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Figure 1. Sample collection in the Hainan Island and metagenomics of rodents according to species and locations. The maps of Haikou City, Baisha County, Dongfang City, Lingao County, Tunchang County, Lingshui County, Ledong County, Chengmai County, and Sanya City in Hainan Island, showing the locations of the samples. Rodent numbers and species are also shown on the map with different shapes, colours, and sizes.
Figure 2. (a-d). Comparison of the number of total contigs and proportions of viral reads from the six rodent species. Comparison of the numbers of total reads and proportions of viral reads from the fifteen sampling locations. (e). The proportions of the number of reads assigned to each viral family in each of the 28 pools are shown in the bar graph.
Figure 3. Rodent-related virome profile in the transcriptomic data from the 28 pools. Expression is reported in log2(TPM), where TPM refers to transcripts per million.
Figure 4. Phylogenetic tree of arenaviruses (AreVs). The phylogenetic tree is based on the partial L protein (RdRp) acid sequences of AreVs. Phylogenetic trees were constructed by the maximum likelihood method using the best-fit models (LG+G+I). AreVs identified in this study are labelled in red. Host genus and location of each virus are labelled by the 5-point stars and dots of different colours. The outer colour rings represent additional taxonomic information about these viruses.
Figure 5 . Phylogenetic tree of coronaviruses (CoVs). (a) The phylogenetic tree is based on the amino acid sequences of complete RNA-dependent RNA polymerase (RdRp) genes and S (spike) genes of CoVs. (b)Phylogenetic trees were constructed by the maximum likelihood method using the best-fit models (WAG+G). All CoVs identified in this study are labelled in red. Host genus and location of each virus are labelled by the 5-point stars and dots of different colours. The outer colour rings represent additional taxonomic information about these viruses.
Figure 6 . Phylogenetic tree of pestiviruses (PestVs). The phylogenetic tree is based on the amino acid sequences of complete RNA-dependent RNA polymerase (RdRp) (NS5) genes of PestVs. Phylogenetic trees were constructed by the maximum likelihood method using the best-fit models (rtREV+G). All PestVs identified in this study are labelled in red. Host genus and location of each virus are labelled by the 5-point stars and dots of different colours. The outer colour rings represent additional taxonomic information about these viruses.
Figure 7 . Phylogenetic tree of astroviruses (AstroVs). (a-b) The phylogenetic tree is based on the amino acid sequences of complete RNA-dependent RNA polymerase (RdRp) genes and CP genes. Phylogenetic trees were constructed by the maximum likelihood method using the best-fit models (mtREV+G+I). All AstroVs identified in this study are labelled in red. Host genus and location of each virus are labelled by the 5-point stars and dots of different colours. The outer colour rings represent additional taxonomic information about these viruses.
Figure 8 . Phylogenetic tree of parvoviruses (ParVs) and papillomaviruses (PVs). (a) Phylogenetic tree based on the amino acid sequences of complete NS5 genes of ParVs. Phylogenetic trees were constructed by the maximum likelihood method using the best-fit models (rtREV+G+I). (b) Phylogenetic trees are based on the amino acid sequences of complete L genes of PVs and constructed by the maximum likelihood method using the best-fit models (LG+G). All ParVs and PVs identified in this study are labelled in red. Host genus and location of each virus are labelled by the 5-point stars and dots of different colours. The outer colour rings represent additional taxonomic information about these viruses.