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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...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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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. |
format | Online Article Text |
id | pubmed-10145014 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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