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Codon bias is an important factor affecting gene expression, and it is also one of the key clues to reflect gene evolution. Orchidaceae plants are the "flagship" group in plant protection, and most species have medicinal and ornamental values, but seeds are not easy to germinate. ABI3 (abscisic acid insensitive 3) gene is the central regulator of ABA signal transduction, involved in seed development and dormancy processes, and is the key factor to regulate plant seed germination. Therefore, in-depth study of codon bias of orchid ABI3 gene can lay a foundation for analyzing the function of the gene and optimizing the codon composition. Using Arabidopsis thaliana ABI3 gene as a probe, 45 Orchidaceae ABI3 genes were screened from the public database (NCBI), and the codon use patterns and preferences were analyzed by bioinformatics programs such as CodonW, SPSS and MEGA. The ENC (effective number of codon) value of the genes ranged from 40.84 to 58.46, of which 82.2% was greater than 52. The average value of CAI (codon adaptation index) was 0.203, far less than 1, indicating that the codon usage bias of ABI3 gene was relatively weak. Neutral plot analysis showed that the slope of the regression curve between GC12 and GC3 was 0.6103, R2=0.7928 (P<0.05), indicating that the base composition has an important influence on codon bias. In ENC plot analysis, the ENC value of all genes was lower than the expected value, but the difference was small, indicating that the codon of orchid ABI3 gene is mainly affected by base mutation and other factors such as selection pressure. Parity preference analysis showed that most genes were distributed in the right region of the plan, and the use frequency of A/T (U) at codon 3 was higher than that of G/C. Through RSCU and ΔRSCU analysis, 26 optimal codons were identified, including 14 codons ending in A/T (U) and 10 codons ending in T (U), indicating that ABI3 gene of orchid plants relatively prefers to use codons ending in A/T (U), especially codons ending in T (U), which is different from that of most monocotyledonous plants. This study may provide a theoretical basis for the phylogenetic and functional elucidation of ABI3 genes in Orchidaceae and for improving ABI3 gene expression efficiency, as well as facilitating codon biology in plants and the improvement of exogenous genes.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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