The analysis of rRNA sequence-structure in phylogenetics: An application to the family Pectinidae (Mollusca: Bivalvia)

Several studies pointed out the relevance of integrating secondary structure information in sequence analysis and phylogenetics, both in terms of phylogenetic resolution and of marker suitability for phylogenetic reconstruction at higher taxonomic-rank. In this study we explore in a phylogenetic framework the primary and secondary structure information from nuclear (ITS2) and mitochondrial (16S) ribosomal DNA sequences from the Pectinidae, commonly known as scallops. Primary sequences were analysed under neighbour-joining, maximum parsimony, maximum likelihood, and Bayesian approaches. The individual RNA secondary structures were analysed alone and with primary sequences employing a combined model of sequence-structure evolution. The information from primary sequences and secondary structure of the ITS2 are concordant and provide good phylogenetic resolution, while the mitochondrial marker 16S fails to resolve the relationships between the major clades and shows a lack of structural signals. Our phylogenetic reconstruction provided evidence for the monophyly of the subfamily Pectininae and the tribes Aequipectinini and Pectinini while the subfamily Chlamydinae, although recovered in some analyses, did not receive good support. The secondary structure analysis of the derived pectinid ITS2 rRNA sequence revealed three striking differences between Pectininae and Chlamydinae subfamilies: (a) Chlamydinae ITS2 rRNA folding shows the typical four domains architecture, while the one of Pectininae only three; (b) the Pectinidae basal DI pairing shows a different sequence-structure consensus between Pectininae and Chlamydinae; (c) the Pectininae DIII domain holds a specific short secondary stem (Pec STEM). Furthermore, the scallop ITS2 rRNA folding analysis has shown the presence of a conserved sequence motif (invariably located on apical portion of the DIII domain) which emerges as a common feature across Bivalvia. The combined sequence-structure approach employed in this study, corroborates the deep significance of including the secondary structure information in phylogenetic analysis both as combined sequence-structure alignment as well as pointing out conserved elements of the RNA folding