In this study, we analysed the nuclear ITS2 rRNA primary sequence and secondary structure in Veneridae and comparatively with 20 Bivalvia taxa to test the phylogenetic resolution of this marker and its suitability for molecular diagnosis at different taxonomic levels. Maximum-Likelihood and Bayesian trees based on primary sequences were congruent with (Profile-) Neighbor-Joining trees based on a combined model of sequence-structure evolution. ITS2 showed higher resolution below the subfamily level, up to the intraspecific level, providing a phylogenetic signal comparable to (mitochondrial and/or nuclear) gene fragments two-five times longer. Structural elements of the ITS2 folding, such as specific mismatch pairing and compensatory base changes, provided further support for the monophyly of some groups and for their phylogenetic relationships. Veneridae ITS2 folding is structured in six domains (DI-VI) and shows five striking sequence-structure features. Two of them, the Basal and Apical STEMs, are common to Bivalvia, while the presence of both the Branched STEM and the Y/R stretches occurs in five superfamilies of the two Heterodonta orders Myoida and Veneroida, thus questioning their reciprocal monophyly. Our results validated the ITS2 as a suitable marker tool for venerids phylogenetics and taxonomy, and underlined the significance of including secondary structure information for both applications at several systematic levels within bivalves.

Salvi, D., Mariottini, P. (2012). Molecular phylogenetics in 2D: ITS2 rRNA evolution and sequence-structure barcode from Veneridae to Bivalvia. MOLECULAR PHYLOGENETICS AND EVOLUTION [10.1016/j.ympev.2012.07.017].

Molecular phylogenetics in 2D: ITS2 rRNA evolution and sequence-structure barcode from Veneridae to Bivalvia

MARIOTTINI, Paolo
2012-01-01

Abstract

In this study, we analysed the nuclear ITS2 rRNA primary sequence and secondary structure in Veneridae and comparatively with 20 Bivalvia taxa to test the phylogenetic resolution of this marker and its suitability for molecular diagnosis at different taxonomic levels. Maximum-Likelihood and Bayesian trees based on primary sequences were congruent with (Profile-) Neighbor-Joining trees based on a combined model of sequence-structure evolution. ITS2 showed higher resolution below the subfamily level, up to the intraspecific level, providing a phylogenetic signal comparable to (mitochondrial and/or nuclear) gene fragments two-five times longer. Structural elements of the ITS2 folding, such as specific mismatch pairing and compensatory base changes, provided further support for the monophyly of some groups and for their phylogenetic relationships. Veneridae ITS2 folding is structured in six domains (DI-VI) and shows five striking sequence-structure features. Two of them, the Basal and Apical STEMs, are common to Bivalvia, while the presence of both the Branched STEM and the Y/R stretches occurs in five superfamilies of the two Heterodonta orders Myoida and Veneroida, thus questioning their reciprocal monophyly. Our results validated the ITS2 as a suitable marker tool for venerids phylogenetics and taxonomy, and underlined the significance of including secondary structure information for both applications at several systematic levels within bivalves.
2012
Salvi, D., Mariottini, P. (2012). Molecular phylogenetics in 2D: ITS2 rRNA evolution and sequence-structure barcode from Veneridae to Bivalvia. MOLECULAR PHYLOGENETICS AND EVOLUTION [10.1016/j.ympev.2012.07.017].
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11590/122416
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