Classification of introns, which is crucial to understanding their evolution and splicing, has historically been binary and has resulted in the naming of major and minor introns that are spliced by their namesake spliceosome. However, a broad range of intron consensus sequences exist, leading us to here reclassify introns as minor, minor-like, hybrid, major-like, major and non-canonical introns in 263 species across six eukaryotic supergroups. Through intron orthology analysis, we discovered that minor-like introns are a transitory node for intron conversion across evolution. Despite close resemblance of their consensus sequences to minor introns, these introns possess an AG dinucleotide at the –1 and –2 position of the 5′ splice site, a salient feature of major introns. Through combined analysis of CoLa-seq, CLIP-seq for major and minor spliceosome components, and RNAseq from samples in which the minor spliceosome is inhibited we found that minor-like introns are also an intermediate class from a splicing mechanism perspective. Importantly, this analysis has provided insight into the sequence elements that have evolved to make minor-like introns amenable to recognition by both minor and major spliceosome components. We hope that this revised intron classification provides a new framework to study intron evolution and splicing.

中文翻译：

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内含子的分类和小内含子的进化


内含子的分类对于理解其进化和剪接至关重要，历史上一直是二元的，并导致了由同名剪接体剪接的主要和次要内含子的命名。然而，存在广泛的内含子共有序列，导致我们在这里将内含子重新分类为 6 个真核超类群 263 个物种的小内含子、小内含子、混合内含子、类大内含子、大内含子和非规范内含子。通过内含子同源分析，我们发现次要内含子是进化过程中内含子转换的过渡节点。尽管它们的共有序列与次要内含子非常相似，但这些内含子在 5' 剪接位点的 –1 和 –2 位置具有 AG 二核苷酸，这是主要内含子的显着特征。通过对主要和次要剪接体成分的 CoLa-seq、CLIP-seq 以及来自次要剪接体被抑制的样本的 RNAseq 的组合分析，我们发现从剪接机制的角度来看，次要类内含子也是一个中间类。重要的是，该分析提供了对序列元素的深入了解，这些序列元素已经进化到使次要样内含子易于被次要和主要剪接体成分识别。我们希望这一修订后的内含子分类为研究内含子进化和剪接提供一个新的框架。