Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA.
G3 (Bethesda). 2023 Jan 12;13(1). doi: 10.1093/g3journal/jkac285.
The fungal genus Aspergillus contains a diversity of species divided into taxonomic sections of closely related species. Section Flavi contains 33 species, many of industrial, agricultural, or medical relevance. Here, we analyze the mitochondrial genomes (mitogenomes) of 20 Flavi species-including 18 newly assembled mitogenomes-and compare their evolutionary history and codon usage bias patterns to their nuclear counterparts. Codon usage bias refers to variable frequencies of synonymous codons in coding DNA and is shaped by a balance of neutral processes and natural selection. All mitogenomes were circular DNA molecules with highly conserved gene content and order. As expected, genomic content, including GC content, and genome size differed greatly between mitochondrial and nuclear genomes. Phylogenetic analysis based on 14 concatenated mitochondrial genes predicted evolutionary relationships largely consistent with those predicted by a phylogeny constructed from 2,422 nuclear genes. Comparing similarities in interspecies patterns of codon usage bias between mitochondrial and nuclear genomes showed that species grouped differently by patterns of codon usage bias depending on whether analyses were performed using mitochondrial or nuclear relative synonymous usage values. We found that patterns of codon usage bias at gene level are more similar between mitogenomes of different species than the mitogenome and nuclear genome of the same species. Finally, we inferred that, although most genes-both nuclear and mitochondrial-deviated from the neutral expectation for codon usage, mitogenomes were not under translational selection while nuclear genomes were under moderate translational selection. These results contribute to the study of mitochondrial genome evolution in filamentous fungi.
真菌属曲霉包含了多样性的物种，分为密切相关的物种分类群。黄曲霉组包含 33 个物种，其中许多具有工业、农业或医学相关性。在这里，我们分析了 20 种黄曲霉的线粒体基因组（线粒体基因组）-包括 18 个新组装的线粒体基因组-并比较了它们的进化历史和密码子使用偏好模式与其核对应物。密码子使用偏性是指编码 DNA 中同义密码子的可变频率，由中性过程和自然选择之间的平衡所塑造。所有的线粒体基因组都是圆形 DNA 分子，具有高度保守的基因内容和顺序。正如预期的那样，基因组内容，包括 GC 含量和基因组大小，在线粒体和核基因组之间有很大的差异。基于 14 个串联线粒体基因的系统发育分析预测的进化关系与基于 2422 个核基因构建的系统发育预测的进化关系基本一致。比较线粒体和核基因组之间物种间密码子使用偏好模式的相似性表明，根据使用线粒体或核相对同义使用值进行分析，物种的分组方式因密码子使用偏好模式而异。我们发现，不同物种的线粒体基因组之间的基因水平的密码子使用偏好模式更为相似，而同一物种的线粒体基因组和核基因组之间则不那么相似。最后，我们推断，尽管大多数基因-无论是核基因还是线粒体基因-都偏离了密码子使用的中性预期，但线粒体基因组不受翻译选择的影响，而核基因组则受到中度翻译选择的影响。这些结果为丝状真菌线粒体基因组进化的研究做出了贡献。
