2.4 Sequence analysis
Nucleotide compositional skew was calculated according to the formulae: AT-skew = (A−T)/(A+T) and GC-skew = (G−C)/(G+C) [42]. The Sequence Manipulation Suite program package (http://www.bioinformatics.org/sms2/codon_usage.html) was used to analyze codon usage based on genetic code “4” [43]. Genetic distances between each pair of the 14 core PCGs (atp6, atp8, atp9, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5, andnad6 ) were calculated with MEGA X [44], using the Kimura−2-parameter (K2P) substitution model. DnaSP v6 [45] was used to calculate the nonsynonymous (Ka) and synonymous (Ks) substitution rates for the 14 core PCGs among the four mitogenomes. Genomic synteny among the four mitogenomes was analyzed using the Mauve v2.4.0 program [46].