Election on codon WWU bias (Table two). Compared with other species, the usage Species SSU SSC WWC P2 values of SSU and WWU were larger, and the values of SSC and WWC were decrease in B. hispida 4.92 5.08 two.67 3.21 0.5120 cucumber and melon, indicating extra preference 2.71U within the third position of 0.5116 of for codons C. lanatus 4.90 5.06 3.24 them.maxima In cucumber, the P2 was 0.5201, and inside the 2.83 nine species, the values were all other C. 4.81 4.85 three.46 0.C. melo C. moschata C. pepo C. sativus L. siceraria S. edule T. anguina five.06 four.81 four.88 5.11 4.92 four.68 four.76 5.ten four.83 four.86 five.11 five.08 four.96 5.00 two.57 2.83 2.79 two.53 two.70 2.93 two.81 three.17 3.47 3.46 three.17 three.21 3.36 3.30 0.5176 0.5194 0.5216 0.5201 0.5110 0.5047 0.Table 2. The P2 analysis of CUB in ten species of Cucurbitaceae.3.two.5. Correlation Evaluation To reflect the partnership amongst various indicators of codon usage, specially involving them plus the two primary axes, the correlation involving them was calculated (Table S1). In cucumber, the first axis significantly correlated with GC3s, ENC, codon adaptation index (CAI), and protein length (r = 0.893, 0.357, 0.302, and -0.282, respectively, p 0.01), indicating that Cuminaldehyde Biological Activity nucleotide composition had a much more essential influence on CUB. So, the correlation in between GC3s and other people was additional explored. There were also significant correlations existing in GC3s and ENC (r = 0.350, p 0.01), GC3s and CAI (r = 0.230, p 0.01), GC3s and protein length (r = -0.279, p 0.01). Such correlations among indicators have been like these in other species except for chayote. Within the chayote, there had been no significant correlations between the very first axis and ENC (p 0.05) and none amongst the GC3s and ENC (p 0.05). Other substantial correlations detected in cucumber also existed in chayote. These results inferred that the nucleotide composition had a vital impact around the formation of codon usage bias in cucumber and relative species. 3.three. Application of CUB Determined by the analysis of codon usage patterns of cucumber and its close species, the optimal codons had been additional identified, assisting to improve the efficiency of genetic transformation and analyzing the connection between these ten species in Cucurbitaceae determined by their respective RSCU values at the genomic level.Agronomy 2021, 11,12 of3.three.1. Identification of Optimal Codons To determine optimal codons, we firstly chose two datasets comparing 5 of the total genes applying the ENC index from the extreme ideal and left based on the principal trend, namely axis 1 (which represented main trend changes of codon usage). Then, we used the two-way chi-square test to recognize codons with important differences in two biased sets. The results show that there have been 30 optimal codons for 18 amino acids identified in cucumber, such as 16, 12, and two U, A, and G-ending codons (Table 3). Leucine has the biggest number of optimal codons, i.e., four. The same results have been identified in melon, wax gourd, bottle gourd, and watermelon. In three species of Cucurbita and snake gourd, there was one far more optimal codon in every species, namely CGU for arginine, even though in chayote, there had been two far more optimal codons, namely CGU and CGA for arginine. These benefits may provide Piperonylic acid supplier beneficial data for the genetic transformation with the gourd crop in the future.Table three. Optimal codons identified in ten species of Cucurbitaceae. Amino Acids Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Phe Pro Ser Thr Tyr Val Optimal Codons A-Ending GCA AGA (CGA) AGG.