Codon usage patterns and analysis of blue light receptor gene AmCRY1 in Amaranthus tricolor L.

Abstract

To explore the codon usage bias, homology with CRY1 genes in different species and genetic transformation receptors of amaranth AmCRY1 gene can be used. In this study, CodonW, EMBOSS, Excel 2017, SPSS 24, Origin 2018, and other software were used to analyze the codon bias of CRY1 gene in amaranth and other species to compare the codon use frequency of AmCRY1 gene and model organisms. The effective number of codons (ENc) of AmCRY1 in amaranth was 54.42, and the content of GC and GC3 were lower than 50%. This indicated that AmCRY1 preferred codons ending with A/T, and the content of A + T in the coding region was higher than that of G + C. Among the codons of amar anth AmCRY1, 29 codons (RSCU > 1) had a strong preference, and one codon (RSCU > 2) had the strongest preference. Among them, 22 codons ended with A/T, respectively. This indicated that codons of amaranth AmCRY1 preferred to end with A/T, and some amino acids preferred codon usage. The codon preference of AmCRY1 in amaranth was more affected by mutation pressure in the process of evolution because the codon loci of AmCRY1 in amaranth were closer to the expected curve in ENC mapping. The codon usage preference parameters of amaranth AmCRY1 gene were similar to those of caryophylla species, and the codon usage preference was similar to species with similar homology. From the analysis of codon usage frequency, the yeast expression system was more suitable for heterologous expression of amaranth AmCRY1. Arabidopsis thaliana, tobacco, and tomato can be used as genetic transformation receptors of amaranth AmCRY1. Sugar beet with similar metabolic pathways of amaranth can also be used as the transient expression receptors of amaranth AmCRY1. In this study, the codon preference of amaranth AmCRY1 ended with A/T and was affected by mutation pressure that provided a reference for further functional research, especially for the verification of heterologous expression.