Insight into higher-level phylogeny of Neuropterida: Evidence from secondary structures of mitochondrial rRNA genes and mitogenomic data - PubMed (original) (raw)

Insight into higher-level phylogeny of Neuropterida: Evidence from secondary structures of mitochondrial rRNA genes and mitogenomic data

Nan Song et al. PLoS One. 2018.

Abstract

It is well known that the rRNA structure information is important to assist phylogenetic analysis through identifying homologous positions to improve alignment accuracy. In addition, the secondary structure of some conserved motifs is highly stable among distantly related taxa, which can provide potentially informative characters for estimating phylogeny. In this paper, we applied the high-throughput pooled sequencing approach to the determination of neuropteran mitogenomes. Four complete mitogenome sequences were obtained: Micromus angulatus (Hemerobiidae), Chrysoperla nipponensis (Chrysopidae), Rapisma sp. (Ithonidae), and Thaumatosmylus sp. (Osmylidae). This allowed us to sample more complete mitochondrial RNA gene sequences. Secondary structure diagrams for the complete mitochondrial small and large ribosomal subunit RNA genes of eleven neuropterid species were predicted. Comparative analysis of the secondary structures indicated a closer relationship of Megaloptera and Neuroptera. This result was congruent with the resulting phylogeny inferred from sequence alignments of all 37 mitochondrial genes, namely the hypothesis of (Raphidioptera + (Megaloptera + Neuroptera)).

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1

Fig 1. Secondary structure drawing of the complete mitochondrial rrnS gene for Chrysoperla nipponensis EMHAU-15090613.

The grey boxes indicated the helices aligned across all eleven sampled neuropterids.

Fig 2

Fig 2. Secondary structure drawing of the complete mitochondrial rrnL gene for Chrysoperla nipponensis EMHAU-15090613.

The grey boxes indicated the helices aligned across all eleven sampled neuropterids.

Fig 3

Fig 3. Phylogenetic reconstruction and secondary structure drawings of the helices.

(A) Phylogenetic reconstruction from PCG12RNA using software IQ-TREE under the partitioned models automatically selected. Node values represent bootstrap values (left) and posterior probabilities (right). The “-” indicates the relationship not being retrieved by the data set of PCG12RNA using software PhyloBayes under CAT-GTR model. Asterisks designate the species newly sequenced in this study. (B) Secondary structure drawings of the helix 47 in rrnS for eleven representative neuropterid species. (C) Secondary structure drawings of the helix 837 in rrnL for eleven representative neuropterid species.

Fig 4

Fig 4. Alignments of helices for eleven representative neuropterid species.

(A) Alignments of the helix 47 in rrnS. (B) Alignments of the helix 837 in rrnL. Helices are highlighted by grey box and numbered as diagrams of the full secondary structures. No color areas in each helix indicate the unpaired regions.

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Grants and funding

This research is supported by grants from the National Natural Science Foundation of China (no. 31402002), Key Scientific Research Projects of Henan Province (grant no. 16A210029), and Henan Academician Workstation of Pest Green Prevention and Control for Plants in Southern Henan (YZ201601). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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