Computational protocol: Rapid Evolution of the Mitochondrial Genome in Chalcidoid Wasps (Hymenoptera: Chalcidoidea) Driven by Parasitic Lifestyles

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Protocol publication

[…] The protein-coding and rRNA genes were identified by Blast searches in GenBank and aligned to the orthologous mitochondrial genes of Nasonia and Apis mellifera. Positional confirmation and annotation of the tRNAs was accomplished by using the online software of tRNAscan-SE 1.21 . The detection of repeats used Tandem repeats finder . [...] The combined sequences were aligned by using ClustalW and the software package DnaSP 5.0 was used to compute nucleotide divergence, the ratio of Ka (the number of synonymous substation per synonymous site) and Ks (the number of nonsynonymous substation per nonsynonymous site). Based on genetic divergence, Co1 and co2 were inferred to be the most conserved protein-coding genes. They were employed for hypothesizing the phylogenetic relationships of the hymenoptera by using MrBayes 3.12 . Twenty-four mitochondrial genome sequences (accession numbers for the downloaded genomes: EU746610-EU746612, NC_011923, NC_010967, NC_004529, NC_014295, NC_001566, NC_014272, NC_014278, NC_012708, NC_014677, NC_014669, NC_014672, NC_015075, NC_011520, NC_013238, NC_008323, NC_012688, NC_014485, NC_012689.) were used for phylogenetic inference and gene rearrangement analyses. Orussus occidentalis was chosen as the outgroup. We used The MrModeltest 2 to select the best-fit model for Bayesian analysis. Bayesian calculations used 1 million generations while sampling a tree every 100 generations. A 50% majority rule consensus tree was calculated from the sampled trees. […]

Pipeline specifications

Software tools tRNAscan-SE, TRF, Clustal W, DnaSP, MrBayes, MrModelTest
Applications Genome annotation, Phylogenetics
Organisms Ceratosolen solmsi