Genomic analysis of Poxviridae and exploring qualified gene sequences for phylogenetics

Yu, Zehui; Zhang, Wenjie; Fu, Huancheng; Zou, Xiang; Zhao, Mingde; Liang, Sisi; Gu, Chunping; Yang, Qian; He, Manli; Xiao, Qihai; Xiao, Wudian; He, Lvqin; Lü, Muhan

doi:10.1016/j.csbj.2021.09.031

Cited by 16 publications

(13 citation statements)

References 26 publications

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“…FSMs in 13 virus families. We downloaded and analyzed randomly selected gene sequences of randomly selected viruses from 11 randomly selected RNA virus families and 2 randomly selected DNA virus families, including the newly established virus families of Hantaviridae, Nairoviridae, Peribunyaviridae, and Phenuiviridae (10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22). These sequences constituted 604 fas files, which harbored 400, 167, 195, and 244 groups with intra-group sequence identities of 90.0%−99.9%, 80.0%−89.9%, 70.0%−79.9%, and 60.0%−69.9%, respectively (Fig.…”

Section: Resultsmentioning

confidence: 99%

Frameshift Mutations in the Microevolution and Macroevolution of Viruses

Shao

Sun

et al. 2022

Preprint

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Some nucleotide insertions or deletions (indels) in protein-coding open reading frames lead to frameshift mutations (FSMs) which can change amino acid sequences drastically. FSMs are widely distributed in the genomes of many organisms. However, few studies have been reported regarding frequencies of FSMs in microevolution or macroevolution. Many viruses evolve much more rapidly than cellular organisms, and they are hence suitable to investigate frequencies of FSMs in microevolution or macroevolution. In this report, we identified 667 FSMs in gene sequences of 13 virus families and each FSM changed approximately 11 amino acid residues on average. Of the FSMs, 89.21% were 2-indel compensatory FSMs, and the remaining were 1-, 3-, 4-, 5-indel FSMs. We found that FSMs usually occurred more frequently in the viruses of the same family with smaller sequence identities, and FSMs occurred in the sequences of with identities of 60.0−69.9% more frequently than in the sequences with identities of 90.0−99.9% or 80.0−89.9% by approximately 34.9 or 13.1 times on average. We also found FSMs occurred at different frequencies among genes in the same virus genome, among species in the same virus family, or among virus families (e.g., more frequently in Coronaviridae than in Orthomyxoviridae). These results suggest that FSMs are more frequent in the inter-species or macroevolution than in the intra-species or microevolution of viruses. They provide novel evidence for the hopeful monster hypothesis in evolutionary biology. They inspire researchers to investigate the roles, frequencies, features, and functions of FSMs in other viruses and cellular organisms.

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Section: Resultsmentioning

confidence: 99%

Frameshift Mutations in the Microevolution and Macroevolution of Viruses

Shao

Sun

et al. 2022

Preprint

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“…Over the sequence length of 81,000 bp, all monkeypox virus (txid10244) nucleotide sequences were downloaded from the NCBI GenBank on July 5, 2022 (n = 402). Phylogenetic analysis was based on four viral genes, recommended by Yu et al [ 3 ], as for the family Poxviridae , the comparison between the analysis of these four-genes-concatenates and that of whole genomic amino acid sequences or poxvirus core genes conveyed similar results; and the results of the concatenate phylogenetic analysis has mirrored the classification of the family Poxviridae accurately. Viral sequences were annotated according to strain Zaire-96-I-16 (NC_003310) using VAPiD 1.2 [ 4 , 5 ], and the early transcription factor (E6R, GeneID: 928933), DNA-directed RNA polymerase (A25R, 928976), RNA polymerase-associated transcription-specificity factor (H4L, 928896), and DNA-dependent RNA polymerase gene (L6R, 929036) nucleotide sequences were extracted from these using Geneious.…”

Section: Methodsmentioning

confidence: 99%

Phylogenetic analysis of all available monkeypox virus strains shows the close relatedness of contemporary ones

Benkő

Harrach

Kaján

2023

Heliyon

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“…Phylogenetic analysis was conducted for the following poxvirus core genes ( 11 ) (ORF numbers designated according to PPV ORFs ( 12 )): DNA polymerase (ORF025), early transcription factor VETFL (ORF083), DNA-directed RNA polymerase subunit RPO132 (ORF101), and DNA topoisomerase type 1 (ORF062) (Figure). Consistent with earlier observations based on partial sequences of ORF11 and ORF056, F14.1158H grouped clearly closer to PPVs than other poxviruses (Figure A), although distinctly separate from the five currently recognized species (Figure B-D).…”

Section: Textmentioning

confidence: 99%

“…Phylogenetic analysis was conducted for the following poxvirus core genes (11) between the five previously recognized PPV species (Table S2). Within the PPVs, F14.1158H generally showed the second lowest pairwise nucleotide identity of the group (after the most divergent Grey sealpox virus) (Table ) with identities to other PPVs being 74-83% (ORF025), 73-83% (ORF083), 78-87% (ORF101), and 84-91% (ORF062).…”

Section: Textmentioning

confidence: 99%