Background: Epinephelus fuscoguttatus is one of the rare marine economic fishes with high economic value. At present, the researches on grouper mainly focus on artificial propagation, physiology and biochemistry, diseases and so on. However, there are few reports on mitochondrial genome level. The research aimed to analyze composition characteristics and usage preference of codon of mitochondrial genome in E. fuscoguttatus, and explored main factors of affecting the formation of codon preference, thereby providing theoretical basis for studying species evolution, genetics and breeding, and improving expression efficiency of exogenous genes.
Results: GC content of mitochondrial genome of E. fuscoguttatus changed between 44.00% and 46.30%, with 45.40% of mean. Change range of CAI value was between 0.125 and 0.202, and the mean was 0.155. Effective number of codons (ENC) changed between 36.08 and 49.55, with 44.98 of mean. There were 32 codons that relative synonymous codon usage (RSCU) was more than 1, mainly ended with A/C. ENC-plot analysis found that all the genes were in the lower middle of the standard curve, and there was larger difference between actual and theoretical ENC, illustrating that codon bias was mainly affected by the choice. Correspondence analysis showed that the first axis contributed 58.85% of the difference, while the second, third and fourth axes contributed 14.59%, 7.66% and 5.43% of the difference respectively. Cumulative contribution rate of the first four vectors was 85.53%. Finally, nine optimal codons were selected: CUU, AUC, GUU, CCU, GCA, UAU, CGC, AGC and GGC.
Conclusions: Codon usage preference of mitochondrial genome of E. fuscoguttatus was weak, and it preferred to use A/C terminated codon, and preference was mainly influenced by choice.