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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Elsevier
2023-09-01
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Series: | Virus Research |
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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. |
first_indexed | 2024-03-12T17:52:41Z |
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institution | Directory Open Access Journal |
issn | 1872-7492 |
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last_indexed | 2024-03-12T17:52:41Z |
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publisher | Elsevier |
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series | Virus Research |
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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