser F;Bancroft I
多倍体经常导致基因表达发生相当大的变化，无论是立即还是在进化过程中。多倍体的形成往往会产生新的表型，这可能有助于多倍体在自然界的适应性或它们在农业上的选择。油菜（Brassica napus）被广泛用于研究人工重组和自然形态的多倍体过程。mRNA-Seq是最近开发的一种利用深度测序技术进行转录组分析的方法，是多倍体基因表达研究的微阵列的替代方法。Illumina mRNA-Seq在转录物定量方面与微阵列分析相当，但灵敏度更高，而且非常重要的是，它有可能区分多倍体中的同源基因。使用一种新的固化工艺，我们将从油菜a和C基因组的est中获得的共识参考序列改编为包含94,558个原始unigenes中的每个a和C基因组版本的参考序列。我们将来自甘蓝型油菜的reads与这个固化的参考文献比对，发现来自重组系的reads多出38%，来自自然系的reads多出28%。当A和C版本在单核苷酸位置不同时，称为同源间多态性（IHPs），我们能够在A和C基因组同源物之间分配多倍体中的表达。43,761个单基因至少含有一个IHP，平均频率为每kb单基因序列10.5个。在重组的甘蓝型油菜中，6350个具有IHPs的同源基因对之间存在差异表达。3212个单基因在一系列天然甘蓝型油菜作物品种中表现出相似的差异表达模式，其中995个与重组甘蓝型油菜相同。功能分类在与剂量敏感性无关的基因本体类别中表现出过度代表性。mRNA-Seq是测量多倍体转录物丰度的首选方法，因为它能够测量同源物对基因表达的贡献。在新合成的多倍体和天然甘蓝型油菜中发现了大量差异表达基因，证实了多倍体发生后同源基因对的表达会发生直接和长期的变化。
Polyploidy often results in considerable changes in gene expression, both immediately and over evolutionary time. New phenotypes often arise with polyploid formation and may contribute to the fitness of polyploids in nature or their selection for use in agriculture. Oilseed rape (Brassica napus) is widely used to study the process of polyploidy both in artificially resynthesised and natural forms. mRNA-Seq, a recently developed approach to transcriptome profiling using deep-sequencing technologies is an alternative to microarrays for the study of gene expression in a polyploid. Illumina mRNA-Seq is comparable to microarray analysis for transcript quantification but has increased sensitivity and, very importantly, the potential to distinguish between homoeologous genes in polyploids. Using a novel curing process, we adapted a reference sequence that was a consensus derived from ESTs from both Brassica A and C genomes to one containing separate A and C genome versions for each of the 94,558 original unigenes. We aligned reads from B. napus to this cured reference, finding 38% more reads mapping from resynthesised lines and 28% more reads mapping from natural lines. Where the A and C versions differed at single nucleotide positions, termed inter-homoeologue polymorphisms (IHPs), we were able to apportion expression in the polyploid between the A and C genome homoeologues. 43,761 unigenes contained at least one IHP, with a mean frequency of 10.5 per kb unigene sequence. 6,350 of the unigenes with IHPs were differentially expressed between homoeologous gene pairs in resynthesised B. napus. 3,212 unigenes showed a similar pattern of differential expression across a range of natural B. napus crop varieties and, of these, 995 were in common with resynthesised B. napus. Functional classification showed over-representation in gene ontology categories not associated with dosage-sensitivity. mRNA-Seq is the method of choice for measuring transcript abundance in polyploids due to its ability to measure the contributions of homoeologues to gene expression. The identification of large numbers of differentially expressed genes in both a newly resynthesised polyploid and natural B. napus confirms that there are both immediate and long-term alterations in the expression of homoeologous gene pairs following polyploidy.
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影响因子：
8
作者：
Marguerat, Samuel;Baehler, Juerg
通讯作者：
Baehler, Juerg
DOI：
10.1111/j.1469-8137.2009.03087.x
发表时间：
2010-04
期刊：
The New phytologist
影响因子：
--
作者：
Birchler JA;Veitia RA
通讯作者：
Veitia RA
影响因子：
9.4
作者：
Dong, Shaowei;Adams, Keith L.
通讯作者：
Adams, Keith L.
DOI：
10.1073/pnas.94.13.6809
发表时间：
1997-06-24
影响因子：
11.1
作者：
Gaut, BS;Doebley, JF
通讯作者：
Doebley, JF
影响因子：
4.9
作者：
Hegarty, MJ;Jones, JM;Hiscock, SJ
通讯作者：
Hiscock, SJ