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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.