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Comprehensive identification of protein orthologs in the family Ascoviridae facilitates an understanding of phylogenomics, protein conservation, and phosphorylation

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Abstract

Analysis of orthology is important for understanding protein conservation, function, and phylogenomics. In this study, we performed a comprehensive analysis of gene orthology in the family Ascoviridae based on identification of 366 protein homologue groups and phylogenetic analysis of 34 non-single-copy proteins. Our findings revealed 90 newly annotated proteins, five newly identified core proteins for the family Ascoviridae, and 14 core proteins for the genus Ascovirus. A phylogenomic tree of 11 Ascoviridae members was constructed based on a concatenation of 35 of the 45 ortholog groups. In combination with phosphoproteomic results and conservation estimations, 30 conserved phosphorylation sites on 17 phosphoproteins were identified from a total of 176 phosphosites on 57 phosphoproteins from Heliothis virescens ascovirus 3h (HvAV-3h), providing potential research targets for investigating the role of these protein in the regulation of viral infection. This study will facilitate genome annotation and comparison of further Ascoviridae members as well as functional genomic investigations.

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Acknowledgements

This research was funded by the Shandong Provincial Natural Science Foundation (No. ZR2020QC014), the National Natural Science Foundation of China (No. 31872027), and the Doctoral Fund of Weifang Medical University (No. 02181801). We also thank LetPub (www.letpub.com) for its linguistic assistance during the preparation of this manuscript.

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  1. Yanhua Shi, Weiping Lin and Jinxin Chu have contributed equally to this work.

Authors and Affiliations

  1. School of Life Science and Technology, Weifang Medical University, Weifang, 261053, People’s Republic of China

    Yanhua Shi, Weiping Lin, Jinxin Chu, Guohui Wang, Punan Zhao & Dianhai Hou

  2. Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan, 410128, People’s Republic of China

    Guo-hua Huang

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Contributions

Conceptualization: WL, DH, and GH. Formal analysis: WL, YS, and DH. Writing—original draft preparation: WL, YS, PZ, and DH. Writing—review and editing: JC, DH, and GH. Revision: GW, DH, and GH. Supervision: DH and GH. Funding acquisition: DH and GH. All authors have read and agreed to the published version of the manuscript.

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Correspondence to Guo-hua Huang or Dianhai Hou.

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705_2022_5402_MOESM1_ESM.tif

Fig. S1 Schematic diagram of the work flow for identification of homologue groups and analysis of orthology among Ascoviridae genomes (TIF 2932 KB)

705_2022_5402_MOESM2_ESM.tif

Fig. S2 Phylogenetic analysis based on alignments of complete amino acid (aa) sequences of Putative S1/P1 nuclease (HvAV-3h ORF88/ORF139) (A), HvAV-3h ORF31/ORF34 (B), HvAV-3g ORF10 (C), TnAV-6a ORF71 (D), and HR (E) homologues. Phylogenetic analysis was performed using the ML method in IQ-TREE with 1000 bootstrap replicates with a protein model of LG+I, FLU+R2, JTT, LG+G4, and JTT+R2 for Putative S1/P1 nuclease (HvAV-3h ORF88/ORF139), HvAV-3h ORF31/ORF34, HvAV-3g ORF10, TnAV-6a ORF71, and HR, respectively. The orthologous groups were identified based on a phylogenetic analysis each of homologue group. The scale bar of branch length is shown at the bottom left of each phylogenetic tree. See full names of viruses in Table S1 (TIF 58960 KB)

705_2022_5402_MOESM3_ESM.tif

Fig. S3 Phylogenetic analysis based on alignments of complete amino acid (aa) sequences of TnAV-6a ORF27 (A), TnAV-6a ORF36 (B), TnAV-6a ORF66 (C), TnAV-6a ORF70 (D) and TnAV-6a ORF73 (E) homologues. Phylogenetic analysis was performed using the ML method in IQ-TREE with 1000 bootstrap replicates with a protein model of FLU+I, FLU+R2, Blosum62, FLU and PMB for TnAV-6a ORF27, TnAV-6a ORF36, TnAV-6a ORF66, TnAV-6a ORF70, and TnAV-6a ORF73, respectively. Pairs of orthologous groups were identified based on a phylogenetic analysis each of homologue group. The scale bar of branch length is shown at the bottom left of each phylogenetic tree. * Newly annotated in this study. See full names of viruses in Table S1 (TIF 64239 KB)

705_2022_5402_MOESM4_ESM.tif

Fig. S4 Phylogenetic and structural analysis based on alignments of complete aa sequences of ARO homologues. A Phylogenetic analysis was performed using the maximum-likelihood method in IQ-TREE with 1000 bootstrap replicates with a protein model of VT+I+G4. The scale bar of branch length is shown at the bottom left of each phylogenetic tree. See full names of viruses in Table S1. B The corresponding polypeptide sequences of AROs at the terminal of each phylogenetic tree is represented as rectangles, with small rectangles in different colors corresponding to motifs found using MEME. All AROs shared the DUF5862 domain with unknown function. C The motifs corresponding to different colored rectangles (TIF 20558 KB)

705_2022_5402_MOESM5_ESM.tif

Fig. S5 Phylogenetic analysis based on alignments of complete aa sequences of BRO homologues. Phylogenetic analysis was performed using the maximum-likelihood method in IQ-TREE with 10,000 ultrafast bootstrap replicates with a protein model of Dayhoff+F+R7. The scale bar of branch length is shown at the bottom left of each phylogenetic tree. See full names of viruses in Table S1 (TIF 8401 KB)

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Shi, Y., Lin, W., Chu, J. et al. Comprehensive identification of protein orthologs in the family Ascoviridae facilitates an understanding of phylogenomics, protein conservation, and phosphorylation. Arch Virol 167, 1075–1087 (2022). https://doi.org/10.1007/s00705-022-05402-0

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