Comparative Inference of Duplicated Genes Produced by Polyploidization in Soybean Genome

Soybean (Glycine max) is one of the most important crop plants for providing protein and oil. It is important to investigate soybean genome for its economic and scientific value. Polyploidy is a widespread and recursive phenomenon during plant evolution, and it could generate massive duplicated genes which is an important resource for genetic innovation. Improved sequence alignment criteria and statistical analysis are used to identify and characterize duplicated genes produced by polyploidization in soybean. Based on the collinearity method, duplicated genes by whole genome duplication account for 70.3% in soybean. From the statistical analysis of the molecular distances between duplicated genes, our study indicates that the whole genome duplication event occurred more than once in the genome evolution of soybean, which is often distributed near the ends of chromosomes. 1. Introduction There is an important economic and scientific value of study on soybean genome. First, soybean (Glycine max) is one of the most important crops for producing protein and oil. Second, it has the capacity to fix nitrogen which is one of the major problems of life science. Biological nitrogen fixation provides all the plants with 75% of nitrogen, which plays an important work in the practical production. The completions of genome sequencing in legumes provide new ideas for the studying of symbiotic nitrogen fixation on the genome level [1]. Large-scale duplication events have been considered important for the evolution of many organisms. About 70% of angiosperm evolution has experienced one or more polyploidization events. Polyploidy is a widespread and recursive phenomenon during plant evolution, and it could generate massive duplicated genes which is an important resource of genetic innovation [2–6]. This process greatly increases the complexity of the plant and improves the adaptive capacity to new environments. Soybean is a well documented paleopolyploid [7]. Despite some analysis of soybean [8], the in-depth study of evolution after polyploidization is also needed. For comparative genomics analysis, this paper aims to study the evolution laws of duplicated genes in soybean after polyploidization. Our study identifies significant duplicated genes on the evolutionary of the two species, soybean and Arabidopsis thaliana, and indicates that the whole genome duplication (WGD) event occurred more than once in the genome evolution of soybean. 2. Materials and Methods 2.1. Sequence Data Soybean (Glycine max) [1] and Arabidopsis thaliana [9] genome sequences were downloaded