Fig 1.
Flow diagram depicting experimental procedures and the number of analyzed samples.
The numbers in rectangles indicate those of samples from P. americana (first sampling), P. americana (second sampling), B. dubia and G. oblongonota, respectively. For samples from the first sampling of P. americana, the intestines from 4 cockroaches were pooled.
Table 1.
The list of the sequences used in this study.
Fig 2.
SSU rDNA-based phylogenetic tree of 134 Entamoeba sequences from cockroaches.
SSU rDNA sequences were aligned using MAFFT v7.187. Unambiguously aligned sequences composed of 1,023 nucleotides were selected by Gblocks and manual inspection. Maximum-likelihood (ML) tree was inferred by RAxML 8.1.17 using GTRGAMMA model. The number of bootstrap pseudoreplicate trees was 1,000. ML tree was visualized using FigTree 1.4.0 and Keynote 6.6.2. Bootstrap values for major nodes are shown on each node. Nine groups (A to I) were shown to be monophyletic with high bootstrap support values. Representative sequences of each group used in Fig 3 or Fig 4 are indicated by green circles or magenta circles, respectively.
Fig 3.
SSU rDNA-based cladogram of major eukaryotic supergroups including representative cockroach-derived Entamoeba.
SSU rDNA sequences were aligned using MAFFT v7.187. Unambiguously aligned sequences composed of 914 nucleotides were selected by Gblocks and manual inspection. Maximum-likelihood (ML) tree was inferred by RAxML 8.1.17 using GTRGAMMA model. The number of bootstrap pseudoreplicate trees was 1,000. ML tree was visualized as a cladogram using FigTree 1.4.0 and Keynote 6.6.2. Note that all representative sequences of cockroach-derived Entamoeba are new Entamoeba ribosomal lineages, and their monophyly was supported by the high bootstrap value (100%; black arrow). The size and colors of circles at the nodes indicate the approximate bootstrap value.
Fig 4.
Phylogenetic tree of SSU rDNA of Group C sequences of cockroach-derived Entamoeba.
SSU rDNA sequences were aligned using MAFFT v7.187. Unambiguously aligned sequences composed of 1,224 nucleotides were selected by Gblocks and manual inspection. Maximum-likelihood (ML) tree was inferred by RAxML 8.1.17 using GTRGAMMA model. The number of bootstrap pseudoreplicate trees was 1,000. ML tree was visualized using FigTree 1.4.0 and Keynote 6.6.2. Bootstrap values for major nodes are shown on each node.
Fig 5.
Phylogenetic tree of SSU rDNA of representative cockroach-derived Entamoeba ribosomal lineages and other Archamoebae species.
SSU rDNA sequences were aligned using MAFFT v7.187. Well-aligned 1,224 nucleotide positions were selected by Gblocks and manual operation. Maximum-likelihood (ML) tree was inferred by RAxML 8.1.17 using GTRGAMMA model. The number of bootstrap pseudoreplicate trees was 1,000. ML tree was visualized using FigTree 1.4.0 and Keynote 6.6.2. Bootstrap values (over 60%) are shown on each branch. Monophyly of Entamoeba is strongly supported with high bootstrap value (97%; gray arrow head). Commencing with Pa_27–2 and Bd_21–3, all cockroach-derived Entamoeba are positioned at the base of Entamoeba clade.
Table 2.
The number of Entamoeba groups found in each P. americana.
Table 3.
The number of Entamoeba groups found in each G. oblongonota.
Table 4.
The number of Entamoeba groups found in each B. dubia.
Table 5.
Sequence percentage identities among representative members of the clades in group C.