Table 1.
Number of both M35 family and M36 family genes in different fungal species.
Figure 1.
ML tree based on amino acid sequences of 105 M35 family genes.
The tree was performed using PHYML 3.0[17]. The best-fitting model WAG+I+G and their parameters (I = 0.03, G = 1.912) which were estimated by program ProtTest [50] were used in the ML analysis. The reliability of the tree topology was evaluated using bootstrap support [20] with 100.
Figure 2.
ML tree based on amino acid sequences of 58 M36 family genes.
The tree was performed using PHYML 3.0[17]. The best-fitting model WAG+I+G and their parameters (I = 0.038, G = 1.149) which were estimated by program ProtTest [50] were used in the ML analysis. The reliability of the tree topology was evaluated using bootstrap support [20] with 100.
Figure 3.
Duplication and loss events of M35 family genes and M36 family genes in Onygenales fungi.
The reconciliation between species tree and gene tree of Onygenales fungi along with the confirmation of the gene loss/duplication scenario were determined by using Notung 2.6 [21]. The species tree of Onygenales fungi is shown as Fig. S7. Putative duplication events are indicated with solid cycles, while loss events are indicated with thick branches. a, duplication and loss events of M35 family genes. b, duplication and loss events of M36 family genes.
Figure 4.
Duplication and loss events of M35 family genes in Eurotiales fungi.
The reconciliation between species tree and gene tree of Eurotiales fungi along with the confirmation of the gene loss/duplication scenario were determined by using Notung 2.6 [21]. The species tree of Eurotiale fungi is shown as Fig. S8. Putative duplication events are indicated with solid cycles, while loss events are indicated with thick branches. 1, the lineage includes species of A. fumigatus, N. fischeri and A. clavatus. 2, the lineage includes species of A. nidulans, A. terreus, A. oryza and A. flavus.
Figure 5.
Phylogenetic tree of 62 M35 family genes used for codon-based maximum likelihood analysis in PAML.
Phylogenetic trees were collapsed with inconsistent nodes from different tree-building methods and poor statistical supports into polytomy. Branches a-s indicated putative duplication events in Onygenales fungi. The branches with significant evidence of positive selection are indicated as a thick branch. The putative positively selected residues along these branches were shaded in grey.
Table 2.
CODEML analyses of selective pattern for M35 family genes.
Table 3.
CODEML analyses of selective pattern for M36 family genes.
Figure 6.
Phylogenetic tree of 38 M36 family genes used for codon-based maximum likelihood analysis in PAML.
Phylogenetic trees were collapsed with inconsistent nodes from different tree-building methods and poor statistical supports into polytomy. Branches a-j indicated putative duplication events in Onygenales fungi. The branches with significant evidence of positive selection are indicated as a thick branch. The putative positively selected residues along these branches were shaded in grey.