Secondary structure models of 18S and 28S rRNAs of the true bugs based on complete rDNA sequences of Eurydema maracandica Oshanin, 1871 (Heteroptera, Pentatomidae)

Abstract

The sequences of 18S and 28S rDNAs have been used as molecular markers to resolve phylogenetic relationships of Heteroptera for two decades. The complete sequences of 18S rDNAs have been used in many studies, while in most studies only partial sequences of 28S rDNAs have been used due to technical difficulties of amplifying the complete lengths. In this study, we amplified the complete 18S and 28S rDNA sequences of Eurydema maracandica Oshanin, 1871, and reconstructed the secondary structure models of the corresponding rRNAs. In addition, and more importantly, all of the length variable regions of 18S rRNA were compared among 37 families of Heteroptera based on 140 sequences, and the D3 region of 28S rRNA was compared among 51 families based on 84 sequences. It was found that 8 length variable regions could potentially serve as molecular synapomorphies for some monophyletic groups. Therefore discoveries of more molecular synapomorphies for specific clades can be anticipated from amplification of complete 18S and 28S rDNAs of more representatives of Heteroptera.

Extracting ‘legacy loci’ from an invertebrate sequence capture data set

“…To determine the complete sequence lengths of ribosomal nucDNA (i.e. 28S and 18S rRNA), literature searches were performed (DeLeo et al., 2018; Tautz et al., 1988; Xie et al., 2013). For most protein‐coding nucDNA (i.e.…”

Molecular Apomorphies in the Secondary and Tertiary Structures of Length-Variable Regions (LVRs) of 18S rRNA Shed Light on the Systematic Position of the Family Thaumastellidae (Hemiptera: Heteroptera: Pentatomoidea)

“…Analyses based on the sequence alignment using relevant models for nucleotide substitution are now widely accepted in molecular systematics [7][8][9][10][11][12][13]. However, the increase in the application of rRNA secondary structures in hexapod phylogenetics is less pronounced and, as far as the tertiary structures are concerned, progress is still not satisfactory [4,5,[14][15][16][17][18][19].…”

“…Unfortunately, the usefulness of the secondary structures of nuclear 18S rRNA sequences in resolving the phylogenetic problems in Hemiptera in general, and Heteroptera in particular, has only been considered sporadically [9,10,[19][20][21]. Nevertheless, the results have been promising, suggesting that the secondary structures of 18S rRNA could be a crucial new parameter in insect phylogenetic reconstructions.…”

“…Nevertheless, the results have been promising, suggesting that the secondary structures of 18S rRNA could be a crucial new parameter in insect phylogenetic reconstructions. The heteropteran superfamily Pentatomoidea is the only taxon in which such analyses have been conducted comprehensively [19,20]. Unfortunately, only one study [20] considered the pentatomoid family Thaumastellidae, the within-subfamily systematic position of which is ambiguous.…”

“…The SSU nrDNA (coding 18S rRNA) is one of the most frequently sequenced genes in insect molecular studies [1][2][3][6][7][8][9][10][11]15,[19][20][21]35,36,40]. However, in Heteroptera, its primary structure (i.e., aligned sequences) is usually used in phylogenetic reconstructions [6][7][8][9][10][11]13,35,36,40,44,[51][52][53].…”