Abstract:

【Objective】To explore the codon usage pattern of Fusarium oxysporum genome-wide and to assess the factors influencing the codon composition and coding characteristics.【Methods】Using software CodonW and R to analyze the codon preference and its influencing factors on genome-wide data from F. oxysporum.【Results】A total of 18 125 sequences was obtained. The average GC content of F. oxysporum was 51.46%. The ENC value ranged from 24.31 to 61.00,and 94.41% of the ENC values were more than 45. Leucine and Alanine were the major amino acids,and accounted for 8.86% and 8.29% respectively. While Tryptophan and Cysteine accounted for only 1.61% and 1.34% respectively. F. oxysporum had 33 high-frequency codons and 19 optimal codons,with the majority of the codons ending in G/C. The correlation study of basic codon parameters revealed that the correlation between GC1 and GC2 was extreme significant(P<0.01),while the correlation between GC3 and ENC was the strongest(P<0.01).【Conclusion】Natural selection is the primary factor influencing the codon preference of Fusarium oxysporum. The correlation between GC3 and ENC was the strongest. 33 high-frequency codons and 19 optimal codons primarily ending in G/C.

Key words: Fusarium oxysporum, Codon usage preference, Optimal codon, Effective codon