Department of Infectious Diseases, Section for Clinical Virology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
Laboratory of Molecular Biology and Bioinformatics, Institute of Botany, Czech Academy of Sciences, Prague, Czechia.
Commun Biol. 2024 Oct 30;7(1):1412. doi: 10.1038/s42003-024-07098-1.
The genomic signature of an organism captures the characteristics of repeated oligonucleotide patterns in its genome , such as oligomer frequencies, GC content, and differences in codon usage. Viruses, however, are obligate intracellular parasites that are dependent on their host cells for replication, and information about genomic signatures in viruses has hitherto been sparse.Here, we investigate the presence and specificity of genomic signatures in 2,768 eukaryotic viral species from 105 viral families, aiming to illuminate dependencies and selective pressures in viral genome evolution. We demonstrate that most viruses have highly specific genomic signatures that often also differ significantly between species within the same family. The species-specificity is most prominent among dsDNA viruses and viruses with large genomes. We also reveal consistent dissimilarities between viral genomic signatures and those of their host cells, although some viruses present slight similarities, which may be explained by genetic adaptation to their native hosts. Our results suggest that significant evolutionary selection pressures act upon viral genomes to shape and preserve their genomic signatures, which may have implications for the field of synthetic biology in the construction of live attenuated vaccines and viral vectors.
生物体的基因组特征捕获了其基因组中重复寡核苷酸模式的特征，例如寡核苷酸频率、GC 含量和密码子使用差异。然而，病毒是专性细胞内寄生虫，其复制依赖于宿主细胞，而关于病毒基因组特征的信息迄今一直很匮乏。在这里，我们研究了来自 105 种病毒科的 2768 种真核病毒物种中的基因组特征的存在和特异性，旨在阐明病毒基因组进化中的依赖性和选择压力。我们证明，大多数病毒具有高度特异性的基因组特征，这些特征在同一科内的不同物种之间也常常有很大的差异。这种物种特异性在双链 DNA 病毒和基因组较大的病毒中最为明显。我们还揭示了病毒基因组特征与宿主细胞之间的一致性差异，尽管有些病毒表现出轻微的相似性，这可能可以通过遗传适应其天然宿主来解释。我们的研究结果表明，显著的进化选择压力作用于病毒基因组，以塑造和保留其基因组特征，这可能对合成生物学领域构建活减毒疫苗和病毒载体产生影响。
