Ansai Satoshi, Toyoda Atsushi, Yoshida Kohta, Kitano Jun
Laboratory of Genome Editing Breeding, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan.
Mol Ecol. 2024 Dec;33(24):e17222. doi: 10.1111/mec.17222. Epub 2023 Nov 28.
The karyotype, which is the number and shape of chromosomes, is a fundamental characteristic of all eukaryotes. Karyotypic changes play an important role in many aspects of evolutionary processes, including speciation. In organisms with monocentric chromosomes, it was previously thought that chromosome number changes were mainly caused by centric fusions and fissions, whereas chromosome shape changes, that is, changes in arm numbers, were mainly due to pericentric inversions. However, recent genomic and cytogenetic studies have revealed examples of alternative cases, such as tandem fusions and centromere repositioning, found in the karyotypic changes within and between species. Here, we employed comparative genomic approaches to investigate whether centromere repositioning occurred during karyotype evolution in medaka fishes. In the medaka family (Adrianichthyidae), the three phylogenetic groups differed substantially in their karyotypes. The Oryzias latipes species group has larger numbers of chromosome arms than the other groups, with most chromosomes being metacentric. The O. javanicus species group has similar numbers of chromosomes to the O. latipes species group, but smaller arm numbers, with most chromosomes being acrocentric. The O. celebensis species group has fewer chromosomes than the other two groups and several large metacentric chromosomes that were likely formed by chromosomal fusions. By comparing the genome assemblies of O. latipes, O. javanicus, and O. celebensis, we found that repositioning of centromere-associated repeats might be more common than simple pericentric inversion. Our results demonstrated that centromere repositioning may play a more important role in karyotype evolution than previously appreciated.
核型，即染色体的数量和形态，是所有真核生物的一个基本特征。核型变化在进化过程的许多方面都起着重要作用，包括物种形成。在具有单着丝粒染色体的生物体中，以前认为染色体数量的变化主要是由着丝粒融合和分裂引起的，而染色体形态的变化，即臂数的变化，主要是由于臂间倒位。然而，最近的基因组和细胞遗传学研究揭示了一些其他情况的例子，如串联融合和着丝粒重新定位，这些情况在物种内部和物种之间的核型变化中都有发现。在这里，我们采用比较基因组方法来研究在青鳉鱼类的核型进化过程中是否发生了着丝粒重新定位。在青鳉科中，三个系统发育组的核型有很大差异。青鳉物种组的染色体臂数比其他组多，大多数染色体是中着丝粒染色体。爪哇青鳉物种组的染色体数量与青鳉物种组相似，但臂数较少，大多数染色体是端着丝粒染色体。西里伯斯青鳉物种组的染色体比其他两组少，并且有几条可能由染色体融合形成的大型中着丝粒染色体。通过比较青鳉、爪哇青鳉和西里伯斯青鳉的基因组组装，我们发现着丝粒相关重复序列的重新定位可能比简单的臂间倒位更为常见。我们的结果表明，着丝粒重新定位在核型进化中可能比以前认为的发挥更重要的作用。
