Using informatics tools to compare important species is now feasible as structural genomics continue in importance and establishment of structure-function relationships become a common way of comparative analysis. Currently, many of the technical issues involved in sequencing complete genomes have been solved. The smallness in size of chloroplast genomes facilitates being used for the discovery of disease resistance genes, introgression of important traits in transgenic plants, quantitative trait analysis and phylogenetic studies. Knowledge from this can be extrapolated to important crops like sorghum, millet, taro, and cassava that have not been fully sequenced. This study compared six important crop species using GeneOrder3.0 and CoreGenes2.0 web-based informatics tools using complete chloroplast genomes. Results obtained depict cases of major genome rearrangements, translocation, duplication, inversion and deletion of genes. Members of the poaceae family indicate a close relationship in the nature of conserved sequences while Oryza sativa and Chlorella vulgaris, which are not members of poaceae indicate no synteny. Gene content indicates that there are common sets of putative orthologs across the different species. Zea mays, O. sativa, Nicotiana tabacum, Spinacea oleracea, Triticum aestivum had 71 rows of putative orthologs (355 total) with one hypothetical protein (GI:11465969) in N. tabacum, which is homologous to cemA and ORF230 protein in O. sativa and Z. mays, respectively. There was a clear indication from these sets of putative orthologs that maturase-encoding genes were found only in the terrestrial plants and not in the unicellular organisms.
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