3.2 Protein-Coding Genes and Codon Usage
The total lengths of the 13 PCGs of Amipittia virgata ,Halpe nephele and Onryza maga are 11,190 bp, 11,202 bp and
11,187 bp, respectively (Table 3). In these 3 sequenced species, 9 of 13
PCGs (nad2 , cox1 , cox2 , atp8 , atp6 ,cox3 , nad3 , nad6 , cytb ) are encoded in the
J-strand, and the other 4 (nad5 , nad4 , nad4L ,nad1 ) are located on the N-strand. The size of the 13 PCGs with
the smallest gene for the 13 PCGs is the atp8 and the largest
gene is the nad5 ranging in size from 162 bp to 1,744 bp. The
AT-skew and GC-skew indicate that the T content of PCGs is obviously
higher than that of A among these 3 species, while the content of G and
C is not much different. The AT bias of the bases is more significant in
the third codon, and the AT content of the third codon
(90.5%~ 92.3%) is remarkably higher than that of the
first codon (73.7%~ 74.6%) and the second codon
(70.1%~ 70.5%), which is consistent with the higher
mutation rate of the third codon site compared with the second and first
codon sites (Table 3). All PCGs of these 3 mitogenomes start with
typical ATN (ATG, ATT, ATA) codons except cox1 using CGA, and all
of them use TAA or TAG as the stop codons, with the exception forcox1 , cox2 , nad4 and nad5 , which use a
single T as stop codons (Table 2). Statistics on the relative synonymous
codon usage (RSCU) of the 3 skippers shows that the codon UUA
(Leu2 ), UCU (Ser2 ) and CGA (Arg ) are the 3 used
most frequently, and the codons terminating with A and T also have a
relatively higher frequency (Figure 2).