Genomic Analysis of Amphioxus Reveals a Wide Range of Fragments Homologous to Viral Sequences-Reference-Cited by-同舟云学术

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

Published:2023-03-31 Issue:4 Volume:15 Page:909
ISSN:1999-4915
Container-title:Viruses
language:en
Short-container-title:Viruses

Author:

Du Qiao¹,Peng Fang¹,Xiong Qing²³^ORCID,Xu Kejin¹,Yang Kevin Yi²³^ORCID,Wang Mingqiang²⁴^ORCID,Wu Zhitian¹,Li Shanying¹,Cheng Xiaorui¹,Rao Xinjie¹,Wang Yuyouye¹,Tsui Stephen Kwok-Wing²³^ORCID,Zeng Xi¹^ORCID

Affiliation:

1. Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China

2. School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China

3. Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China

4. Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA

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.

Funder

National Natural Science Foundation of China

Shanghai rising star program

Publisher

MDPI AG

Subject

Virology,Infectious Diseases

Link

https://www.mdpi.com/1999-4915/15/4/909/pdf

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