Faculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, Bodø, 8026, Norway.
BMC Biol. 2024 Nov 27;22(1):275. doi: 10.1186/s12915-024-02059-w.
Primary transcripts are largely comprised of intronic sequences that are excised and discarded shortly after synthesis. In vertebrates, the shape of the intron size distribution is largely constant; however, most teleost fish have a diverged log-bimodal 'teleost distribution' (TD) that is seen only in teleosts. How the TD evolved and to what extent this was affected by adaptative or non-adaptive mechanisms is unknown.
Here, we show that the TD has evolved independently at least six times and that its appearance is linked to the loss of the aKRAB domain from PRDM9. We determined intron size distributions and identified PRDM9 orthologues from annotated genomes in addition to scanning 1193 teleost assemblies for the aKRAB domain. We show that a diverged form of PRDM9 ( ) is predominant in teleosts whereas the version is absent from most species. Only a subset of PRDM9- proteins contain aKRAB, and hence, it is present only in a small number of teleost lineages. Almost all lineages lacking aKRAB (but no species with) had TDs.
In mammals, PRDM9 defines the sites of meiotic recombination through a mechanism that increases structural variance and depends on aKRAB. The loss of aKRAB is likely to have shifted the locations of both recombination and structural variance hotspots. Our observations suggest that the TD evolved as a side-effect of these changes and link recombination to the evolution of intron size illustrating how genome architectures can evolve in the absence of selection.
初级转录本主要由内含子序列组成，这些序列在合成后不久就被切除和丢弃。在脊椎动物中，内含子大小分布的形状基本保持不变；然而，大多数硬骨鱼具有分化的对数双峰“硬骨鱼分布”（TD），这种分布仅见于硬骨鱼。TD 是如何进化的，以及适应或非适应机制在多大程度上影响了它的进化，目前还不得而知。
在这里，我们表明 TD 至少独立进化了六次，并且它的出现与 PRDM9 的 aKRAB 结构域的丢失有关。我们确定了内含子大小分布，并从注释基因组中鉴定了 PRDM9 直系同源物，此外还扫描了 1193 个硬骨鱼组装体以寻找 aKRAB 结构域。我们表明，一种分化形式的 PRDM9（ ）在硬骨鱼中占主导地位，而 版本在大多数物种中不存在。只有一小部分 PRDM9- 蛋白含有 aKRAB，因此，它只存在于少数硬骨鱼谱系中。几乎所有缺乏 aKRAB 的谱系（但没有物种有）都有 TD。
在哺乳动物中，PRDM9 通过一种增加结构变异性的机制来定义减数分裂重组的位点，这种机制依赖于 aKRAB。aKRAB 的缺失很可能改变了重组和结构变异热点的位置。我们的观察结果表明，TD 的进化是这些变化的副作用之一，并将重组与内含子大小的进化联系起来，说明了在没有选择的情况下，基因组结构是如何进化的。
