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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Main Authors: Wenjie Zhang, Ran Wang, Xiaoxia Zou, Congwei Gu, Qian Yang, Manli He, Wudian Xiao, Lvqin He, Mingde Zhao, Zehui Yu
Format: Article
Language:English
Published: Elsevier 2023-09-01
Series:Virus Research
Subjects:
Online Access:http://www.sciencedirect.com/science/article/pii/S0168170223001259
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author Wenjie Zhang
Ran Wang
Xiaoxia Zou
Congwei Gu
Qian Yang
Manli He
Wudian Xiao
Lvqin He
Mingde Zhao
Zehui Yu
author_facet Wenjie Zhang
Ran Wang
Xiaoxia Zou
Congwei Gu
Qian Yang
Manli He
Wudian Xiao
Lvqin He
Mingde Zhao
Zehui Yu
author_sort Wenjie Zhang
collection DOAJ
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 doaj.art-8f0bfcb907734e52a0e89634e2155dd52023-08-03T04:22:32ZengElsevierVirus Research1872-74922023-09-01334199163Comparative genomic analysis of alloherpesviruses: Exploring an available genus/species demarcation proposal and methodWenjie Zhang0Ran Wang1Xiaoxia Zou2Congwei Gu3Qian Yang4Manli He5Wudian Xiao6Lvqin He7Mingde Zhao8Zehui Yu9Laboratory Animal Center, Southwest Medical University, Luzhou Sichuan, PR ChinaLaboratory Animal Center, Southwest Medical University, Luzhou Sichuan, PR ChinaSuining First People's Hospital, Suining, PR ChinaLaboratory Animal Center, Southwest Medical University, Luzhou Sichuan, PR China; Model Animal and Human Disease Research of Luzhou Key Laboratory, PR ChinaLaboratory Animal Center, Southwest Medical University, Luzhou Sichuan, PR China; Model Animal and Human Disease Research of Luzhou Key Laboratory, PR ChinaLaboratory Animal Center, Southwest Medical University, Luzhou Sichuan, PR China; Model Animal and Human Disease Research of Luzhou Key Laboratory, PR ChinaLaboratory Animal Center, Southwest Medical University, Luzhou Sichuan, PR China; Model Animal and Human Disease Research of Luzhou Key Laboratory, PR ChinaLaboratory Animal Center, Southwest Medical University, Luzhou Sichuan, PR China; Model Animal and Human Disease Research of Luzhou Key Laboratory, PR ChinaLaboratory Animal Center, Southwest Medical University, Luzhou Sichuan, PR China; Model Animal and Human Disease Research of Luzhou Key Laboratory, PR ChinaLaboratory Animal Center, Southwest Medical University, Luzhou Sichuan, PR China; Model Animal and Human Disease Research of Luzhou Key Laboratory, PR China; Scholl of Basic Medical Sciences, Zhejiang University, Hangzhou, PR China; Corresponding author at: Laboratory Animal Center, Southwest Medical University, Luzhou, Sichuan, PR China.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.http://www.sciencedirect.com/science/article/pii/S0168170223001259AlloherpesvirusesViral classificationPhylogenetic analysisANI/AAIDot-plot analysisCore-pan analysis
spellingShingle Wenjie Zhang
Ran Wang
Xiaoxia Zou
Congwei Gu
Qian Yang
Manli He
Wudian Xiao
Lvqin He
Mingde Zhao
Zehui Yu
Comparative genomic analysis of alloherpesviruses: Exploring an available genus/species demarcation proposal and method
Virus Research
Alloherpesviruses
Viral classification
Phylogenetic analysis
ANI/AAI
Dot-plot analysis
Core-pan analysis
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 Alloherpesviruses
Viral classification
Phylogenetic analysis
ANI/AAI
Dot-plot analysis
Core-pan analysis
url http://www.sciencedirect.com/science/article/pii/S0168170223001259
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