College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.
Plant J. 2021 Feb;105(4):1072-1082. doi: 10.1111/tpj.15088. Epub 2021 Feb 9.
Eukaryotic genes can be classified into intronless (no introns), intron-poor (three or fewer introns per gene) or intron-rich. Early eukaryotic genes were mostly intron-rich, and their alternative splicing into multiple transcripts, giving rise to different proteins, might have played pivotal roles in adaptation and evolution. Interestingly, extant plant genomes contain many gene families with one or sometimes few sub-families with genes that are intron-poor or intronless, and it remains unknown when and how these intron-poor or intronless genes have originated and evolved, and what their possible functions are. In this study, we identified 33 such gene families that contained intronless and intron-poor sub-families. Intronless genes seemed to have first emerged in early land plant evolution, while intron-poor sub-families seemed first to have appeared in green algae. In contrast to intron-rich genes, intronless genes in intron-poor sub-families occurred later, and were subject to stronger functional constraints. Based on RNA-seq analyses in Arabidopsis and rice, intronless or intron-poor genes in AP2, EF-hand_7, bZIP, FAD_binding_4, STE_STE11, CAMK_CAMKL-CHK1 and C2 gene families were more likely to play a role in response to drought and salt stress, compared with intron-rich genes in the same gene families, whereas intronless genes in the B_lectin and S_locus_glycop gene family were more likely to participate in epigenetic processes and plant development. Understanding the origin and evolutionary trajectory, as well as the potential functions, of intronless and intron-poor sub-families provides further insight into plant genome evolution and the functional divergence of genes.
真核生物基因可分为无内含子（无内含子）、内含子贫乏（每个基因有 3 个或更少的内含子）或内含子丰富。早期真核生物基因大多是内含子丰富的，其通过可变剪接成多个转录本，产生不同的蛋白质，可能在适应和进化中发挥了关键作用。有趣的是，现存植物基因组包含许多基因家族，其中一个或有时只有少数亚家族的基因是内含子贫乏或无内含子的，而这些内含子贫乏或无内含子的基因是何时以及如何起源和进化的，以及它们可能的功能是什么，目前还不清楚。在这项研究中，我们鉴定了 33 个这样的基因家族，其中包含无内含子和内含子贫乏的亚家族。无内含子基因似乎首先出现在早期陆地植物进化中，而内含子贫乏的亚家族似乎首先出现在绿藻中。与内含子丰富的基因相比，内含子贫乏亚家族中的无内含子基因出现得较晚，并且受到更强的功能约束。基于拟南芥和水稻的 RNA-seq 分析，AP2、EF-hand_7、bZIP、FAD_binding_4、STE_STE11、CAMK_CAMKL-CHK1 和 C2 基因家族中的无内含子或内含子贫乏基因比同一基因家族中的内含子丰富基因更有可能在响应干旱和盐胁迫中发挥作用，而 B_lectin 和 S_locus_glycop 基因家族中的无内含子基因更有可能参与表观遗传过程和植物发育。了解无内含子和内含子贫乏亚家族的起源和进化轨迹以及潜在功能，为植物基因组进化和基因功能分化提供了进一步的认识。
