@ARTICLE{TreeBASE2Ref25043, author = {Nan Song}, title = {The mitochondrial genome of the Rhopalosiphum padi and an application of mitogenomic analysis to the Hemiptera phylogeny}, year = {2015}, keywords = {Rhopalosiphum padi, mitochondrial genome, aphid, Hemiptera, phylogeny}, doi = {}, url = {http://}, pmid = {}, journal = {Gene}, volume = {}, number = {}, pages = {}, abstract = {The nearly complete nucleotide sequence of the mitochondrial genome (mitogenome) was determined for the aphid species of Rhopalosiphum padi by the RNAseq plus gap filling method. The 15,113-bp mitogenome include all mitochondrial genes except for the trnF. As a whole, the organization and size of the newly sequenced mitogenome of R. padi are similar to those previously reported for other aphid species. In addition, three tandem repeat regions were discovered in the putative control region. Phylogenetic analyses (maximum likelihood and Bayesian inference) were performed on all mitochondrial genes in combination with already published mitogenome sequence data of 102 species of Hemiptera, and 19 species of Orthoptera, Psocoptera, Phthiraptera and Thysanoptera. The phylogenetic results are sensitive to method of analysis, model selection, taxon sampling and data treatment. The monophyly of Aphidoidea is strongly supported. Within the Aphididae, R. padi is consistently recovered as a sister group of Schizaphis graminum. The seven species representing Aleyrodidae exhibited extremely long branches irrespective of the phylogenetic inference method used, and they frequently clustered 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 site-heterogeneous CAT model showed improvement in suppressing long-branch effect. Within Hemiptera, the basal placement of Sternorrhyncha was supported. } }

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