A 454 sequencing approach to dipteran mitochondrial genome research

Abstract

The availability of complete mitochondrial genome (mtgenome) data for Diptera, one of the largest metazoan orders, in public databases is limited. The advent of high throughput sequencing technology provides the potential to generate mtgenomes for many species affordably and quickly. However, these technologies need to be validated for dipterans as the members of this clade play important economic and research roles. Illumina and 454 sequencing platforms are widely used in genomic research involving non-model organisms. The Illumina platform has already been utilized for generating mitochondrial genomes without using conventional long range PCR for insects whereas the power of 454 sequencing for generating mitochondrial genome drafts without PCR has not yet been validated for insects. Thus, this study examines the utility of 454 sequencing approach for dipteran mtgenomic research. We generated complete or nearly complete mitochondrial genomes for Cochliomyia hominivorax, Haematobia irritans, Phormia regina and Sarcophaga crassipalpis using a 454 sequencing approach. Comparisons between newly obtained and existing assemblies for C. hominivorax and H. irritans revealed no major discrepancies and verified the utility of 454 sequencing for dipteran mitochondrial genomes. We also report the complete mitochondrial sequences for two forensically important flies, P. regina and S. crassipalpis, which could be used to provide useful information to legal personnel. Comparative analyses revealed that dipterans follow similar codon usage and nucleotide biases that could be due to mutational and selection pressures. This study illustrates the utility of 454 sequencing to obtain complete mitochondrial genomes for dipterans without the aid of conventional molecular techniques such as PCR and cloning and validates this method of mtgenome sequencing in arthropods.

Mitochondrial genomes of the hoverflies Episyrphus balteatus and Eupeodes corollae (Diptera: Syrphidae), with a phylogenetic analysis of Muscomorpha

“…We included two superfamilies of Platypezoidea and Syrphoidea from Aschiza. Platypezoidea was sister to all other species of Muscomorpha, which is congruent with previous studies1141. The five genera of Syrphidae (Syrphoidea) clustered as ((unknown Syrphidae sp.)…”

“…The novel life history of the species from Fergusoninidae might affect the evolutionary pattern of their mitochondrial genomes2. The long-branch of Opomyzoidea was also found in previous study based on mitochondrial genome sequences41. Phylogenetic relationships of other groups included in our analyses, i.e.…”

Phylogenetic analysis of the complete mitogenome sequence of the raspberry weevil, Aegorhinus superciliosus (Coleoptera: Curculionidae), supports monophyly of the tribe Aterpini

“…This difference could be explained by deletions of tandem sections in the POR, which has been reported in other insects (De Ré et al, 2014;Elbrecht et al, 2013). Nevertheless, a more plausible explanation for this result is the apparent difficulty of the 454 sequencing approach to recover the mitochondrial control region in insects, basically due to the presence of complex repeats that are difficult to sequence and/or assemble (Cameron et al, 2008;Mao et al, 2012;Ramakodi et al, 2014).…”

The complete mitochondria genome of Aldrichina grahami (Diptera: Calliphoridae)

“…The sequence data from GenBank which are A. grahami, C. vicina, C. rufifacies, P. terraenovae, four L. cuprina, two L. sericata of Calliphoridae and S. crassipalpis, S. similis from family Sarcophagidae. Except A. grahami and S. crassipalpis, the other Calliphoridae genomes originally published in Nelson LA's paper (Nelson et al 2012b), S. similis published in Yan's (Yan et al 2014b) and S. crassipalpis published in Ramakodi MP's (Ramakodi et al 2015). Each of the 12 mt genomes was aligned separately using Vector NTI 9.0.…”