Departamento de Genética, Laboratório de Citogenética Evolutiva e Conservação Animal (LabCECA), Universidade Federal do Paraná, Curitiba, PR 80060-000, Brazil.
Departamento de Genética, Programa de Pós-Graduação em Genética (PPG-GEN), Universidade Federal do Paraná (UFPR), Curitiba, PR 80060-000, Brazil.
G3 (Bethesda). 2022 Feb 4;12(2). doi: 10.1093/g3journal/jkab391.
Anuran genomes have a large number and diversity of transposable elements, but are little explored, mainly in relation to their molecular structure and evolutionary dynamics. Here, we investigated the retrotransposons containing tyrosine recombinase (YR) (order DIRS) in the genome of Xenopus tropicalis and Xenopus laevis. These anurans show 2n = 20 and the 2n = 36 karyotypes, respectively. They diverged about 48 million years ago (mya) and X. laevis had an allotetraploid origin (around 17-18 mya). Our investigation is based on the analysis of the molecular structure and the phylogenetic relationships of 95 DIRS families of Xenopus belonging to DIRS-like and Ngaro-like superfamilies. We were able to identify molecular signatures in the 5' and 3' noncoding terminal regions, preserved open reading frames, and conserved domains that are specific to distinguish each superfamily. We recognize two ancient amplification waves of DIRS-like elements that occurred in the ancestor of both species and a higher density of the old/degenerate copies detected in both subgenomes of X. laevis. More recent amplification waves are seen in X. tropicalis (less than 3.2 mya) and X. laevis (around 10 mya) corroborating with transcriptional activity evidence. All DIRS-like families were found in both X. laevis subgenomes, while a few were most represented in the L subgenome. Ngaro-like elements presented less diversity and quantity in X. tropicalis and X. laevis genomes, although potentially active copies were found in both species and this is consistent with a recent amplification wave seen in the evolutionary landscape. Our findings highlight a differential diversity-level and evolutionary dynamics of the YR retrotransposons in X. tropicalis and X. laevis species expanding our comprehension of the behavior of these elements in both genomes during the diversification process.
爪蟾属基因组中含有大量的转座元件，具有丰富的多样性，但对其分子结构和进化动态的研究却很少，主要是因为这方面的研究。在这里，我们研究了爪蟾属基因组中的含有酪氨酸重组酶（YR）（DIRS 类群）的反转录转座子。这两种爪蟾分别具有 2n = 20 和 2n = 36 的染色体核型。它们大约在 4800 万年前（mya）分化，而 X. laevis 具有 allotetraploid 起源（约 17-18 mya）。我们的研究基于对 95 个属于 DIRS 样和 Ngaro 样超家族的 Xenopus DIRS 家族的分子结构和系统发育关系的分析。我们能够识别出 5'和 3'非编码末端区域、保存的开放阅读框和保守结构域的分子特征，这些特征是区分每个超家族的特异性标志。我们识别出两个发生在这两个物种祖先中的 DIRS 样元件的古老扩增波，以及在 X. laevis 的两个亚基因组中检测到的更高密度的旧/退化拷贝。在 X. tropicalis（小于 3.2 mya）和 X. laevis（约 10 mya）中发现了更近的扩增波，这与转录活性证据相符。所有的 DIRS 样家族都存在于 X. laevis 的两个亚基因组中，而少数家族在 L 亚基因组中更为突出。Ngaro 样元件在 X. tropicalis 和 X. laevis 基因组中的多样性和数量较少，尽管在这两个物种中都发现了潜在的活跃拷贝，这与进化景观中观察到的最近的扩增波一致。我们的研究结果突出了 YR 反转录转座子在 X. tropicalis 和 X. laevis 物种中的差异多样性水平和进化动态，扩大了我们对这两个基因组在多样化过程中这些元件行为的理解。
