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Comparative genomic analysis of alloherpesviruses: Exploring an available genus/species demarcation proposal and method

The family Alloherpesviridae contains herpesviruses of fish and amphibians. Due to the significant economic losses to aquaculture that herpesviruses can cause, the primary areas of research interest are concerning their pathogenesis and prevention. Despite alloherpesvirus genomic sequences becoming...

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Autores principales: Zhang, Wenjie, Wang, Ran, Zou, Xiaoxia, Gu, Congwei, Yang, Qian, He, Manli, Xiao, Wudian, He, Lvqin, Zhao, Mingde, Yu, Zehui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10410580/
https://www.ncbi.nlm.nih.gov/pubmed/37364814
http://dx.doi.org/10.1016/j.virusres.2023.199163
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author Zhang, Wenjie
Wang, Ran
Zou, Xiaoxia
Gu, Congwei
Yang, Qian
He, Manli
Xiao, Wudian
He, Lvqin
Zhao, Mingde
Yu, Zehui
author_facet Zhang, Wenjie
Wang, Ran
Zou, Xiaoxia
Gu, Congwei
Yang, Qian
He, Manli
Xiao, Wudian
He, Lvqin
Zhao, Mingde
Yu, Zehui
author_sort Zhang, Wenjie
collection PubMed
description The family Alloherpesviridae contains herpesviruses of fish and amphibians. Due to the significant economic losses to aquaculture that herpesviruses can cause, the primary areas of research interest are concerning their pathogenesis and prevention. Despite alloherpesvirus genomic sequences becoming more widely accessible, methods regarding their genus/species classification are still relatively unexplored. In the present study, the phylogenetic relationships between 40 completely sequenced alloherpesviruses were illustrated by the viral proteomic tree (ViPTree), which was divided into three monophyletic groups, namely Cyprinivirus, Ictalurivirus and Batrachovirus. Additionally, average nucleotide identity (ANI) and average amino acid identity (AAI) analyses were performed across all available sequences and clearly displayed species boundaries with the threshold value of ANI/AAI set at 90%. Subsequently, core-pan analysis uncovered 809 orthogroups and 11 core genes shared by all 40 alloherpesvirus genome sequences. For the former, a 15 percent identity depicts a clear genus boundary; for the latter, 8 of them may be qualified for phylogenetic analysis based on amino acid or nucleic acid sequences after being verified using maximum likelihood (ML) or neighbor-joining (NJ) phylogenetic trees. Finally, although the dot plot analysis was valid for the members within Ictalurivirus, it was unsuccessful for Cyprinivirus and Batrachovirus. Taken together, the comparison of individual methodologies provides a wide range of alternatives for alloherpesviruses classification under various circumstances.
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spelling pubmed-104105802023-08-10 Comparative genomic analysis of alloherpesviruses: Exploring an available genus/species demarcation proposal and method Zhang, Wenjie Wang, Ran Zou, Xiaoxia Gu, Congwei Yang, Qian He, Manli Xiao, Wudian He, Lvqin Zhao, Mingde Yu, Zehui Virus Res Article The family Alloherpesviridae contains herpesviruses of fish and amphibians. Due to the significant economic losses to aquaculture that herpesviruses can cause, the primary areas of research interest are concerning their pathogenesis and prevention. Despite alloherpesvirus genomic sequences becoming more widely accessible, methods regarding their genus/species classification are still relatively unexplored. In the present study, the phylogenetic relationships between 40 completely sequenced alloherpesviruses were illustrated by the viral proteomic tree (ViPTree), which was divided into three monophyletic groups, namely Cyprinivirus, Ictalurivirus and Batrachovirus. Additionally, average nucleotide identity (ANI) and average amino acid identity (AAI) analyses were performed across all available sequences and clearly displayed species boundaries with the threshold value of ANI/AAI set at 90%. Subsequently, core-pan analysis uncovered 809 orthogroups and 11 core genes shared by all 40 alloherpesvirus genome sequences. For the former, a 15 percent identity depicts a clear genus boundary; for the latter, 8 of them may be qualified for phylogenetic analysis based on amino acid or nucleic acid sequences after being verified using maximum likelihood (ML) or neighbor-joining (NJ) phylogenetic trees. Finally, although the dot plot analysis was valid for the members within Ictalurivirus, it was unsuccessful for Cyprinivirus and Batrachovirus. Taken together, the comparison of individual methodologies provides a wide range of alternatives for alloherpesviruses classification under various circumstances. Elsevier 2023-07-26 /pmc/articles/PMC10410580/ /pubmed/37364814 http://dx.doi.org/10.1016/j.virusres.2023.199163 Text en © 2023 The Authors. Published by Elsevier B.V. https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Zhang, Wenjie
Wang, Ran
Zou, Xiaoxia
Gu, Congwei
Yang, Qian
He, Manli
Xiao, Wudian
He, Lvqin
Zhao, Mingde
Yu, Zehui
Comparative genomic analysis of alloherpesviruses: Exploring an available genus/species demarcation proposal and method
title Comparative genomic analysis of alloherpesviruses: Exploring an available genus/species demarcation proposal and method
title_full Comparative genomic analysis of alloherpesviruses: Exploring an available genus/species demarcation proposal and method
title_fullStr Comparative genomic analysis of alloherpesviruses: Exploring an available genus/species demarcation proposal and method
title_full_unstemmed Comparative genomic analysis of alloherpesviruses: Exploring an available genus/species demarcation proposal and method
title_short Comparative genomic analysis of alloherpesviruses: Exploring an available genus/species demarcation proposal and method
title_sort comparative genomic analysis of alloherpesviruses: exploring an available genus/species demarcation proposal and method
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10410580/
https://www.ncbi.nlm.nih.gov/pubmed/37364814
http://dx.doi.org/10.1016/j.virusres.2023.199163
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