Table 1.
Genome features of the P. vivax-like Pvl01 (Illumina HiSeq sequenced) and Pvl06 (PacBio sequenced) strains, P. vivax reference strains SalI and PvP01 [15], P. cynomolgi B and M isolates [8,17], and P. knowlesi H strain [18].
Table 2.
Number of detected copies of multigene family members in the genomes of P. vivax-like (Pvl01 and Pvl06), P. vivax strains SalI and PvP01 [15], P. cynomolgi B and M isolates [8,17], and P. knowlesi H strain [18].
Fig 1.
rbp genes in P. vivax-like and P. vivax.
(A) Maximum likelihood phylogenetic tree of all full-length rbp genes in P. vivax-like Pvl01 (in blue), P. vivax SalI and PvP01 strains (in green), P. cynomolgi B strain, and P. knowlesi H strain (in black). Bootstrap values, calculated by RAxML bootstrapping posterior probability, are indicated. The different subclasses of rbp are indicated as rbp1, rbp2, and rbp3. The black stars indicate pseudogenes. The animal pictograms indicate the primate host. (B) Table representing the number of variants (including the ones that are pseudogenized) observed in each rbp subclass in P. vivax-like (Pvl01), P. vivax (SalI and PvP01), P. cynomolgi (B and M strains), and P. knowlesi (H strain). Pseudogenes detected among each subclass of rbp are indicated within each subclass between brackets. The alignment of the rbp sequences with their accession numbers indicated and the inferred RAxML tree are available as the supplemental files in S2 Data. RBP, reticulocyte-binding protein.
Fig 2.
Relative divergence dating between P. vivax and P. vivax-like.
Maximum likelihood phylogenetic tree of 13 Plasmodium species, including P. vivax and P. vivax-like. The analysis was based on an alignment of 2,784 one-to-one orthologous groups across the 13 Plasmodium reference genomes (see Materials and methods section). Values indicated at the nodes are the 95% CIs of the relative splits estimated using the method developed by Silva and colleagues [29] (values in blue) and the RelTime method [69] (values in red; ×100). Results are given for the analyses performed considering the JTT model of evolution. For the Silva method [29], we gave for the internal nodes the minimal and maximal values of the lower and upper limits of the 95% CI of all possible pairwise species combinations. The table gives the ratio between the relative divergence times of the human–nonhuman Plasmodium species pairs. The final alignment of the 2,784 one-to-one orthologues—excluding ambiguities, lox-complexity regions, and poorly aligned regions—and the tree are available as supplemental files in S3 Data. CI, confidence interval; JTT, Jones, Taylor, and Thornton; Pf, P. falciparum; Pkn, P. knowlesi; Pm, P. malariae; Pml, P. malariae-like; Poc, P. ovale curtisi; Pow, P. ovale wallikeri; Pprf, P. praefalciparum; Pv, P. vivax; Pvl, P. vivax-like.
Fig 3.
ML phylogenetic tree with 1,000 bootstraps computed by alignment to the P. cynomolgi B strain genome, based on 100,616 SNVs shared by 11 P. vivax-like and 19 P. vivax samples.
A position was considered an SNV if at least one sample carried a different nucleotide compared with the PvP01 reference. No missing data were allowed, and a minimum depth of 5 reads per position was considered. To overcome issues relating to multiple infections, we considered the dominant infection only by selecting the dominant allele (see Materials and methods for details). Bootstrap values superior to 70% are indicated. The host in which the Plasmodium parasite was detected is indicated by the pictograms (human, chimpanzee, and An. moucheti). This phylogeny showed the presence of a significantly distinct clade (high bootstrap values associated with each clade) composed of P. vivax-like strains on one side (light blue) and human P. vivax isolates on the other side (light green). Data (the alignment and the tree file obtained by the ML phylogenetic analysis) can be found in S5 Data. ML, maximum likelihood; SNV, single nucleotide variant.