Codon usage bias analysis in mitochondrial genome of Melo melo

【Objective】The use preference of mitochondrial whole genome codon of Melo melo was investigated，and the factors affecting codon preference were analyzed，to improve gene expression efficiency，study the characteristics， ecological adaptation and evolutionary direction of mitochondrial genome of M. melo.【Method】Based on the mitochondrial genome sequence of M. melo，eleven non-repetitive sequences with length more than 300 bp and ATG as the starting codon were selected as the research objects，and the codon bias was analyzed by using the softwares of CodonW 1.4.2， Excel 2017，SPSS 22.0.【Result】The G+C content corresponding to codon positions of different gene sequence varies，including GC（1 G+C content represented by codon position 1），GC（2 G+C content represented by codon position 2），GC₃ （G+C content represented by codon position 3），was 35.20%-51.90%，16.40%-40.60%，13.10%-34.90%，corresponding average of 41.15%，32.29%，and 23.71%，respectively. The content of GC₁ and GC₂ was higher than that of GC₃. The codon adaptation index（CAI ）value ranged from 0.110 to 0.180，with an average of 0.137. The codonbiasindex（CBI） was at -0.272 to -0.090，with an average of -0.175. The optimal codon usage frequency（FOP）was from 0.216-0.339， with an average of 0.277. The effective codon number（ENC）ranged from 36.84 to 53.75，with an average of 45.59； grand average of hydropathy（GRAVY）ranged from 0.480 to 1.394，with an average of 0.968. There were 30 codons with relative synonymous codon usage（RSCU）>1.00，mainly ending with A/U. Neutral mapping analysis showed that the correlation coefficient between the mean of GC₁ and GC（2 GC₁₂）and GC₃ was -0.438，the correlation was not significant（P>0.05，the same below）. ENC-plot analysis showed that all genes were located near the standard curve，among them，NAD4，COX2 and NAD3 genes were located above the standard curve，and eight genes including COX1，ATP6， NAD1，NAD6，COB，NAD5，COX3 and NAD2 were located below the standard curve. Correspondence analysis showed that the first，second，third and fourth axis contributed 23.12%，15.19%，13.17% and 9.63% of the difference，respectively. The total contribution rate of the first four vectors was 61.12%. Combining high frequency codons and high expression codons，four optimal codons（UUU，GUU，ACU and CAU）were selected，all ending with U.【Conclusion】The whole mitochondrial genome codon of M. melo mainly prefers to use the codon ending in A/U，and the four selected optimal codons（UUU，GUU，ACU，and CAU）end with U. In addition to dominating natural selection in genome-wide codon preference formation in M. melo mitochondria，mutational pressure and base composition also influence their codon preference. Codon optimization of the target gene can effectively improve the foreign gene expression and optimize the trait determination gene，so as to accelerate the process of excellent parental cultivation.