BACKGROUND It is widely accepted that the last eukaryotic common ancestor and early eukaryotes were intron-rich and intron loss dominated subsequent evolution, thus the presence of only very few introns in some modern eukaryotes must be the consequence of massive loss. But it is striking that few eukaryotes were found to have completely lost introns. Despite extensive research, the causes of massive intron losses remain elusive. Actually the reverse question -- how the few introns can be retained under the evolutionary selection pressure of intron loss -- is equally significant but was rarely studied, except that it was conjectured that the essential functions of some introns prevent their loss. The situation that extremely few (eight) spliceosome-mediated cis-spliced introns present in the relatively simple genome of Giardia lamblia provides an excellent opportunity to explore this question. RESULTS Our investigation found three types of distribution patterns of the few introns in the intron-containing genes: ancient intron in ancient gene, later-evolved intron in ancient gene, and later-evolved intron in later-evolved gene, which can reflect to some extent the dynamic evolution of introns in Giardia. Without finding any special features or functional importance of these introns responsible for their retention, we noticed and experimentally verified that some intron-containing genes form sense-antisense gene pairs with transcribable genes on their complementary strands, and that the introns just reside in the overlapping regions. CONCLUSIONS In Giardia's evolution, despite constant evolutionary selection pressure of intron loss, intron gain can still occur in both ancient and later-evolved genes, but only a few introns are retained; at least the evolutionary retention of some of the introns might not be due to the functional constraint of the introns themselves but the causes outside of introns, such as the constraints imposed by other genomic functional elements overlapping with the introns. These findings can not only provide some clues to find new genomic functional elements -- in the areas overlapping with introns, but suggest that "functional constraint" of introns may not be necessarily directly associated with intron loss and gain, and that the real functions are probably still outside of our current knowledge. REVIEWERS This article was reviewed by Mikhail Gelfand, Michael Gray, and Igor Rogozin.

中文翻译：

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有义-反义基因重叠可能是在贾第鞭毛虫基因组中保留少数内含子的原因及其影响。

背景技术广泛接受的是，最后的真核生物共同祖先和早期的真核生物富含内含子，内含子丢失主导了随后的进化，因此在某些现代真核生物中只有极少的内含子必须是大量丢失的结果。但令人惊讶的是，几乎没有发现真核生物完全丧失了内含子。尽管进行了广泛的研究，大量内含子损失的原因仍然难以捉摸。实际上，相反的问题-在内含子丢失的进化选择压力下如何保留少数内含子-同样重要，但很少有人研究，只是推测某些内含子的基本功能阻止了它们的丢失。贾第鞭毛虫相对简单的基因组中存在极少（八个）剪接体介导的顺式剪接内含子的情况为探讨这一问题提供了极好的机会。结果我们的研究发现含内含子的基因中少数内含子的三种分布模式：古代基因中的古代内含子，古代基因中的后来进化的内含子和后来进化的基因中的后来进化的内含子，这可以反映出一些贾第虫中内含子的动态进化。在没有发现这些内含子导致它们滞留的任何特殊特征或功能重要性的情况下，我们注意到并通过实验验证了一些含内含子的基因与它们互补链上的可转录基因形成有义反义基因对，并且这些内含子仅位于重叠区域地区。结论在贾第鞭毛虫的进化过程中，尽管内含子丢失的进化选择压力不断，但内含子的获得仍可在古代和后来进化的基因中发生，但只保留了少数内含子。至少某些内含子的进化保留可能不是由于内含子本身的功能限制，而是内含子之外的原因，例如与内含子重叠的其他基因组功能元件所施加的限制。这些发现不仅可以提供一些线索，在与内含子重叠的区域中找到新的基因组功能元件，而且还暗示内含子的“功能限制”不一定与内含子的损失和增益直接相关，而真正的功能是可能仍在我们目前的知识范围之外。