Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective.
Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective.
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DOI：
10.1186/1471-2164-13-406
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发表时间：
2012-08-17
期刊：
影响因子：
4.4
通讯作者：
Mueller LA
中科院分区：
文献类型：
--
作者：
Bombarely A;Edwards KD;Sanchez-Tamburrino J;Mueller LA
多倍化是植物进化的重要机制。通过分析取自异源四倍体烟草和亲本基因组供体 N. sylvesteris (S-Genome) 和 N. tomentosiformis (T-Genome) 的叶子转录组，采用系统发育学方法绘制了该植物中同源基因对的命运图谱。烟草叶转录组中存在的基因与其祖先物种的现代代表基因之间的比较表明，只有 33% 的组装转录本可以根据其序列进行区分。表达高于背景水平（超过 5 个读段）的绝大多数基因（83.6% 的非亲本可区分簇和 87.2% 的系统发育拓扑分析簇）显示出相似的总体表达水平。可以鉴定出 968 个基因簇的同源序列，并且该组中的 90%（所有基因的 6%）仅保持一种烟草同源物的表达。当两种同源物都表达时，只有 15%（总数的 0.5%）显示出差异表达的证据，提供了有限的亚功能化证据。比较同义核苷酸取代（Ks）和非同义核苷酸取代（Kn）的比率为自多倍化事件发生以来烟草进化过程中的正选择提供了有限的证据。多倍化是植物物种形成的一种强大机制，可在一代内发生。然而，重复基因可能需要数百万代才能获得新功能。对烟叶转录组的分析表明，即使在烟草等年轻的四倍体中，多倍体化也会导致基因表达的复杂变化。基因丢失和基因沉默或亚功能化可以解释为什么相关基因不表达两种同源物。在全基因组复制（WGD）事件中，多倍体基因组通常保持高比例的基因重复。数据几乎没有提供T基因组或S基因组基因表达优先维持的证据。此外，烟草中几乎没有新功能化的证据表明它在年轻的多倍体中发生的频率较低。
Polyploidization is an important mechanism in plant evolution. By analyzing the leaf transcriptomes taken from the allotetraploid Nicotiana tabacum (tobacco) and parental genome donors, N. sylvesteris (S-Genome) and N. tomentosiformis (T-Genome), a phylogenomic approach was taken to map the fate of homeologous gene pairs in this plant. A comparison between the genes present in the leaf transcriptomes of N. tabacum and modern day representatives of its progenitor species demonstrated that only 33% of assembled transcripts could be distinguished based on their sequences. A large majority of the genes (83.6% of the non parent distinguishable and 87.2% of the phylogenetic topology analyzed clusters) expressed above background level (more than 5 reads) showed similar overall expression levels. Homeologous sequences could be identified for 968 gene clusters, and 90% (6% of all genes) of the set maintained expression of only one of the tobacco homeologs. When both homeologs were expressed, only 15% (0.5% of the total) showed evidence of differential expression, providing limited evidence of subfunctionalization. Comparing the rate of synonymous nucleotide substitution (Ks) and non-synonymous nucleotide substitution (Kn) provided limited evidence for positive selection during the evolution of tobacco since the polyploidization event took place. Polyploidization is a powerful mechanism for plant speciation that can occur during one generation; however millions of generations may be necessary for duplicate genes to acquire a new function. Analysis of the tobacco leaf transcriptome reveals that polyploidization, even in a young tetraploid such as tobacco, can lead to complex changes in gene expression. Gene loss and gene silencing, or subfunctionalization may explain why both homeologs are not expressed by the associated genes. With Whole Genome Duplication (WGD) events, polyploid genomes usually maintain a high percentage of gene duplicates. The data provided little evidence of preferential maintenance of gene expression from either the T- or S-genome. Additionally there was little evidence of neofunctionalization in Nicotiana tabacum suggesting it occurs at a low frequency in young polyploidy.
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DOI：
10.1111/j.1469-8137.2009.03087.x
发表时间：
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期刊：
The New phytologist
影响因子：
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作者：
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