Duplicate genes increase expression diversity in closely related species and allopolyploids
Duplicate genes increase expression diversity in closely related species and allopolyploids
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DOI：
10.1073/pnas.0807350106
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发表时间：
2009-02-17
影响因子：
11.1
通讯作者：
Chen, Z. Jeffrey
中科院分区：
文献类型：
--
作者：
Ha, Misook;Kim, Eun-Deok;Chen, Z. Jeffrey
多倍体或全基因组复制（WGD）为重复基因的序列和表达进化提供了原始遗传材料。然而，WGD重复基因在密切相关的物种和经常性异源多倍体之间的表达分歧的模式和克里思知之甚少。拟南芥是一个合适的系统，用于测试的假设，重复基因增加表达多样性和调控网络。在拟南芥中，WGD在拟南芥和Arabidopsis arenosa之间分裂之前发生了不止一次，并且天然和人造的异源四倍体都是可用的。比较基因组杂交分析表明，WGD后的单拷贝和重复基因在A.和拟南芥A. arenosa。基因表达微阵列的分析表明，重复基因通常有较高水平的表达差异两个密切相关的物种比单拷贝基因。在人工合成的异源四倍体和天然异源四倍体中，非加性表达的祖细胞重复基因的比例显著高于单拷贝基因。与环境胁迫相关的重复基因倾向于差异表达，多拷贝重复基因可能在祖细胞和异源四倍体中分化表达。与单拷贝基因相比，重复基因倾向于包含TATA盒和启动子区域较少的DNA甲基化，从而通过结合转录因子和/或顺式和反式作用蛋白来促进转录调控。这些数据表明，WGD重复基因在调节不同的和新的基因表达变化中的重要作用，以响应外部环境线索和内部遗传混乱，如经常性的多倍性事件。
Polyploidy or whole genome duplication (WGD) provides raw genetic materials for sequence and expression evolution of duplicate genes. However, the mode and tempo of expression divergence between WGD duplicate genes in closely related species and recurrent allopolyploids are poorly understood. Arabidopsis is a suitable system for testing the hypothesis that duplicate genes increase expression diversity and regulatory networks. In Arabidopsis, WGD occurred more than once before the split between Arabidopsis thaliana and Arabidopsis arenosa, and both natural and human-made allotetraploids are available. Comparative genomic hybridization analysis indicated that single-copy and duplicate genes after WGD were well preserved in A. thaliana and A. arenosa. Analysis of gene expression microarrays showed that duplicate genes generally had higher levels of expression divergence between two closely related species than single-copy genes. The proportion of the progenitors' duplicate genes that were nonadditively expressed in the resynthesized and natural allotetraploids was significantly higher than that of single-copy genes. Duplicate genes related to environmental stresses tended to be differentially expressed, and multicopy duplicate genes were likely to diverge expression between progenitors and in the allotetraploids. Compared with single-copy genes, duplicate genes tended to contain TATA boxes and less DNA methylation in the promoter regions, facilitating transcriptional regulation by binding transcription factors and/or cis- and trans- acting proteins. The data suggest an important role of WGD duplicate genes in modulating diverse and novel gene expression changes in response to external environmental cues and internal genetic turmoil such as recurrent polyploidy events.