Department of Biology, McGill University, Montreal, Quebec, Canada.
PLoS Genet. 2012 Sep;8(9):e1002931. doi: 10.1371/journal.pgen.1002931. Epub 2012 Sep 6.
The benefits of ever-growing numbers of sequenced eukaryotic genomes will not be fully realized until we learn to decipher vast stretches of noncoding DNA, largely composed of transposable elements. Transposable elements persist through self-replication, but some genes once encoded by transposable elements have, through a process called molecular domestication, evolved new functions that increase fitness. Although they have conferred numerous adaptations, the number of such domesticated transposable element genes remains unknown, so their evolutionary and functional impact cannot be fully assessed. Systematic searches that exploit genomic signatures of natural selection have been employed to identify potential domesticated genes, but their predictions have yet to be experimentally verified. To this end, we investigated a family of domesticated genes called MUSTANG (MUG), identified in a previous bioinformatic search of plant genomes. We show that MUG genes are functional. Mutants of Arabidopsis thaliana MUG genes yield phenotypes with severely reduced plant fitness through decreased plant size, delayed flowering, abnormal development of floral organs, and markedly reduced fertility. MUG genes are present in all flowering plants, but not in any non-flowering plant lineages, such as gymnosperms, suggesting that the molecular domestication of MUG may have been an integral part of early angiosperm evolution. This study shows that systematic searches can be successful at identifying functional genetic elements in noncoding regions and demonstrates how to combine systematic searches with reverse genetics in a fruitful way to decipher eukaryotic genomes.
直到我们学会破译大量的非编码 DNA 序列，其中主要由可转座元件组成，不断增加的真核生物基因组测序的好处才会完全实现。可转座元件通过自我复制而持续存在，但曾经由可转座元件编码的一些基因，通过一个称为分子驯化的过程，进化出了增加适应性的新功能。尽管它们带来了许多适应性，但这种驯化的可转座元件基因的数量仍然未知，因此它们的进化和功能影响无法得到全面评估。利用基因组自然选择的特征进行系统搜索，已经被用于识别潜在的驯化基因，但它们的预测尚未得到实验验证。为此，我们研究了一个称为 MUSTANG（MUG）的驯化基因家族，该基因家族是在之前对植物基因组的生物信息学搜索中发现的。我们表明 MUG 基因是有功能的。拟南芥 MUG 基因突变体通过减小植物大小、延迟开花、花器官发育异常以及显著降低繁殖力，导致植物适应性严重降低。MUG 基因存在于所有开花植物中，但不存在于任何非开花植物谱系中，如裸子植物，这表明 MUG 的分子驯化可能是早期被子植物进化的一个组成部分。这项研究表明，系统搜索可以成功地识别非编码区域中的功能性遗传元件，并展示了如何将系统搜索与反向遗传学相结合，以有效地破译真核生物基因组。
