从水稻的纯化选择和表达谱推断pack - mule在水稻中的功能作用[W]

Kousuke Hanada, Veronica A. Vallejo, K. Nobuta, R. Slotkin, D. Lisch, B. Meyers, Shin-Han Shiu, Ning Jiang
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引用次数: 90

摘要

基因复制是新基因进化的重要机制。在植物中,一组特殊的转座因子,称为Pack-MULEs或transduplduplicate,能够大规模地复制和扩增基因或基因片段。尽管有大量的pack - mule,但这些复制体的功能尚不清楚。在此,我们对水稻(Oryza sativa)中2809个packmules的表达和纯化选择进行了综合分析,这些基因来源于1501个亲本基因。至少22%的Pack-MULEs被转录,28个Pack-MULEs有翻译的直接证据。嵌合Pack-MULEs包含来自多个基因的基因片段,比仅来自单个基因的片段表达频率高得多。此外,pack - mule通常与小rna相关。这些小rna的存在与pack - mule及其亲本基因的表达减少有关。此外,使用非同义(Ka)和同义(Ks)替代率的比率对pack - mule的选择压力进行评估表明,相当数量的pack - mule可能处于选择约束之下。在感向表达的Pack-MULE中,Pack-MULE和亲本基因对的Ka/Ks值较低。综上所述,我们的分析表明,大量pack - mule被表达并受到纯化选择的影响,其中一些与小rna相关。因此,至少有一部分pack - mule可能是功能性的,并且在调节基因表达以及提供新的编码能力方面具有很大的潜力。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
The Functional Role of Pack-MULEs in Rice Inferred from Purifying Selection and Expression Profile[W]
Gene duplication is an important mechanism for evolution of new genes. In plants, a special group of transposable elements, called Pack-MULEs or transduplicates, is able to duplicate and amplify genes or gene fragments on a large scale. Despite the abundance of Pack-MULEs, the functionality of these duplicates is not clear. Here, we present a comprehensive analysis of expression and purifying selection on 2809 Pack-MULEs in rice (Oryza sativa), which are derived from 1501 parental genes. At least 22% of the Pack-MULEs are transcribed, and 28 Pack-MULEs have direct evidence of translation. Chimeric Pack-MULEs, which contain gene fragments from multiple genes, are much more frequently expressed than those derived only from a single gene. In addition, Pack-MULEs are frequently associated with small RNAs. The presence of these small RNAs is associated with a reduction in expression of both the Pack-MULEs and their parental genes. Furthermore, an assessment of the selection pressure on the Pack-MULEs using the ratio of nonsynonymous (Ka) and synonymous (Ks) substitution rates indicates that a considerable number of Pack-MULEs likely have been under selective constraint. The Ka/Ks values of Pack-MULE and parental gene pairs are lower among Pack-MULEs that are expressed in sense orientations. Taken together, our analysis suggests that a significant number of Pack-MULEs are expressed and subjected to purifying selection, and some are associated with small RNAs. Therefore, at least a subset of Pack-MULEs are likely functional and have great potential in regulating gene expression as well as providing novel coding capacities.
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