Analysis Of Codon Usage In Zea Mays

Maize, as important foodstuff and forage crop, has been recently made great effort on functional gene and genome researches. The draft genome sequences has been determined and published in February, 2008, which could provide abundant data resources for further basic biological studies on the whole genomic level by techniques of bioinformatics. In this study, we investigate the molecular basis and the genetic mechanism of glutinous phenotype with six southwestern local varieties of waxy corn by the alignment analysis on DNA, CDS and protein sequences, which is based on the cloning full-length coding regions of waxy gene through polymerase chain reaction. We get the basic information of codon usage through the sequences analysis of waxy. Taking the hot research points in to consideration, we performed detailed codon usage patterns of waxy, maize nuclear genes, mitochondrial genome and chloroplast genome and major factors shaping codon usage by the methods of bioinformatics,multielement statistical analysis and correlation analysis.Optimal codons were determined and compared with other plants and model organisms. The results are of important reference value to guide gene-transformation and molecular modification of gene to increase the expression efficiency in maize, to consummate gene prediction software and to improve accuracy of gene prediction and genome annotation, and meanwhile could provide theoretical basis for the further research on gene structure and function, molecular evolution and so on. The main results were summarized as follows:1. There are multiple different kinds of insertion/deletion mutation in the first intron and the second, the ninth and the tenth exon regions of the waxy genes of the six southwestern waxy corn. The single base mutations exist in the splice receptor site of the second intron and the splice donor site of the eighth intron, respectively. At the same time, there are different types of repetitive sequence mutant in many other intron regions. All the mutant sites and patterns are different from the reported waxy mutant and it can be recognized as new mutant type of waxy. The mutation of bases insertion or deletion in the second exons and the ninth exons might lead to frame-shift mutation. The deletion of fifteen bases in the tenth exon is the starting point of the conserved domain of granule bound starch synthase, and it could induce inactivation of the enzyme. Therefore, insertion/deletion occurred in coding regions and mutation in splicing sites might be the key points that led to the glutinous phenotype in part of southwestern waxy corns.2. The synonymous codon usage bias is strong for each amino acid of waxy, with a common tendency of preferring the codons ending with C or G base, and less use or no use of the codons ending with A or T. Compared with the codon usage frequency between maize waxy and prokaryotic expression system of E. coli and eukaryotic expression system of yeast, respectively, there are 24 and 37 codons varied greatly, respectively.3. Compared with other graminaceous crops and a part of dicotyledons, codon usages of waxy gene in maize are coincident with the earlier one but opposite to dicotyledons such as Arabidopsis thaliana and Pisum sativum which prefer the codons ending with A or T base. This is main difference between mono- and di-cotyledons in codon usages of waxy gene.4. GC content varies widely from one gene to another in maize nuclear genes, many of which have high GC content and prefer the codons ending with G or C base. The results of correspondence analysis and correlation analysis indicated that multiple factors shaped the codon usage of maize, such as base compositions, gene expression levels, gene length, encoding protein hydrophobicity and so on, among which the earlier two were the most important factors.5. Codon usage patterns of maize nuclear genes are varied in distinct degree with mono-and di-cotyledons and different kinds of mode organisms. We compared the codon preferences of maize with those of human, E.coli, yeast and fruit fly. There are 14 codons showing distinct usage differences between maize and human, 24 between maize and E.coli, 41 between maize and yeast and 11 between maize and fruit fly. Meanwhile, There are 37 codons showing distinct usage differences between maize and A. thaliana, 41 between maize and tobacco, but only two codons between maize and rice and wheat, respectively. Finally, twenty-seven codons ending with a G or C base have been defined firstly as "optimal codons".6. Both of mitochondria and chloroplast are crucial organelle in maize. It is similar on codon usage patterns of them, but they vary from host genome. The genes of mitochondria and chloroplast with low GC content are preferred to codons with A and T at the third codon position. There might be several factors shaping the codon usage in mitochondria and chloroplast genes of maize, but base compositions and gene expression levels were relatively major factors. Additional twenty-nine and twenty-five codons have been defined firstly as "optimal codons" for mitochondria and chloroplast, respectively.