Bioinformatics comparison of codon usage of genes encoding phosphate transporter in terms of salt tolerance, day length, temperature and pollination in different plants
Journal Title: International journal of Advanced Biological and Biomedical Research - Year 2014, Vol 2, Issue 2
Abstract
In order to study and compare the phosphate transporter gene codon usage and it's respond to the traits like salt tolerance, day length, Pollination and temperature in different plants, 100 isoform from 10 plants are extracted from NCBI website and then analyzed with Gene Infinity and Minitab 16 software. The result shows that the highest codon usage similarity (81.95%) was for wheat and oryza (annual, self-polinated and Psychrophilic) from Poaceae family. The result for poaceae family shows that the highest mean abundance was for codons that have U or G at the end. In this study Cucurbita maxima (salt tolerance, annual and cross pollinated) have the lowest codon usage similarity (70.37%) in compare with other plants in this study. The highest difference between families was for Fabaceae (77.64%) but they are divided in one group at the cluster. So the results show that the families that have lowest distance have the highest codon usage similarity in terms of salt tolerance, day length, Pollination and temperature. It is conceivable that a direct relationship would exist between preferred codons and division of plant families.
Authors and Affiliations
Mohammad Fazel Soltani| Crop Production and Plant Breeding Department, School of Agriculture, Shiraz University, Shiraz, Iran, E-mail: Fazel_royan@yahoo.com, Morteza Hadizadeh| Department of Genetic and Animal Breeding, Agriculture Faculty, Shahid Bahonar University of Kerman, Iran, Mohammad Javad Soltani Banavandi| Departments of Microbiology, Faculty of Basic sciences, Islamic Azad University, Kerman Branch, Kerman, Iran, Azadeh Yazdizadeh| Departments of Medicine, Medicinal University, Shiraz University, Shiraz, Iran, Abbas Alemzadeh| Crop Production and Plant Breeding Department, School of Agriculture, Shiraz University, Shiraz, Iran
Keywords
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