Codon Bias Analysis of Prunus salicina 'Huangguan' Malate Transporter ALMT4, ALMT9 and tDT Genes
WU Wei-Feng1,2,3, CHEN Ming-Jie2, CHEN Fa-Xing1,*
1 College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350000, China; 2 Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350000, China; 3 Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China
Abstract：Aluminum-activated malate transporter 4 gene (ALMT4), aluminum-activated malate transporter 9 gene (ALMT9) and tonoplast dicarboxylate transporter gene (tDT) may be important genes involved in malate transportation and accumulation in plum (Prunus salicina) fruit, to analyze their codon bias is of great significance for subsequent research of gene function. This study used CodonW and CUSP programs to analyze the codon bias of ALMT4, ALMT9 and tDT genes in Prunus salicina 'Huangguan' and compared with the codon bias of the genome of the model species contained Escherichia coli, Saccharomyces cerevisiae, Nicotiana tabacum, Arabidopsis thaliana and Lycopersicon esculentum etc. The results showed that the effective number of codons (ENC) of ALMT4, ALMT9 and tDT genes in Prunus salicina ‘Huangguan’ were much higher than 35, close to 61, and the codon adaptation index (CAI) was much less than 1, close to 0, which indicated their codon bias were weak. ALMT4 and ALMT9 preferred to the codons ending with A or U(T), tDT preferred to the codons ending with U(T) or C. GCA, AGA, UGU, GGU, CCU, ACU, UAU, UUU, GAA, CAU, AAU, GAU were the high frequency codons of ALMT4, GCA, AGG, GGA, CAU, UUG, UCA, ACA, AAU, GAU, UUU, UAC were the high frequency codons of ALMT9, GCU, AGG, CGA, UGC, GAG, GGA, UUG, AGC, UCC, UAU, GAU, CAA, AAG were the high frequency codons of tDT. The gene tree was more able to reflect the botanical classification relationship of species than the cluster tree constructed based on relative synonymous codon usage (RSCU). Considering codon bias differences, cost, convenience and other factors, S. cerevisiae was an ideal heterologous protein expression system for ALMT4, ALMT9, and tDT genes in P. salicina 'Huangguan', and L. esculentum was an ideal heterologous plant expression system. Furthermore, S. cerevisiae and L. esculentum were used as examples to optimize the CDs sequences of ALMT4, ALMT9 and tDT genes in P. salicina 'Huangguan', the modified gene sequences had codon bias features of S. cerevisiae and L. esculentum genome. These results provide a theoretical basis for subsequent research of genes function.
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