Genomic Analysis of Amphioxus Reveals a Wide Range of Fragments Homologous to Viral Sequences
Open Access
- 31 March 2023
- Vol. 15 (4), 909
- https://doi.org/10.3390/v15040909
Abstract
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 (Branchiostoma belcheri beihai) was examined using virus sequence queries. In this study, 347 homologous fragments (HFs) of viruses were identified in the genome of B. belcheri 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 Histone or Histone H2B domains of viruses. Together, this comprehensive analysis of viral HFs provides insights into the neglected role of viral integration in the evolution of amphioxus.Keywords
Funding Information
- National Natural Science Foundation of China (31900479, 82072759)
- Shanghai Rising Star Program (20QA1412000)
This publication has 84 references indexed in Scilit:
- Endogenous viruses: insights into viral evolution and impact on host biologyNature Reviews Genetics, 2012
- Viral Proteins Acquired from a Host Converge to Simplified Domain ArchitecturesPLoS Computational Biology, 2012
- Eukaryotic Gene Prediction Using GeneMark.hmm‐E and GeneMark‐ESCurrent Protocols in Bioinformatics, 2011
- Discovery and Characterization of Mammalian Endogenous ParvovirusesJournal of Virology, 2010
- A neurotropic herpesvirus infecting the gastropod, abalone, shares ancestry with oyster herpesvirus and a herpesvirus associated with the amphioxus genomeVirology Journal, 2010
- Endogenous non-retroviral RNA virus elements in mammalian genomesNature, 2010
- The amphioxus genome and the evolution of the chordate karyotypeNature, 2008
- MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomesGenome Research, 2007
- Tunicates and not cephalochordates are the closest living relatives of vertebratesNature, 2006
- De novo identification of repeat families in large genomesBioinformatics, 2005