The SSU rRNA secondary structures of Trematoda reflect life cycle strategies of parasites and possess promising barcode regions

Abstract The small subunit ribosomal RNA (SSU rRNA) is widely used phylogenetic marker in broad groups of organisms and its secondary structure increasingly attracts the attention of researchers as supplementary tool in sequence alignment and advanced phylogenetic studies. Its comparative analysis provides a great contribution to evolutionary biology, allowing find out how the SSU rRNA secondary structure originated, developed and evolved. Herein, we provide the first data on the putative SSU rRNA secondary structures of the Trematoda species. The structures were found to be quite conserved across broad range of species studied, well compatible with those of others eukaryotic SSU rRNA and possessed some peculiarities: cross-shaped structure of the ES6b, additional shortened ES6c2 helix, and elongated ES6a helix and h39 + ES9 region. The secondary structures of variable regions reflect parasites' life-cycle strategies including their tissue specificity (ES3 and ES7) and possess promising barcodes at family level (ES6 and ES9). Their uniqueness more depends on the length than on the nucleotide diversity of primary sequences which evolutionary rates well differ. The findings have important implications for understanding rRNA evolution, developing molecular taxonomy and systematics of Trematoda as well as for constructing new anthelmintic drugs.