Computational protocol: The mitochondrial genome of the land snail Camaenacicatricosa (Müller, 1774) (Stylommatophora, Camaenidae): the first complete sequence in the family Camaenidae

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[…] Raw sequences were proof-read and aligned into contigs with BioEdit v. (). The tRNA genes were identified with tRNAscan-SE Search Server v.1.21 () and DOGMA (), while others that could not be determined by these two tools were predicted by similarity comparison with other published land snails (; ; ; ; ; ). The PCGs and rRNA genes were annotated by BLAST in Genbank with published available mitochondrial sequences of terrestrial snails.PCGs were aligned with Clustal X (). The nucleotide composition and codon usage were analyzed with MEGA 5.0 (). Strand asymmetry was denoted by skew values, which were calculated according to the formulas: AT skew = [A−T]/[A+T] and GC skew = [G−C]/[G+C] ().Phylogenetic analyses were performed based on 11 representative gastropod mt genomes from GenBank (Table ) using maximum likelihood (ML) and maximum parsimony (MP) methods. One species of Opisthobranchia was selected as outgroup. A DNA alignment with 9,892bp length was inferred from the amino acid alignment of 13 PCGs using MEGA 5.0 (). The selection of best-fit-substitution model for ML estimation was performed using MEGA 5.0 with corrected Akaike information criterion (AIC). Node supports for ML and MP analyses were calculated through 1000 bootstrap replicates. All other settings were kept as default. […]

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