Evolutionary dynamics of the LTR-retrotransposon crapaud in the Podospora anserina species complex and the interaction with repeat-induced point mutations

IF 4.7 2区 生物学 Q1 GENETICS & HEREDITY Mobile DNA Pub Date : 2024-01-13 DOI:10.1186/s13100-023-00311-8
Ivar Westerberg, S. Lorena Ament-Velásquez, Aaron A. Vogan, Hanna Johannesson
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Abstract

The genome of the filamentous ascomycete Podospora anserina shows a relatively high abundance of retrotransposons compared to other interspersed repeats. The LTR-retrotransposon family crapaud is particularly abundant in the genome, and consists of multiple diverged sequence variations specifically localized in the 5’ half of both long terminal repeats (LTRs). P. anserina is part of a recently diverged species-complex, which makes the system ideal to classify the crapaud family based on the observed LTR variation and to study the evolutionary dynamics, such as the diversification and bursts of the elements over recent evolutionary time. We developed a sequence similarity network approach to classify the crapaud repeats of seven genomes representing the P. anserina species complex into 14 subfamilies. This method does not utilize a consensus sequence, but instead it connects any copies that share enough sequence similarity over a set sequence coverage. Based on phylogenetic analyses, we found that the crapaud repeats likely diversified in the ancestor of the complex and have had activity at different time points for different subfamilies. Furthermore, while we hypothesized that the evolution into multiple subfamilies could have been a direct effect of escaping the genome defense system of repeat induced point mutations, we found this not to be the case. Our study contributes to the development of methods to classify transposable elements in fungi, and also highlights the intricate patterns of retrotransposon evolution over short timescales and under high mutational load caused by nucleotide-altering genome defense.
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Podospora anserina物种群中LTR-反转座子Crapaud的进化动态以及与重复诱导点突变的相互作用
与其他穿插重复子相比,丝状无丝菌Podospora anserina的基因组显示出较高的反转座子丰度。LTR-retrotransposon 家族 crapaud 在基因组中的含量尤其丰富,它由多个不同的序列变异组成,特异性地定位于两个长末端重复序列(LTR)的 5' 半部。P.anserina是最近分化的物种复合体的一部分,这使得该系统非常适合根据观察到的LTR变异对crapaud家族进行分类,并研究其进化动态,如在最近的进化过程中元素的多样化和突变。我们开发了一种序列相似性网络方法,将代表P. anserina物种群的7个基因组中的Crapaud重复序列分为14个亚科。这种方法不使用共识序列,而是将在设定序列覆盖范围内具有足够序列相似性的拷贝连接起来。根据系统发生学分析,我们发现螯虾重复序列很可能在该复合体的祖先中发生了多样化,并在不同亚科的不同时间点具有活性。此外,虽然我们假设进化成多个亚家族可能是逃避重复点突变基因组防御系统的直接结果,但我们发现情况并非如此。我们的研究有助于开发真菌中转座元件的分类方法,同时也凸显了在核苷酸改变基因组防御系统造成的高突变负荷下,逆转录转座子在短时间内进化的复杂模式。
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来源期刊
Mobile DNA
Mobile DNA GENETICS & HEREDITY-
CiteScore
8.20
自引率
6.10%
发文量
26
审稿时长
11 weeks
期刊介绍: Mobile DNA is an online, peer-reviewed, open access journal that publishes articles providing novel insights into DNA rearrangements in all organisms, ranging from transposition and other types of recombination mechanisms to patterns and processes of mobile element and host genome evolution. In addition, the journal will consider articles on the utility of mobile genetic elements in biotechnological methods and protocols.
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