Additional file 1 of Association of virome dynamics with mosquito species and environmental factors
Creators: name: Liu, Qing
name: Cui, Feng
name: Liu, Xiang
name: Fu, Yumei
name: Fang, Wenjing
name: Kang, Xun
name: Lu, Hong
name: Li, Siping
name: Liu, Biao
name: Guo, Wei
name: Xia, Qianfeng
name: Kang, Le
name: Jiang, Feng
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: Cancer
subject: Plant Biology
subject: Virology

description: Additional file 1: Fig. S1. Phylogeny of viral RdRp protein sequences in the phylum Lenarviricota. The red star indicates bootstrap support &gt;90%. Branch lengths are measured by a scale bar. The RNA virus identified in this study is labeled by red branches. The red circle represents the novel virus identified in this study, and the blue circle represents the previously described virus. Fig. S2. Phylogeny of viral RdRp protein sequences in the family Partitiviridae. The red star indicates bootstrap support &gt;90%. Branch lengths are measured by a scale bar. The RNA virus identified in this study is labeled by red branches. The red circle represents the novel virus identified in this study, and the blue circle represents the previously described virus. Fig. S3. Phylogeny of viral RdRp protein sequences in the family Iflaviridae. The red star indicates bootstrap support &gt;90%. Branch lengths are measured by a scale bar. The RNA virus identified in this study is labeled by red branches. The red circle represents the novel virus identified in this study, and the blue circle represents the previously described virus. Fig. S4. Phylogeny of viral RdRp protein sequences in the family Secoviridae. The red star indicates bootstrap support &gt;90%. Branch lengths are measured by a scale bar. The RNA virus identified in this study is labeled by red branches. The red circle represents the novel virus identified in this study, and the blue circle represents the previously described virus. Fig. S5. Phylogeny of viral RdRp protein sequences in the family Dicistroviridae. The red star indicates bootstrap support &gt;90%. Branch lengths are measured by a scale bar. The RNA virus identified in this study is labeled by red branches. The red circle represents the novel virus identified in this study, and the blue circle represents the previously described virus. Fig. S6. Phylogeny of viral RdRp protein sequences in the family Polycipiviridae. The red star indicates bootstrap support &gt;90%. Branch lengths are measured by a scale bar. The RNA virus identified in this study is labeled by red branches. The red circle represents the novel virus identified in this study, and the blue circle represents the previously described virus. Fig. S7. Phylogeny of viral RdRp protein sequences in the families Picornaviridae and Solinviviridae. The red star indicates bootstrap support &gt;90%. Branch lengths are measured by a scale bar. The RNA virus identified in this study is labeled by red branches. The red circle represents the novel virus identified in this study, and the blue circle represents the previously described virus. Fig. S8. Phylogeny of viral RdRp protein sequences in the family Endornaviridae. The red star indicates bootstrap support &gt;90%. Branch lengths are measured by a scale bar. The RNA virus identified in this study is labeled by red branches. The red circle represents the novel virus identified in this study, and the blue circle represents the previously described virus. Fig. S9. Phylogeny of viral RdRp protein sequences in the family Virgaviridae. The red star indicates bootstrap support &gt;90%. Branch lengths are measured by a scale bar. The RNA virus identified in this study is labeled by red branches. The red circle represents the novel virus identified in this study, and the blue circle represents the previously described virus. Fig. S10. Phylogeny of viral RdRp protein sequences in the family Tymoviridae. The red star indicates bootstrap support &gt;90%. Branch lengths are measured by a scale bar. The RNA virus identified in this study is labeled by red branches. The red circle represents the novel virus identified in this study, and the blue circle represents the previously described virus. Fig. S11. Phylogeny of viral RdRp protein sequences in the family Flaviviridae. The red star indicates bootstrap support &gt;90%. Branch lengths are measured by a scale bar. The RNA virus identified in this study is labeled by red branches. The red circle represents the novel virus identified in this study, and the blue circle represents the previously described virus. Fig. S12. Phylogeny of viral RdRp protein sequences in the family Nodaviridae. The red star indicates bootstrap support &gt;90%. Branch lengths are measured by a scale bar. The RNA virus identified in this study is labeled by red branches. The red circle represents the novel virus identified in this study, and the blue circle represents the previously described virus. Fig. S13. Phylogeny of viral RdRp protein sequences in the families Totiviridae and Chrysoviridae. The red star indicates bootstrap support &gt;90%. Branch lengths are measured by a scale bar. The RNA virus identified in this study is labeled by red branches. The red circle represents the novel virus identified in this study, and the blue circle represents the previously described virus. Fig. S14. Phylogeny of viral RdRp protein sequences in the order Reovirales. The red star indicates bootstrap support &gt;90%. Branch lengths are measured by a scale bar. The RNA virus identified in this study is labeled by red branches. The red circle represents the novel virus identified in this study, and the blue circle represents the previously described virus. Fig. S15. Phylogeny of viral RdRp protein sequences in the order Bunyavirales. The red star indicates bootstrap support &gt;90%. Branch lengths are measured by a scale bar. The RNA virus identified in this study is labeled by red branches. The red circle represents the novel virus identified in this study, and the blue circle represents the previously described virus. Fig. S16. Phylogeny of viral RdRp protein sequences in the family Orthomyxoviridae. The red star indicates bootstrap support &gt;90%. Branch lengths are measured by a scale bar. The RNA virus identified in this study is labeled by red branches. The red circle represents the novel virus identified in this study, and the blue circle represents the previously described virus. Fig. S17. Phylogeny of viral RdRp protein sequences in the family Rhabdoviridae. The red star indicates bootstrap support &gt;90%. Branch lengths are measured by a scale bar. The RNA virus identified in this study is labeled by red branches. The red circle represents the novel virus identified in this study, and the blue circle represents the previously described virus. Fig. S18. Phylogeny of viral RdRp protein sequences in the family Xinmoviridae. The red star indicates bootstrap support &gt;90%. Branch lengths are measured by a scale bar. The RNA virus identified in this study is labeled by red branches. The red circle represents the novel virus identified in this study, and the blue circle represents the previously described virus. Fig. S19. Phylogeny of viral RdRp protein sequences in the family Birnaviridae. The red star indicates bootstrap support &gt;90%. Branch lengths are measured by a scale bar. The RNA virus identified in this study is labeled by red branches. The red circle represents the novel virus identified in this study, and the blue circle represents the previously described virus. Fig. S20. Saturation analysis of the identified viral family across sequencing samples. Ar.sub, Armigeres subalbatus; Ae.alb, Aedes albopictus; Ae.vex, Aedes vexans; Cx.gel, Culex gelidus; Cx.pal, Culex pallidothorax; Cx.pip, Culex pipiens quinquefasciatus; Cx.tri, Culex tritaeniorhynchus; Cx.vis, Culex vishnui. Fig. S21. Random validation of plant-derived RNAs and RNA viruses based on RT‒PCR Sanger sequencing. Cx.pip, Culex pipiens quinquefasciatus; Ae.vex, Aedes vexans; Cx.pal, Culex pallidothorax; Cx.gel, Culex gelidus; HMOV5, Hainan Mosquito Virus 5. Fig. S22. The observed richness of operational taxonomic units of RNA viruses (A) and RNA virus abundance (B) in different sequencing libraries across mosquito species. *P &lt; 0.05; **P &lt; 0.001. Ae.alb, Aedes albopictus; Ae.aeg, Aedes aegypti; Cx.pip, Culex pipiens quinquefasciatus; Ar.sub, Armigeres subalbatus; Cx.tri, Culex tritaeniorhynchus; Cx.pal, Culex pallidothorax; Ae.vex, Aedes vexans; Cx.vis, Culex vishnui; Cx.fus, Culex fuscocephala; Cx.sit, Culex sitiens; Cx.pse, Culex pseudovishnui; An.vag, Anopheles vagus; Cx.lut, Culex (Lutzia) fuscanus; Ae.mal, Aedes malayensis; Cx.gel, Culex gelidus. Fig. S23. Multiple scaling analysis for RNA virome composition across mosquito species using a Euclidean distance matrix. BS, Baisha. DF, Dongfang. DZ, Danzhou. HK, Haikou. LD, Ledong. LG, Lingao. LS, Lingshui. QH, Qionghai. SY, Sanya. TC, Tunchang. WC, Wenchang. WN, Wanning. WZS, Wuzhishan. Fig. S24. Heatmap plot showing the presence of virus OTUs over the three consecutive years from 2018 to 2020 in three mosquito species. Ae.alb, Aedes albopictus; Ar.sub, Armigeres subalbatus; Cx.pip, Culex pipiens quinquefasciatus. Fig. S25. Shannon index of operational taxonomic units of RNA viruses across collection locations. Statistically significant differences were detected using a Kruskal‒Wallis test in cases of multiple comparisons. In pairwise comparisons, significant differences were detected by pairwise Wilcoxon rank sum tests. *P &lt; 0.05; **P &lt; 0.001. BS, Baisha; DF, Dongfang; DZ, Danzhou; HK, Haikou; LD, Ledong; LG, LinGao; LS, Lingshui; QH, Qionghai; SY, Sanya; TC, Tunchang; WC, Wenchang; WN, Wanning; WZS, Wuzhishan. Fig. S26. The observed richness of operational taxonomic units of RNA viruses (A, C, E) and RNA virus abundance (B, D, F) between Hainan Island and other collection locations in Yunnan (inland China, Asia), California (United States, North America) and Sweden (Europe). In pairwise comparisons, Wilcoxon rank sum tests were applied to detect significant differences. *P &lt; 0.05; **P &lt; 0.01. Ae.alb, Aedes albopictus; Cx.pip, Culex pipiens quinquefasciatus. Fig. S27. Bubble plot showing the distribution of food sources derived from animals and plants in Aedes albopictus and Culex pipiens quinquefasciatus in Hainan Island. The shared families are linked using blue lines. Ae.alb, Aedes albopictus;Cx.pip, Culex pipiens quinquefasciatus. Fig. S28. Bubble plot showing the distribution of food sources derived from animals and plants in Aedes albopictus (left) and Culex pipiens quinquefasciatus (right) in the four continental regions. The shared families are linked using blue lines.