Fig. 4.

Secondary structures of protostome TRs. (A) Evolutionary relationship of protostome phyla and classes with TR identified. The numbers of TRs identified in this study for each class are indicated. An asterisk denotes the classes for which the TR secondary structure of a representative species is shown in B–D. Fungi represents the outgroup in the phylogenetic tree. (B–D) Representative TR secondary structures determined by phylogenetic comparative sequence analyses are shown; Pomacea diffusa (apple snail) from phylum mollusca (B), Eisenia fetida (earth worm) from phylum annelida (C), and Lingula anatina (tongue shell) from phylum brachipoda (D). The conserved TR structural domains are shaded in blue. The eCR4/5 domain is shaded in red. Universal covariations (thick lines), invariant residues, and residues with >80% conservation are based on the sequence alignment of 55 previously identified animal TRs and 82 novel metazoan TRs identified in this study. Group-specific covariations (thick lines) are indicated and based on the sequence alignment of TRs from individual groups including 21 mollusca, 7 annelida, 1 brachiopda, and 1 phoronida TRs, respectively.