Grass MicroRNA Gene Paleohistory Unveils New Insights into Gene Dosage Balance in Subgenome Partitioning after Whole-Genome Duplication
Grass MicroRNA Gene Paleohistory Unveils New Insights into Gene Dosage Balance in Subgenome Partitioning after Whole-Genome Duplication
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DOI：
10.1105/tpc.112.095752
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发表时间：
2012-05-01
期刊：
影响因子：
11.6
通讯作者：
Salse, Jerome
中科院分区：
文献类型：
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作者：
Abrouk, Michael;Zhang, Rongzhi;Salse, Jerome
最近可用的植物基因组序列，结合强大的现代单子叶植物和真双子叶植物核型从他们的二倍体祖先的进化方案，提供了一个机会，以获得深入了解microRNA（miRNA）基因在植物的古历史。对植物中miRNA和相关蛋白质编码靶标的表征和比较使我们能够揭示（1）全基因组复制（WGD）后单子叶植物和真双子叶植物中miRNA的对比基因组保守模式，（2）单子叶植物基因组中的祖先miRNA创始人库可以追溯到1亿年前，（3）在WGD后二倍化过程中miRNA亚基因组优势，选择性miRNA缺失补充可能的转座元件介导的回流，以及（4）遵循基因剂量平衡规则的miRNA/靶点相互作用指导的miRNA差异丢失/保留。总之，我们的数据表明，草基因组中过度保留的miRNA可能与胁迫反应的相关基因调控有关，这对植物适应至关重要，对作物品种创新也很有用。
The recent availability of plant genome sequences, combined with a robust evolutionary scenario of the modern monocot and eudicot karyotypes from their diploid ancestors, offers an opportunity to gain insights into microRNA (miRNA) gene paleohistory in plants. Characterization and comparison of miRNAs and associated protein-coding targets in plants allowed us to unravel (1) contrasted genome conservation patterns of miRNAs in monocots and eudicots after whole-genome duplication (WGD), (2) an ancestral miRNA founder pool in the monocot genomes dating back to 100 million years ago, (3) miRNA subgenome dominance during the post-WGD diploidization process with selective miRNA deletion complemented with possible transposable element-mediated return flows, and (4) the miRNA/target interaction-directed differential loss/retention of miRNAs following the gene dosage balance rule. Together, our data suggest that overretained miRNAs in grass genomes may be implicated in connected gene regulations for stress responses, which is essential for plant adaptation and useful for crop variety innovation.