Department of Bioscience, School of Science, Kitasato University, Kanagawa 252-0373, Japan.
Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan.
Genome Biol Evol. 2024 Sep 3;16(9). doi: 10.1093/gbe/evae179.
In certain tetraploid species resulting from interspecific hybridization, one parent's subgenome is known to selectively undergo DNA loss. The molecular mechanisms behind this remain unclear. In our study, we compared the genomes of a standard diploid species with two allotetraploid species from the Xenopus genus, both possessing L (longer) and S (shorter) homoeologous subgenomes. We observed substantial gene losses and intergenic DNA deletions in both the S and L subgenomes of the tetraploid species. Gene losses were around 1,000 to 3,000 for L and 4,000 to 6,000 for S, with especially prominent losses in the S subgenome. Many of these losses likely occurred shortly after interspecific hybridization in both L/S subgenomes. We also deduced frequent large inversions in the S subgenome. Upon reassessing transposon dynamics using updated genome databases, we reaffirmed heightened DNA transposon activity during the hybridization, as previously reported. We next investigated whether S subgenome-biased DNA loss could be correlated with the activation of DNA transposons following hybridization. Notably, distinct patterns were observed in the dynamics of DNA transposons between the L and S subgenomes. Several DNA transposon subfamilies correlated positively with DNA deletions in the S subgenome and negatively in the L subgenome. Based on these results, we propose a model that, upon and after hybridization between two related diploid Xenopus species, the mixture of their genomes resulted in the derepression of DNA transposons, especially in the S subgenome, leading to selective DNA loss in the S subgenome.
在某些由种间杂交产生的四倍体物种中，已知一个亲本的亚基因组会选择性地发生 DNA 丢失。其背后的分子机制尚不清楚。在我们的研究中，我们比较了一个标准二倍体物种和两个来自 Xenopus 属的异源四倍体物种的基因组，这两个物种都拥有 L（较长）和 S（较短）同源亚基因组。我们观察到四倍体物种的 S 和 L 亚基因组中都存在大量的基因丢失和基因间 DNA 缺失。L 亚基因组的基因丢失约为 1000 到 3000 个，S 亚基因组的基因丢失约为 4000 到 6000 个，S 亚基因组的基因丢失尤为明显。这些丢失很可能在 L/S 亚基因组的种间杂交后不久就发生了。我们还推断出 S 亚基因组中频繁发生的大型倒位。在使用更新的基因组数据库重新评估转座子动态时，我们再次证实了杂交过程中转座子的 DNA 活性增加，正如之前报道的那样。接下来，我们研究了 S 亚基因组偏向性的 DNA 丢失是否与杂交后 DNA 转座子的激活有关。值得注意的是，我们在 L 和 S 亚基因组中转座子的动态中观察到了明显不同的模式。几个 DNA 转座子亚家族与 S 亚基因组中的 DNA 缺失呈正相关，而与 L 亚基因组中的 DNA 缺失呈负相关。基于这些结果，我们提出了一个模型，即在两个相关的二倍体 Xenopus 物种杂交之后，它们基因组的混合导致 DNA 转座子的去抑制，特别是在 S 亚基因组中，从而导致 S 亚基因组的选择性 DNA 丢失。
