Computational protocol: The complete mitochondrial genome sequence of the indigenous I pig (Sus scrofa) in Vietnam

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Protocol publication

[…] The PCR products were sequenced using ABI3500 DNA sequencer. The DNA sequences were assembled using DNA Dragon v1.6.0 software and exported to FASTA file. The complete sequence was annotated using MITOS and DOGMA. The mitochondrial circle structure was built using GenomeVx and the tRNAs structure was downloaded from online report of MITOS analysis result. The C, G, A, T frequencies and A+T-content of the entire mitochondrial genome were calculated using DAMBE v6.3.17 []. After that, skewness for each protein coding gene was evaluated using the following formulas: GC skew = (G−C)/(G+C) and AT skew = (A−T)/(A+T). [...] The D loop and full sequence of I pig were aligned with other pig sequences using MUSCLE algorithm [] of MEGA6 []. The best model for full mitochondrial genome group was HKY+G and TN93+I. We used Bayesian phylogenetic analysis in BEAST v1.8.3 [] with Yule process and MCMC 10000000 to calculate the alignment data and Figure Tree v1.4.2 to build the phylogenetic trees. […]

Pipeline specifications

Software tools DNA Dragon, MITOS, GenomeVx, DAMBE, MUSCLE, MEGA, BEAST
Applications Genome annotation, Phylogenetics, Sanger sequencing, Nucleotide sequence alignment, Genome data visualization
Organisms Sus scrofa, Sus scrofa domesticus
Diseases Ataxia Telangiectasia