Additional file 1.
Table S1 and Figures S1-S12. Table S1: Catalogs of cytoplasmic and transferred organelle ribosomal protein genes. Figure S1: Occurrence frequency of RPGs in 132 plant chloroplast and 25 plant mitochondrial genomes. (A) More than half of chloroplast RPGs are absent in most chloroplast genomes of 132 plants surveyed (green dash line), providing a raw estimate of the lower bound of transfer frequency of cpRPGs. (B) Similarly, there are over 50 RPGs in Rickettsia prowazekii str. Madrid E (α-proteobacteria, an ancient cousin of mitochondrion), whereas only 18 mtRPGs can be found in the union of all 25 plant mitochondrial genomes and most mtRPGs are absent in over half studied species (red dash line). Genes with zero occurrence frequency are present in corresponding ancient cousin but absent in chloroplast/mitochondria of all studied plants. Figure S2: Protein expression correlation of mtRPGs, cpRPGs and euRPGs in A. thaliana. Each element of the matrix represents the Pearson's correlation coefficient between the expression profiles of two ribosomal proteins. Figure S3: RNA expression correlation of mtRPGs, cpRPGs and euRPGs in different tissues of several developmental stages in A. thaliana. 7th day (A), 17th day (B), 21st day (C) and 8th week (D) corresponds to stage of seedling, leaf, flower and seed of A. thaliana, respectively. Each element of the matrix represents the Pearson's correlation coefficient of the expression profiles of each two RPGs. Color code is illustrated in bottom panel. Figure S4: Putative promoter motifs only enriched in one of cpRPGs, mtRPGs, and euRPGs in A. thaliana. The number on the left of each logo is E-value of MEME prediction. Figure S5: Putative promoter motifs predicted by AlignACE and DME. The number on the left of each logo is score of AlignACE and DME prediction. Figure S6: Expression correlation between RPGs with telo-box and those without telo-box. Telo-box here indicates the sequence AAACCCT or AACCCTA. The error-bar is the standard deviation of expression correlation. A symbol of the three stars (***) indicates the p-value is less than 0.001. Figure S7: The phylogenetic relationship of all investigated species. The phylogenetic relationship of angiospermae is derived according to the 16S rRNA of chloroplast genome in each species, using the neighbor-joining method. Both gene expression data and genome sequence data are available for O. sativa, A. thaliana, P. trichocarpa, M. truncatula and E. siliculosus, whereas only genome sequence data are available for P. patens and S. moellendorffii. The current gene expression data for C. reinhardtii do not include mtRPGs. Gray fonts indicate species that are not sequenced yet. Branch lengths are not scaled to time. Figure S8: Alignment of Purα proteins in all studied land plants. Some species have two Purα proteins. Here three highly conserved domains of Purα are shown. The tree on the left is drawn based on the sequences of Purα proteins with neighbor-joining method. The sequence labeled with the cyan line is involved in DNA-binding. Asterisks, colons, and dots indicate identical (red), strongly similar (green) and weakly similar (blue) residues, respectively. Figure S9: The occurrence of telo-boxes (A) and non-RPGs with telo-box (B) relative to mtRPGs or cpRPGs: (A) The star symbol indicates the significance of the occurrence within -1kb for mtRPGs. (B) The insets indicates mean distances of mtRPGs (cyan) and cpRPGs (magenta) relative to their closest upstream (left) or downstream (right) non-ribosomal protein genes (non-RPGs) with telo-box, respectively. The error-bar in the insets is the standard deviation of the distances. Figure S10: RNA Expression correlation of mtRPGs, cpRPGs and euRPGs in brown (A) and green (B) algae. Each element of the matrix represents the Pearson's correlation coefficient between the expression profiles of two RPGs. RNA expression level is measured by RT-PCR experiment for green algae C. reinhardtii (see Methods). Figure S11: Positional distribution of Site II, GAAGAA and telo-box of RPGs in A. thaliana. Site II motif (GCCCA, magenta line), GAAGAA (dark green line) and telo-box motif (AAACCCT, cyan line) are close to each other in promoter regions of RPGs. Figure S12: Promoter motifs of nuclear-encoded chloroplast genes in A. thaliana. (A) The logos of the motifs are predicted with MEME. The upper-left number of each logo is E-value. (B) The motif density of nuclear-encoded chloroplast genes (NCGs) in A. thaliana (Ath) and corresponding genes in Synechocystis sp. PCC6803 (Syn). The nuclear-encoded chloroplast genes in A. thaliana are identified by Martin et al. (2002).
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Wang et al. BMC Evolutionary Biology 2011 11:161 doi:10.1186/1471-2148-11-161