The <em>Agaricus bisporus cox1</em> Gene: The Longest Mitochondrial Gene and the Largest Reservoir of Mitochondrial Group I Introns

In eukaryotes, introns are located in nuclear and organelle genes from several kingdoms. Large introns (up to 5 kbp) are frequent in mitochondrial genomes of plant and fungi but scarce in Metazoa, even if these organisms are grouped with fungi among the Opisthokonts. Mitochondrial introns are classified in two groups (I and II) according to their RNA secondary structure involved in the intron self-splicing mechanism. Most of these mitochondrial group I introns carry a “Homing Endonuclease Gene” (heg) encoding a DNA endonuclease acting in transfer and site-specific integration (“homing”) and allowing intron spreading and gain after lateral transfer even between species from different kingdoms. Opposed to this gain mechanism, is another which implies that introns, which would have been abundant in the ancestral genes, would mainly evolve by loss. The importance of both mechanisms (loss and gain) is matter of debate. Here we report the sequence of the cox1 gene of the button mushroom Agaricus bisporus, the most widely cultivated mushroom in the world. This gene is both the longest mitochondrial gene (29,902 nt) and the largest group I intron reservoir reported to date with 18 group I and 1 group II. An exhaustive analysis of the group I introns available in cox1 genes shows that they are mobile genetic elements whose numerous events of loss and gain by lateral transfer combine to explain their wide and patchy distribution extending over several kingdoms. An overview of intron distribution, together with the high frequency of eroded heg, suggests that they are evolving towards loss. In this landscape of eroded and lost intron sequences, the A. bisporus cox1 gene exhibits a peculiar dynamics of intron keeping and catching, leading to the largest collection of mitochondrial group I introns reported to date in a Eukaryote.在真核生物中，内含子（intron）存在于多个界的核基因与细胞器基因中。长度可达5千碱基对（kbp）的大型内含子在植物与真菌的线粒体基因组中较为常见，但在后生动物（Metazoa）中却十分罕见——即便后生动物与真菌同属于后鞭毛生物（Opisthokonts）。根据内含子自剪接机制所依赖的RNA二级结构，线粒体内含子可分为两组（I组与II组）。此类线粒体I组内含子大多携带一段归巢内切酶基因（Homing Endonuclease Gene，heg），该基因编码一种可参与转移与位点特异性整合（即“归巢”）的DNA内切酶，能够在侧向转移后促成内含子在不同界的物种间扩散与获得。与这种获得机制相对的是另一种演化路径：祖先基因中原本丰度较高的内含子主要通过丢失的方式完成演化。这两种机制（丢失与获得）的相对重要性目前仍存在争议。本研究报道了全球栽培最广泛的双孢蘑菇（Agaricus bisporus）的细胞色素c氧化酶亚基1（cox1）基因序列。该基因不仅是目前已知最长的线粒体基因（全长29902个核苷酸，nt），同时也是截至目前已报道的最大I组内含子存储库，共包含18个I组内含子与1个II组内含子。对已报道的cox1基因中的I组内含子进行的全面分析显示，此类内含子属于可移动遗传元件（mobile genetic elements）；大量通过侧向转移发生的获得与丢失事件，共同解释了其在多个界中广泛却斑驳不均的分布模式。综合内含子分布情况与归巢内切酶基因的高频退化现象，研究结果表明内含子正朝着丢失的方向演化。在这一内含子序列不断退化与丢失的演化图景中，双孢蘑菇的cox1基因却展现出独特的内含子留存与捕获动态，使其成为截至目前已知真核生物中拥有最多线粒体I组内含子的物种。