Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.
Viruses. 2023 Mar 31;15(4):909. doi: 10.3390/v15040909.
Amphioxus species are considered living fossils and are important in the evolutionary study of chordates and vertebrates. To explore viral homologous sequences, a high-quality annotated genome of the Beihai amphioxus ( beihai) was examined using virus sequence queries. In this study, 347 homologous fragments (HFs) of viruses were identified in the genome of beihai, of which most were observed on 21 genome assembly scaffolds. HFs were preferentially located within protein-coding genes, particularly in their CDS regions and promoters. A range of amphioxus genes with a high frequency of HFs is proposed, including histone-related genes that are homologous to the or domains of viruses. Together, this comprehensive analysis of viral HFs provides insights into the neglected role of viral integration in the evolution of amphioxus.
文昌鱼被认为是活化石，在脊索动物和脊椎动物的进化研究中具有重要地位。为了探索病毒同源序列，利用病毒序列查询，对北海文昌鱼的高质量注释基因组进行了检查。在这项研究中，在北海的基因组中鉴定出了 347 个病毒的同源片段（HFs），其中大多数观察到在 21 个基因组组装支架上。HFs 优先位于编码蛋白的基因内，特别是在它们的 CDS 区域和启动子中。提出了一系列具有高频 HFs 的文昌鱼基因，包括与病毒的 或 结构域同源的组蛋白相关基因。总的来说，对病毒 HFs 的综合分析揭示了病毒整合在文昌鱼进化中被忽视的作用。
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