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

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...

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Autores principales: Du, Qiao, Peng, Fang, Xiong, Qing, Xu, Kejin, Yang, Kevin Yi, Wang, Mingqiang, Wu, Zhitian, Li, Shanying, Cheng, Xiaorui, Rao, Xinjie, Wang, Yuyouye, Tsui, Stephen Kwok-Wing, Zeng, Xi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10145014/
https://www.ncbi.nlm.nih.gov/pubmed/37112889
http://dx.doi.org/10.3390/v15040909
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author Du, Qiao
Peng, Fang
Xiong, Qing
Xu, Kejin
Yang, Kevin Yi
Wang, Mingqiang
Wu, Zhitian
Li, Shanying
Cheng, Xiaorui
Rao, Xinjie
Wang, Yuyouye
Tsui, Stephen Kwok-Wing
Zeng, Xi
author_facet Du, Qiao
Peng, Fang
Xiong, Qing
Xu, Kejin
Yang, Kevin Yi
Wang, Mingqiang
Wu, Zhitian
Li, Shanying
Cheng, Xiaorui
Rao, Xinjie
Wang, Yuyouye
Tsui, Stephen Kwok-Wing
Zeng, Xi
author_sort Du, Qiao
collection PubMed
description 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.
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spelling pubmed-101450142023-04-29 Genomic Analysis of Amphioxus Reveals a Wide Range of Fragments Homologous to Viral Sequences Du, Qiao Peng, Fang Xiong, Qing Xu, Kejin Yang, Kevin Yi Wang, Mingqiang Wu, Zhitian Li, Shanying Cheng, Xiaorui Rao, Xinjie Wang, Yuyouye Tsui, Stephen Kwok-Wing Zeng, Xi Viruses Article 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. MDPI 2023-03-31 /pmc/articles/PMC10145014/ /pubmed/37112889 http://dx.doi.org/10.3390/v15040909 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Du, Qiao
Peng, Fang
Xiong, Qing
Xu, Kejin
Yang, Kevin Yi
Wang, Mingqiang
Wu, Zhitian
Li, Shanying
Cheng, Xiaorui
Rao, Xinjie
Wang, Yuyouye
Tsui, Stephen Kwok-Wing
Zeng, Xi
Genomic Analysis of Amphioxus Reveals a Wide Range of Fragments Homologous to Viral Sequences
title Genomic Analysis of Amphioxus Reveals a Wide Range of Fragments Homologous to Viral Sequences
title_full Genomic Analysis of Amphioxus Reveals a Wide Range of Fragments Homologous to Viral Sequences
title_fullStr Genomic Analysis of Amphioxus Reveals a Wide Range of Fragments Homologous to Viral Sequences
title_full_unstemmed Genomic Analysis of Amphioxus Reveals a Wide Range of Fragments Homologous to Viral Sequences
title_short Genomic Analysis of Amphioxus Reveals a Wide Range of Fragments Homologous to Viral Sequences
title_sort genomic analysis of amphioxus reveals a wide range of fragments homologous to viral sequences
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10145014/
https://www.ncbi.nlm.nih.gov/pubmed/37112889
http://dx.doi.org/10.3390/v15040909
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