Secondary Structure Models of 18S and 28S RRNAs of the True Bugs Based on Complete RDNA Sequences of Eurydema Maracandica Oshanin, 1871 (Heteroptera, Pentatomidae)

Overview

Journal Zookeys

Date 2013 Sep 17

PMID 24039531

Citations 8

Authors

Shasha Yu

Yanhui Wang

David Redei

Qiang Xie

Wenjun Bu

Affiliations

Soon will be listed here.

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.

Citing Articles

Phylogenetic placement and comparative analysis of the mitochondrial genomes of Idiostoloidea (Hemiptera: Heteroptera).

Zhang D, Chen X, Yang J, Yi W, Xie Q, Yang H Ecol Evol. 2024; 14(5):e11328.

PMID: 38698924 PMC: 11063732. DOI: 10.1002/ece3.11328.

Inconsistencies in the Classification of the Family Cydnidae (Hemiptera: Heteroptera: Pentatomoidea) Revealed by Molecular Apomorphies in the Secondary and Tertiary Structures of 18S rRNA Length-Variable Region L (LVR L).

Lis J, Domagala P Int J Mol Sci. 2024; 25(2).

PMID: 38256014 PMC: 10815949. DOI: 10.3390/ijms25020939.

Different roles of host and habitat in determining the microbial communities of plant-feeding true bugs.

Yang Z, Luo J, Men Y, Liu Z, Zheng Z, Wang Y Microbiome. 2023; 11(1):244.

PMID: 37932839 PMC: 10629178. DOI: 10.1186/s40168-023-01702-y.

Tribe Acalyptaini (: Tinginae) Revisited: Can Apomorphies in Secondary and Tertiary Structures of Length-Variable Regions (LVRs) Support Tribe Validity?.

Lis B, Domagala P, Lis J Insects. 2023; 14(7).

PMID: 37504606 PMC: 10380217. DOI: 10.3390/insects14070600.

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).

Lis J Int J Mol Sci. 2023; 24(9).

PMID: 37175465 PMC: 10178826. DOI: 10.3390/ijms24097758.

References

Neefs J, Van de Peer Y, De Rijk P, Chapelle S, De Wachter R . Compilation of small ribosomal subunit RNA structures. Nucleic Acids Res. 1993; 21(13):3025-49. PMC: 309731. DOI: 10.1093/nar/21.13.3025. View

Reuter J, Mathews D . RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics. 2010; 11:129. PMC: 2984261. DOI: 10.1186/1471-2105-11-129. View

Campbell B, Steffen-Campbell J, Gill R . Evolutionary origin of whiteflies (Hemiptera: Sternorrhyncha: Aleyrodidae) inferred from 18S rDNA sequences. Insect Mol Biol. 1994; 3(2):73-88. DOI: 10.1111/j.1365-2583.1994.tb00154.x. View

Jung S, Lee S . Molecular phylogeny of the plant bugs (Heteroptera: Miridae) and the evolution of feeding habits. Cladistics. 2021; 28(1):50-79. DOI: 10.1111/j.1096-0031.2011.00365.x. View

Grazia J, Schuh R, Wheeler W . Phylogenetic relationships of family groups in Pentatomoidea based on morphology and DNA sequences (Insecta: Heteroptera). Cladistics. 2021; 24(6):932-976. DOI: 10.1111/j.1096-0031.2008.00224.x. View

Wang Y, Engel M, Rafael J, Dang K, Wu H, Wang Y . A unique box in 28S rRNA is shared by the enigmatic insect order Zoraptera and Dictyoptera. PLoS One. 2013; 8(1):e53679. PMC: 3536744. DOI: 10.1371/journal.pone.0053679. View

Tian Y, Zhu W, Li M, Xie Q, Bu W . Influence of data conflict and molecular phylogeny of major clades in Cimicomorphan true bugs (Insecta: Hemiptera: Heteroptera). Mol Phylogenet Evol. 2008; 47(2):581-97. DOI: 10.1016/j.ympev.2008.01.034. View

Xie Q, Lin J, Qin Y, Zhou J, Bu W . Structural diversity of eukaryotic 18S rRNA and its impact on alignment and phylogenetic reconstruction. Protein Cell. 2011; 2(2):161-70. PMC: 4875256. DOI: 10.1007/s13238-011-1017-2. View

Xie Q, Tian X, Qin Y, Bu W . Phylogenetic comparison of local length plasticity of the small subunit of nuclear rDNAs among all Hexapoda orders and the impact of hyper-length-variation on alignment. Mol Phylogenet Evol. 2008; 50(2):310-6. DOI: 10.1016/j.ympev.2008.10.025. View

10.

Hassouna N, Michot B, Bachellerie J . The complete nucleotide sequence of mouse 28S rRNA gene. Implications for the process of size increase of the large subunit rRNA in higher eukaryotes. Nucleic Acids Res. 1984; 12(8):3563-83. PMC: 318769. DOI: 10.1093/nar/12.8.3563. View

11.

Ellis R, Sulston J, Coulson A . The rDNA of C. elegans: sequence and structure. Nucleic Acids Res. 1986; 14(5):2345-64. PMC: 339662. DOI: 10.1093/nar/14.5.2345. View

12.

Marcilla A, Bargues M, Ramsey J, Magallon-Gastelum E, Salazar-Schettino P, Abad-Franch F . The ITS-2 of the nuclear rDNA as a molecular marker for populations, species, and phylogenetic relationships in Triatominae (Hemiptera: Reduviidae), vectors of Chagas disease. Mol Phylogenet Evol. 2001; 18(1):136-42. DOI: 10.1006/mpev.2000.0864. View

13.

Billoud B, Guerrucci M, Masselot M, Deutsch J . Cirripede phylogeny using a novel approach: molecular morphometrics. Mol Biol Evol. 2000; 17(10):1435-45. DOI: 10.1093/oxfordjournals.molbev.a026244. View

14.

Xie Q, Tian Y, Zheng L, Bu W . 18S rRNA hyper-elongation and the phylogeny of Euhemiptera (Insecta: Hemiptera). Mol Phylogenet Evol. 2008; 47(2):463-71. DOI: 10.1016/j.ympev.2008.01.024. View

15.

Calleros L, Panzera F, Bargues M, Monteiro F, Klisiowicz D, Zuriaga M . Systematics of Mepraia (Hemiptera-Reduviidae): cytogenetic and molecular variation. Infect Genet Evol. 2009; 10(2):221-8. DOI: 10.1016/j.meegid.2009.12.002. View

16.

Hillis D, Dixon M . Ribosomal DNA: molecular evolution and phylogenetic inference. Q Rev Biol. 1991; 66(4):411-53. DOI: 10.1086/417338. View

17.

Xie Q, Bu W, Zheng L . The Bayesian phylogenetic analysis of the 18S rRNA sequences from the main lineages of Trichophora (Insecta: Heteroptera: Pentatomomorpha). Mol Phylogenet Evol. 2004; 34(2):448-51. DOI: 10.1016/j.ympev.2004.10.015. View

18.

Gutell R, Lee J, Cannone J . The accuracy of ribosomal RNA comparative structure models. Curr Opin Struct Biol. 2002; 12(3):301-10. DOI: 10.1016/s0959-440x(02)00339-1. View

19.

Ouvrard D, Campbell B, Bourgoin T, Chan K . 18S rRNA secondary structure and phylogenetic position of Peloridiidae (Insecta, hemiptera). Mol Phylogenet Evol. 2000; 16(3):403-17. DOI: 10.1006/mpev.2000.0797. View

20.

Reineke A, Karlovsky P, Zebitz C . Preparation and purification of DNA from insects for AFLP analysis. Insect Mol Biol. 1998; 7(1):95-9. DOI: 10.1046/j.1365-2583.1998.71048.x. View