CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany.
Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany.
Microbiol Spectr. 2022 Oct 26;10(5):e0034922. doi: 10.1128/spectrum.00349-22. Epub 2022 Aug 16.
Transposable elements (TEs) play a pivotal role in shaping diversity in eukaryotic genomes. The covered smut pathogen on barley, , encountered a recent genome expansion. Using long reads, we assembled genomes of 6 strains and 3 sister species, to study this genome expansion. We found that larger genome sizes can mainly be attributed to a higher genome fraction of long terminal repeat retrotransposons (LTR-RTs). In the studied smut genomes, LTR-RTs fractions are the largest in and are positively correlated with the mating-type locus sizes, which is up to ~560 kb in . Furthermore, LTR-RTs were found to be associated with higher nucleotide substitution levels, as these occur in specific genome regions of smut species with a recent LTR-RT proliferation. Moreover, genes in genome regions with higher nucleotide substitution levels generally reside closer to LTR-RTs than other genome regions. Genome regions with many nucleotide substitutions encountered an especially high fraction of CG substitutions, which is not observed for LTR-RT sequences. The high nucleotide substitution levels particularly accelerate the evolution of secretome genes, as their more accessory nature results in substitutions that often lead to amino acid alterations. Genomic alteration can be generated through various means, in which transposable elements (TEs) can play a pivotal role. Their mobility causes mutagenesis in itself and can disrupt the function of the sequences they insert into. They also impact genome evolution as their repetitive nature facilitates nonhomologous recombination. Furthermore, TEs have been linked to specific epigenetic genome organizations. We report a recent TE proliferation in the genome of the barley covered smut fungus, This proliferation is associated with a distinct nucleotide substitution regime that has a higher rate and a higher fraction of CG substitutions. This different regime shapes the evolution of genes in subjected genome regions. We hypothesize that TEs may influence the error-rate of DNA polymerase in a hitherto unknown fashion.
转座元件 (TEs) 在塑造真核生物基因组多样性方面发挥着关键作用。大麦上的覆盖黑粉菌病原体 最近经历了基因组扩张。我们使用长读长组装了 6 个菌株和 3 个姐妹种的基因组，以研究这种基因组扩张。我们发现较大的基因组大小主要归因于长末端重复反转录转座子 (LTR-RTs) 的更高基因组分数。在所研究的黑粉菌基因组中，LTR-RTs 分数在 中最大，并且与交配型基因座大小呈正相关，在 中高达约 560 kb。此外，LTR-RTs 与更高的核苷酸取代水平相关，因为这些发生在具有近期 LTR-RT 增殖的黑粉菌物种的特定基因组区域中。此外，基因组中具有更高核苷酸取代水平的区域通常比其他基因组区域更靠近 LTR-RTs。具有许多核苷酸取代的基因组区域遇到了特别高的 CG 取代分数，而 LTR-RT 序列则没有观察到这种情况。高核苷酸取代水平特别加速了分泌组基因的进化，因为它们更多的辅助性质导致了经常导致氨基酸改变的取代。基因组的改变可以通过各种方式产生，其中转座元件 (TEs) 可以发挥关键作用。它们的移动性本身就会引起突变，并可以破坏它们插入的序列的功能。由于它们的重复性质促进了非同源重组，它们也会影响基因组的进化。此外，TEs 与特定的表观遗传基因组组织有关。我们报告了大麦覆盖黑粉菌基因组中的近期 TE 增殖。这种增殖与一个独特的核苷酸取代机制相关，该机制具有更高的速率和更高的 CG 取代分数。这种不同的机制塑造了受影响基因组区域的基因进化。我们假设 TEs 可能以迄今为止未知的方式影响 DNA 聚合酶的错误率。
