New Comparative Analysis Based on the Secondary Structure of SSU-rRNA Gene Reveals the Evolutionary Trend and the Family-Genus Characters of Mobilida (Ciliophora, Peritrichia)

Abstract

In order to reveal the structural evolutionary trend of Mobilida ciliates, twenty-six SSU-rRNA sequences of mobilid species, including seven ones newly sequenced in the present work, were used for comparative phylogenic analysis based on the RNA secondary structure. The research results indicate that all the secondary structures except domains Helix 10, Helix 12, and Helix 37 could be regarded as the criterions in classification between the family Trichodinidae and Urceolariida, and four regions including Helix E10-1, Helix 29, Helix 43, and Helix 45-Helix 46 could be as criterions in classification between the genus Trichodinella and Trichodina in family Trichodinidae. After the analysis of common structural feature within the Mobilida, it was found that the secondary structure of V6 could prove the family Urceolariidae primitive status. This research has further suggested that the genus Trichodina could be divergent earlier than Trichodinella in the family Trichodinidae. In addition, the relationship between the secondary structure and topology of phylogenic tree that the branching order of most clades corresponds with the secondary structure of species within each clade of phylogenetic tree was first uncovered and discussed in the present study.

Morphological and Molecular Identification of the New Species,Trichodina pseudoheterodentatasp. n. (Ciliophora, Mobilida, Trichodinidae) from the Channel Catfish,Ictalurus punctatus, in Chongqing China

“…Previous studies indicated that some important regions of the SSU rDNA secondary structure could be used for the identification of Mobilida ciliates (Tang et al 2013b;Zhang et al 2015). In the present study, the comparative analysis of the secondary structures revealed distinct differences in H12, H15, E10_1 regions, especially in the V4 region (Fig.…”

“…; Zhang et al. ). In the present study, the comparative analysis of the secondary structures revealed distinct differences in H12, H15, E10_1 regions, especially in the V4 region (Fig.…”

“…; Zhang et al. ), due to limited molecular data. In this study, SSU rDNA sequences were used to reveal that the new species ( T. pseudoheterodentata ) is distinctly different from the other three species ( T. heterodentata , T. paraheterodentata , and T. nobillis ) in both conservative and variable regions, possessing more than thirteen variation sites.…”

“…Up to date, many parasites or ciliates have been identified molecularly (Alda et al 2015;Chen et al 2013;Li et al 2015;Shigehiko et al 2015;Zhao et al 2013), mainly due to the increased molecular data in GenBank databases. However, molecular identification of trichodinid ciliates is scarce (Irwin and Lynn 2015;Tang and Zhao 2016;Tang et al 2013b;Zhang et al 2015), due to limited molecular data. In this study, SSU rDNA sequences were used to reveal that the new species (T. pseudoheterodentata) is distinctly different from the other three species (T. heterodentata, T. paraheterodentata, and T. nobillis) in both conservative and variable regions, possessing more than thirteen variation sites.…”

Morphological description and molecular identification ofMyxobolus dajiangensisn. sp. (Myxozoa: Myxobolidae) from the gill ofCyprinus carpioin southwest China

“…The predicted secondary structures, based on free energy minimization, were constructed for the selected species using RNA structure 5.2 with default settings. The obtained structures were displayed and manually adjusted using RNAViz 2.0 ( Zhang et al 2015 ). Three hypervariable regions of SSU rRNA (V4, V6 and V7) were selected to study their variability.…”