UBC Botanical Garden and Centre for Plant Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
Mol Biol Evol. 2010 Jul;27(7):1686-97. doi: 10.1093/molbev/msq054. Epub 2010 Feb 25.
Gene duplication at various scales, from single gene duplication to whole-genome (WG) duplication, has occurred throughout eukaryotic evolution and contributed greatly to the large number of duplicated genes in the genomes of many eukaryotes. Previous studies have shown divergence in expression patterns of many duplicated genes at various evolutionary time scales and cases of gain of a new function or expression pattern by one duplicate or partitioning of functions or expression patterns between duplicates. Alternative splicing (AS) is a fundamental aspect of the expression of many genes that can increase gene product diversity and affect gene regulation. However, the evolution of AS patterns of genes duplicated by polyploidy, as well as in a sizable number of duplicated gene pairs in plants, has not been examined. Here, we have characterized conservation and divergence in AS patterns in genes duplicated by a polyploidy event during the evolutionary history of Arabidopsis thaliana. We used reverse transcription-polymerase chain reaction to assay 104 WG duplicates in six organ types and in plants grown under three abiotic stress treatments to detect organ- and stress-specific patterns of AS. Differences in splicing patterns in one or more organs, or under stress conditions, were found between the genes in a large majority of the duplicated pairs. In a few cases, AS patterns were the same between duplicates only under one or more abiotic stress treatments and not under normal growing conditions or vice versa. We also examined AS in 42 tandem duplicates and we found patterns of AS roughly comparable with the genes duplicated by polyploidy. The alternatively spliced forms in some of the genes created premature stop codons that would result in missing or partial functional domains if the transcripts are translated, which could affect gene function and cause functional divergence between duplicates. Our results indicate that AS patterns have diverged considerably after gene and genome duplication during the evolutionary history of the Arabidopsis lineage, sometimes in an organ- or stress-specific manner. AS divergence between duplicated genes may have contributed to gene functional evolution and led to preservation of some duplicated genes.
基因在各种尺度上的重复，从单个基因重复到全基因组（WG）重复，在真核生物进化过程中发生了很多次，极大地促进了许多真核生物基因组中重复基因的数量。先前的研究表明，在不同的进化时间尺度上，许多重复基因的表达模式发生了分歧，并且一个重复基因获得了新的功能或表达模式，或者功能或表达模式在重复基因之间进行了分配。选择性剪接（AS）是许多基因表达的一个基本方面，它可以增加基因产物的多样性并影响基因调控。然而，多倍体复制的基因以及植物中大量重复基因对的 AS 模式的进化尚未被研究。在这里，我们研究了拟南芥进化历史上的多倍体事件复制的基因的 AS 模式的保守性和分歧性。我们使用逆转录-聚合酶链反应（RT-PCR）在六种器官类型和在三种非生物胁迫处理下生长的植物中检测了 104 个 WG 重复，以检测 AS 的器官和胁迫特异性模式。在大多数重复对的基因中，在一个或多个器官中，或在胁迫条件下，发现了剪接模式的差异。在少数情况下，仅在一种或多种非生物胁迫处理下而不是在正常生长条件下或反之，重复基因的 AS 模式相同。我们还检查了 42 个串联重复基因的 AS，发现它们的 AS 模式与多倍体复制的基因大致相当。一些基因的可变剪接形式产生了过早的终止密码子，如果转录本被翻译，将会导致缺失或部分功能域，这可能会影响基因功能并导致重复基因之间的功能分歧。我们的结果表明，在拟南芥谱系的进化历史中，基因和基因组复制后，AS 模式发生了很大的变化，有时是在器官或胁迫特异性的方式下。重复基因之间的 AS 分歧可能有助于基因功能的进化，并导致一些重复基因的保存。
