165
166
1.
la Scola B, Audic S, Robert C, et al (2003) A Giant Virus in Amoebae. Science (New York,
NY) 299:2033. https://doi.org/10.1126/science.1081867
167
168
169
170
2.
Boyer M, Yutin N, Pagnier I, et al (2009) Giant Marseillevirus highlights the role of
amoebae as a melting pot in emergence of chimeric microorganisms. Proceedings of the
National Academy of Sciences 106:21848–21853.
https://doi.org/10.1073/pnas.0911354106
171
172
173
3.
Philippe N, Legendre M, Doutre G, et al (2013) Pandoraviruses: Amoeba Viruses with
Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes. Science 341:281–286.
https://doi.org/10.1126/science.1239181
174
175
176
4.
Yoshikawa G, Blanc-Mathieu R, Song C, et al (2019) Medusavirus, a Novel Large DNA
Virus Discovered from Hot Spring Water. Journal of Virology 93:e02130-18.
https://doi.org/10.1128/JVI.02130-18
177
178
179
5.
Yoshida K, Zhang R, Garcia KG, et al (2021) Draft Genome Sequence of Medusavirus
Stheno, Isolated from the Tatakai River of Uji, Japan. Microbiol Resour Announc 10:.
https://doi.org/10.1128/MRA.01323-20
180
181
182
183
6.
Rolland C, Andreani J, Sahmi-Bounsiar D, et al (2021) Clandestinovirus: A Giant Virus
With Chromatin Proteins and a Potential to Manipulate the Cell Cycle of Its Host
Vermamoeba vermiformis. Front Microbiol 12:715608.
https://doi.org/10.3389/fmicb.2021.715608
184
185
186
7.
Koonin EV, Dolja VV, Krupovic M, et al (2020) Global Organization and Proposed
Megataxonomy of the Virus World. Microbiol Mol Biol Rev 84:e00061-19.
https://doi.org/10.1128/MMBR.00061-19
187
188
189
8.
Aylward FO, Moniruzzaman M, Ha AD, Koonin EV (2021) A phylogenomic framework
for charting the diversity and evolution of giant viruses. PLOS Biology 19:e3001430.
https://doi.org/10.1371/journal.pbio.3001430
190
191
192
9.
Yutin N, Wolf YI, Raoult D, Koonin EV (2009) Eukaryotic large nucleo-cytoplasmic DNA
viruses: Clusters of orthologous genes and reconstruction of viral genome evolution. Virol J
6:223. https://doi.org/10.1186/1743-422X-6-223
193
194
195
196
10. Walker PJ, Siddell SG, Lefkowitz EJ, et al (2021) Changes to virus taxonomy and to the
International Code of Virus Classification and Nomenclature ratified by the International
Committee on Taxonomy of Viruses (2021). Arch Virol 166:2633–2648.
https://doi.org/10.1007/s00705-021-05156-1
197
198
199
200
11.
201
202
203
12. Watanabe R, Song C, Kayama Y, et al Particle Morphology of Medusavirus Inside and
Outside the Cells Reveals a New Maturation Process of Giant Viruses. Journal of Virology
0:e01853-21. https://doi.org/10.1128/jvi.01853-21
204
205
206
13. Pritchard L, Glover RH, Humphris S, et al (2015) Genomics and taxonomy in diagnostics
for food security: soft-rotting enterobacterial plant pathogens. Anal Methods 8:12–24.
https://doi.org/10.1039/C5AY02550H
207
208
14. Emms DM, Kelly S (2019) OrthoFinder: phylogenetic orthology inference for comparative
genomics. Genome Biology 20:238. https://doi.org/10.1186/s13059-019-1832-y
209
210
211
15. Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T (2009) trimAl: a tool for automated
alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972–1973.
https://doi.org/10.1093/bioinformatics/btp348
212
213
16. Katoh K (2005) MAFFT version 5: improvement in accuracy of multiple sequence
alignment. Nucleic Acids Research 33:511–518. https://doi.org/10.1093/nar/gki198
Aylward FO, Abrahão J, Brussaard C, Fischer MG, Moniruzzaman M, Ogata H, Suttle CA
(2022) Create 3 new families, 3 subfamilies, 13 genera, and 20 new species within the order
Imitervirales (phylum Nucleocytoviricota) and rename two existing species.
https://talk.ictvonline.org/files/proposals/taxonomy_proposals_fungal1/m/fung01/13591
214
215
216
17. Minh BQ, Schmidt HA, Chernomor O, et al (2020) IQ-TREE 2: New Models and Efficient
Methods for Phylogenetic Inference in the Genomic Era. Molecular Biology and Evolution
37:1530–1534. https://doi.org/10.1093/molbev/msaa015
217
218
219
18. Kalyaanamoorthy S, Minh BQ, Wong TKF, et al (2017) ModelFinder: fast model selection
for accurate phylogenetic estimates. Nat Methods 14:587–589.
https://doi.org/10.1038/nmeth.4285
220
221
222
19. Hoang DT, Chernomor O, von Haeseler A, et al (2018) UFBoot2: Improving the Ultrafast
Bootstrap Approximation. Molecular Biology and Evolution 35:518–522.
https://doi.org/10.1093/molbev/msx281
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Figures
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Fig. 1 Acanthamoeba castellanii medusavirus J1 (ACMV-J1) replication and its particle feature
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[12]. (a) ACMV-J1 replication in amoeba cell after infection. (b) A cryo-EM image of ACMV-J1.
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Scale 200 nm. (c) A 3D reconstruction of ACMV-J1 virion. Scale 50 nm.
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Fig 2 Maximum-likelihood phylogenetic tree of Nucleocytoviricota. The tree was based on a
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concatenated amino acid sequence alignment of seven marker genes constructed using MAFFT
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(v.7.471) and trimAl (v.1.4.1) and was built using IQ-TREE 2 (v.2.1.3) [15–17]. The model was
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LG+F+R8 selected by the built-in Modelfinder of IQ-TREE 2 [18]. The branch supports were
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computed by 1000 ultrafast bootstrap and SH-aLRT [19]. The tree was visualized by iTOL,
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the round labels on branches represent high confidence supports with Ultrafast bootstrap ≥
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95%, SH-aLRT ≥ 80%. Position of proposed family “Mamonoviridae” is reported in red
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background and marked with stars.
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Fig. 3 Boxplots for (a) tip distance, (b) ANI, (c) TETRA, and (d) normalized OGs sharing level.
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The horizontal black line represents the value between clandestinovirus and Acanthamoeba
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castellanii medusavirus J1 (ACMV-J1), a member of proposed species “Medusavirus
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medusae”.
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