Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns

Genome Research
Javier De Las RivasAngel R Ortiz

Abstract

All protein sequences from 19 complete chloroplast genomes (cpDNA) have been studied using a new computational method able to analyze functional correlations among series of protein sequences contained in complete proteomes. First, all open reading frames (ORFs) from the cpDNAs, comprising a total of 2266 protein sequences, were compared against the 3168 proteins from Synechocystis PCC6803 complete genome to find functionally related orthologous proteins. Additionally, all cpDNA genomes were pairwise compared to find orthologous groups not present in cyanobacteria. Annotations in the cluster of othologous proteins database and CyanoBase were used as reference for the functional assignments. Following this protocol, new functional assignments were made for ORFs of unknown function and for ycfs (hypothetical chloroplast frames), which still lack a functional assignment. Using this information, a matrix of functional relationships was derived from profiles of the presence and/or absence of orthologous proteins; the matrix included 1837 proteins in 277 orthologous clusters. A factor analysis study of this matrix, followed by cluster analysis, allowed us to obtain accurate phylogenetic reconstructions and the detection of genes prob...Continue Reading

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Jul 17, 2008·Comparative and Functional Genomics·Javier De Las Rivas, Alberto de Luis
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