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Comparative Analysis of Chloroplast Genomes: Functional Annotation, Genome-Based Phylogeny, and Deduced Evolutionary Patterns

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dc.creator De Las Rivas, Javier
dc.creator Lozano, Juan José
dc.creator Ortíz, Ángel R.
dc.date 2008-06-16T09:02:37Z
dc.date 2008-06-16T09:02:37Z
dc.date 2002-04
dc.date.accessioned 2017-01-31T01:41:44Z
dc.date.available 2017-01-31T01:41:44Z
dc.identifier Genome Research 12(4): 567–583 (2002)
dc.identifier 1088-9051
dc.identifier http://hdl.handle.net/10261/5105
dc.identifier 10.1101/gr.209402
dc.identifier.uri http://dspace.mediu.edu.my:8181/xmlui/handle/10261/5105
dc.description 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 probably involved in speciation as phylogenetic correlates. Finally, by grouping common evolutionary patterns, we show that it is possible to determine functionally linked protein networks. This has allowed us to suggest putative associations for some unknown ORFs.
dc.description This work was supported by Mount Sinai start-up funds (ARO). J.D.L.R. acknowledges a short-term fellowship from OCDE and support from the Spanish government (grant MCT-DGI-PGC, PB98–0480). J.J.L. is a NATO postdoctoral fellow.
dc.description Peer reviewed
dc.format 25055 bytes
dc.format application/pdf
dc.language eng
dc.publisher Cold Spring Harbor Laboratory. Press
dc.relation http://dx.doi.org/10.1101/gr.209402
dc.rights closedAccess
dc.title Comparative Analysis of Chloroplast Genomes: Functional Annotation, Genome-Based Phylogeny, and Deduced Evolutionary Patterns
dc.type Artículo

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