Computational protocol: The first mitochondrial genomes for Pyralinae (Pyralidae) and Glaphyriinae (Crambidae), with phylogenetic implications of Pyraloidea

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[…] Contiguous sequences were assembled using Staden Package v1.7.0 []. PCGs and rRNA genes were identified based on homologous regions of published Pyraloidea mitogenomes using the Clustal X in MEGA 5 []. The tRNAscan-SE [] was used to predict tRNA genes and their secondary structures. Secondary structures of the two rRNA genes were predicted according to the models for Paracymoriza prodigalis []. The base composition and codon usage were calculated using MEGA 5. [...] Mitogenomic phylogeny of Pyraloidea was reconstructed based on four datasets (PCG123: 13 PCGs including all codon positions; PCG123R: 2 rRNAs, 22 tRNAs and 13PCGs including all codon positions; PCG12: 13 PCGs without third codon positions; PCG12R: 2 rRNAs, 22 tRNAs and 13PCGs without third codon positions) using Bayesian inference (BI) and maximum likelihood (ML) methods. Three species from Thyrididae (Pyrinioides aurea, KT337662) [], Alucitidae (Alucita montana, KJ508059) and Pterophoridae (Emmelina monodactyla, KJ508063) [] were selected as outgroups. Each of 37 mitochondrial gene sequences was aligned with Clustal. Considering partitioning strategy of previous studies [], a similar partitioning scheme (tRNA genes, rRNA genes, and each codon site of PCGs) was employed for phylogenetic analysis. The optimal model (GTR+I+Γ) for each partition was selected using Akaike information criterion in jModelTest []. The BI analyses were implemented in MrBayes 3.1.2 [] with four MCMC chains running for five million generations. Each set was sampled every 200 generations with a burn-in of the first 25% of steps. The ML analyses were performed using RAxML 7.0.3 [] with 1000 bootstrap replicates. […]

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