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. 2016 Sep 16;6:33465.
doi: 10.1038/srep33465.

Application of RNA-seq for Mitogenome Reconstruction, and Reconsideration of Long-Branch Artifacts in Hemiptera Phylogeny

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Application of RNA-seq for Mitogenome Reconstruction, and Reconsideration of Long-Branch Artifacts in Hemiptera Phylogeny

Nan Song et al. Sci Rep. .
Free PMC article

Abstract

Hemiptera make up the largest nonholometabolan insect assemblage. Despite previous efforts to elucidate phylogeny within this group, relationships among the major sub-lineages remain uncertain. In particular, mitochondrial genome (mitogenome) data are still sparse for many important hemipteran insect groups. Recent mitogenomic analyses of Hemiptera have usually included no more than 50 species, with conflicting hypotheses presented. Here, we determined the nearly complete nucleotide sequence of the mitogenome for the aphid species of Rhopalosiphum padi using RNA-seq plus gap filling. The 15,205 bp mitogenome included all mitochondrial genes except for trnF. The mitogenome organization and size for R. padi are similar to previously reported aphid species. In addition, the phylogenetic relationships for Hemiptera were examined using a mitogenomic dataset which included sequences from 103 ingroup species and 19 outgroup species. Our results showed that the seven species representing the Aleyrodidae exhibit extremely long branches, and always cluster with long-branched outgroups. This lead to the failure of recovering a monophyletic Hemiptera in most analyses. The data treatment of Degen-coding for protein-coding genes and the site-heterogeneous CAT model show improved suppression of the long-branch effect. Under these conditions, the Sternorrhyncha was often recovered as the most basal clade in Hemiptera.

Figures

Figure 1
Figure 1
Alternative hypotheses of deep-level relationships within Hemiptera: (A) Campbell et al.; (B) Bourgoin & Campbell paraphyletic Homoptera due to the most basal position of Sternorrhyncha based on 18SrDNA sequences; (C) Cryan & Urban paraphyletic Homoptera due to the most basal position of Sternorrhyncha based on nuclear and mitochondrial gene sequences; (D) Misof et al. paraphyletic Homoptera due to the most basal position of Sternorrhyncha based on genome-scale data; (E) Hamilton monophyletic Homoptera as sister group to Heteropterodea based on morphological characters; and (F) Song et al. monophyletic Homoptera based on limited mitogenomic data.
Figure 2
Figure 2. Graphical representation of the mitochondrial genome of Rhopalosiphum padi.
The coding strand is indicated by think line; and abbreviations are as in the text.
Figure 3
Figure 3. GC-skew values were calculated on dataset of mitochondrial PCGs with all codon positions for Rhopalosiphum padi.
Figure 4
Figure 4. Bayesian tree estimated from dataset of 122taxa_PCGRNA under CATGTR model.
The site-heterogeneous model showed significant improvement in suppressing long-branch attraction, thus this topology is presented as one of the most likely tree structures for deep-level phylogeny of Hemiptera. Node numbers show posterior probabilities (above 0.9), and scale bar represents substitutions/site.
Figure 5
Figure 5. Maximum likelihood tree estimated from the reduced dataset of 106taxa_PCGRNA using data partitions and model selections as in Table S3.
MrBayes analysis recovered a similar topology to ML analysis. Node numbers show bootstrap support values (above 70, right) and posterior probabilities (above 0.9, left). The scale bar represents substitutions/site.

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