Genomic Analysis of Amphioxus Reveals a Wide Range of Fragments Homologous to Viral Sequences

Qiao Du; Fang Peng; Qing Xiong; Kejin Xu; Kevin Yi Yang; Mingqiang Wang; Zhitian Wu; Shanying Li; Xiaorui Cheng; Xinjie Rao; Yuyouye Wang; Stephen Kwok-Wing Tsui; Xi Zeng

doi:10.3390/v15040909

Viruses (Mar 2023)

Genomic Analysis of Amphioxus Reveals a Wide Range of Fragments Homologous to Viral Sequences

Qiao Du,
Fang Peng,
Qing Xiong,
Kejin Xu,
Kevin Yi Yang,
Mingqiang Wang,
Zhitian Wu,
Shanying Li,
Xiaorui Cheng,
Xinjie Rao,
Yuyouye Wang,
Stephen Kwok-Wing Tsui,
Xi Zeng

Affiliations

Qiao Du: Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
Fang Peng: Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
Qing Xiong: School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
Kejin Xu: Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
Kevin Yi Yang: School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
Mingqiang Wang: School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
Zhitian Wu: Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
Shanying Li: Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
Xiaorui Cheng: Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
Xinjie Rao: Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
Yuyouye Wang: Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
Stephen Kwok-Wing Tsui: School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
Xi Zeng: Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China

DOI: https://doi.org/10.3390/v15040909
Journal volume & issue: Vol. 15, no. 4
p. 909

Abstract

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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.

Published in Viruses

ISSN: 1999-4915 (Online)
Publisher: MDPI AG
Country of publisher: Switzerland
LCC subjects: Science: Microbiology
Website: http://www.mdpi.com/journal/viruses

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