Genome Sequencing and Bioinformatics Analyses of Higher Plants Chloroplasts

Chloroplast DNA in higher plants exist as closed circular molecules of about 150 kb (±30), usually presenting inverted repeat sequences separating two single copy regions [1]. It is available the complete chloroplast genomes of around 13 higher plants species available in the gene bank. Our group has completely sequenced the sugarcane chloroplast DNA which is 141182 nucleotides in size. We have used bioinformatics tools Phre, Phrap & Consed [2,3,4] to perform the quality analysis of the nucleotides as well as to assemble the complete sequence and to identify the ORFs for annotation and to allow both, organizational and evolutionary analyses by comparison with the plastid genomes available [5]. By comparative analyses among sugarcane plastome, it was observed that all maize functional gene groups and also ycf ́s (conserved putative plastid genes with unknown function) found in other species plastome were identified in sugarcane. Also, comparisons based on structural organization and gene expression regulation analysis by mRNA editing [6,7] showed higher similarity between sugarcane and maize plastomes than between sugarcane and rice ones. The results suggest a common evolution among C4 grasses and also yield new elements for research on this type of photosynthesis and metabolism, as well as for sugarcane chloroplast transformation technology. REFERENCES[1] Palmer, J.D. Cell organelles. In: Herrmann, R.G.(Ed.) Plant gene research. Vienna: Springer-Verlag, 1992..99-122. [2] Ewing, B.; Hillier, L.; Wendl, M.C.; Green, P. Base-calling of automated sequencer traces using phred.Accuracy assessment. Genome Research. 1998.8:175-185. [3]Ewing, B.; Green, P. Base-calling of automatedsequencer traces using phred. II. Error probabilities.Genome Research, 1998. 8:186-194. [4] Gordon, D.; Abajian, C.; Green, P. Consed: agraphical tool for sequence finishing. GenomeResearch. 1998. 8:195-202.[5] Altschul, S.F.; Gish, W.; Miller, W.; Myers, E.W.;Lipman, D.J. Basic Local alignment search tool.Journal of Molecular Biology, 1990. 215(3):403-410. [6] Maier, R.M.; Neckermann, K.; Igloi, G.L.; Kossel,H. Complete sequence of the maize chloroplastgenome: gene content, hotspots of divergence and fine tuning of genetic information by transcriptediting. Journal of Molecular Biology, 1995.251:614-628. [7] Bock, R. Sense from nonsense: how the geneticinformation of chloroplasts is altered by RNAediting. Biochimie. 2000. Jun-Jul; 82(6-7):549-57.