Molecular adaptation and expression evolution following duplication of genes for organellar ribosomal protein S13 in rosids
© Liu and Adams; licensee BioMed Central Ltd. 2008
Received: 07 August 2007
Accepted: 26 January 2008
Published: 26 January 2008
Gene duplication has been a fundamental process in the evolution of eukaryotic genomes. After duplication one copy (or both) can undergo divergence in sequence, expression pattern, and function. Two divergent copies of the ribosomal protein S13 gene (rps13) of chloroplast origin are found in the nucleus of the rosids Arabidopsis, Gossypium, and Glycine. One encodes chloroplast-imported RPS13 (nucp rps13), while the other encodes mitochondria-imported RPS13 (numit rps13). The rps13 gene has been lost from mitochondrial DNA (mt rps13) of many rosids.
We studied sequence evolution of numit rps13 in comparison with nucp rps13 in seven rosid genera. Ka/Ks analysis and likelihood ratio tests showed considerably higher Ka values and Ka/Ks ratios in numit rps13 than in nucp rps13, indicating increased amino acid sequence divergence in numit rps13. Two positively selected codons were detected in numit RPS13 in regions that are inferred to interact with the 16S rRNA. Several amino acids in numit RPS13 have changed from the one present in nucp RPS13 to the one present in mt RPS13, showing that numit rps13 is becoming more like mt rps13. Comparison of expression patterns and levels of numit rps13 and nucp rps13 in Arabidopsis using microarray data indicated divergence in gene expression. We discovered that in addition to numit rps13, Malus (apple) contains a transcribed mt rps13 gene. To determine if partitioning of expression takes place between numit rps13 and mt rps13, expression of both copies and RNA editing of mt rps13 were examined by RT-PCR, qRT-PCR, and sequencing from 14 different organ types plus seedlings subjected to five different abiotic stresses. Co-expression of numit rps13 and mt rps13 was observed in all the organs and various stress treatments. We determined that purifying selection is acting on both numit rps13 and mt rps13 in Malus.
Our data provide evidence that numit rps13 genes in rosids have experienced adaptive sequence evolution and convergent evolution with mt rps13. Co-expression of numit rps13 and mt rps13 and purifying selection on both genes in Malus suggest that both are functional. The three organellar rps13 genes in rosids provide a distinctive case of gene duplication involving the co-evolution of the nuclear and cytoplasmic genomes.
Gene duplication has been an ongoing process during eukaryotic evolution that has provided genetic raw material for the evolution of new gene functions that can lead to morphological and physiological novelty. Duplicated genes can undergo sequence divergence caused by positive selection or neutral drift [1–3] and divergence in expression patterns and function. Two common fates of retained duplicated genes are neofunctionalization – gain of a new function or expression pattern by one copy  and subfunctionalization – partitioning of ancestral function or expression pattern between both copies [5, 6]. Plant genomes contain large numbers of duplicated genes, derived by polyploidy, segmental duplications, tandem duplications, and retroposition of cDNAs. Many duplicated genes in plant genomes have been preserved and undergone purifying selection, a few have undergone positive selection and functional diversification, and some have experienced subfunctionalization [7–10].
There are three genes that code for organellar ribosomal S13 genes among rosid species. Analysis of rps13 genes in the rosid species Arabidopsis thaliana, cotton (Gossypium arboreum), and soybean (Glycine max) revealed the presence of two expressed copies of rps13 in the nucleus that were derived by gene duplication [11, 12]. Both in vitro and in vivo RPS13 protein import experiments indicated that one copy encodes the chloroplast-imported protein (nucp rps13) while the other encodes mitochondria-imported RPS13 (numit rps13) [11, 12]. It was inferred that the missing mt rps13 gene product has been functionally replaced by the product of numit rps13 in a common ancestor of Arabidopsis, cotton, and legumes. Thus the function of numit rps13 has been modified after gene duplication, and one could argue that numit rps13 has gained a new function because it is operating in a new cellular context (the mitochondrial ribosome instead of the chloroplast ribosome). Subsequently mt rps13 was lost from mitochondrial DNA many times during the evolutionary history of rosids, as inferred from a Southern blot hybridization survey (see Additional File 1). Surprisingly, however, there were many species of rosids that do appear to retain rps13 in the mitochondrion, based on Southern blot hybridizations, but the gene in some species may not be intact or functional.
The organellar rps13 genes in rosids provide an intriguing system to study gene duplication because the subcellular location and site of action of numit RPS13 has changed after gene duplication from the chloroplast to the mitochondrion. We have studied sequence evolution of numit rps13 among rosids to determine what kinds of amino acid changes have taken place and where those amino acids are located in the tertiary structure, as well as to test the hypothesis that there has been adaptive evolution. Also we have examined the divergence of expression patterns between numit rps13 and nucp rps13. After finding intact and expressed numit rps13 and mt rps13 genes in Malus we tested the hypothesis that there has been expression partitioning of the two genes in different organ types and/or stress conditions to preserve both genes.
Identification of numit rps13 in Malus, Populus, and Citrus and phylogenetic analysis
Accelerated nucleotide substitution rates and positive selection on numit rps13
Comparison of Ka/Ks ratios between nucp rps13 and numit rps13.
nucp rps13 (0.06 ± 0.02)a
numit rps13 (0.28 ± 0.08)
Although simple pair-wise comparison of Ka and Ks analysis provides some insights into the accelerated amino acid substitution in numit rps13, branchwise estimation of Ka, Ks values, and Ka/Ks ratios can provide additional information such as positive selection and adaptive molecular evolution along certain branches and clades [22–26]. To detect if there has been positive selection acting on numit rps13 and nucp rps13 in different rosid species, site specific model analysis was conducted using PAML . (Although synonymous and non-synonymous substitutions are abbreviated as dS and dN in PAML analysis, we use the common designations Ks and Ka to refer to synonymous and non-synonymous substitutions, respectively.) Both the rps13 tree (Figure 2) and the species tree that reflects our current understanding of rosid phylogeny  were used for detection of positive selection to determine if the tree topology influenced detection of positively selected sites, and no differences were found in this regard.
LRT statistics of site specific model for numit rps13 and nucp rps13.
Number of sequences
11th class from M8
Selected positive sites
28R, 114R (P > 0.8)
Structural location of positively selected amino acids
Amino acid changes in numit rps13 that increase identity to mt rps13
Because numit rps13 was derived from nucp rps13 and encodes a RPS13 protein that functions in the mitochondria, we were interested in determining if the numit RPS13 has become more like the mt RPS13 amino acid sequence. We determined if there have been mutations in the numit rps13 genes in any of the seven rosid species that change an amino acid to the residue that is present in mt RPS13. In our alignment of nucp RPS13, numit RPS13, and mt RPS13 across different plant species, sixteen sites were identified where numit RPS13 in one or more species has the same amino acid at the corresponding site in mt RPS13 from seven angiosperms, and the amino acid is different from the amino acid(s) present in nucp RPS13 (Figure 4A). The sixteen sites are relatively evenly distributed in the RPS13 tertiary structure (Figure 3). Although little is known about the exact functions of those regions, some of the mutations might help improve the function of numit RPS13 in the mitochondrial ribosome. We plotted the sixteen amino acid changes on the phylogeny of the seven rosid species to infer when they might have occurred (Figure 4B). Mutations are inferred to have occurred along most of the branches, suggesting continuous refinement of the numit rps13 sequence. We infer that three mutations occurred in the common ancestor of all the species, with a subsequent mutation at site 80 in Arabidopsis from D to E (a conservative substitution) and at site 110 in Gossypium from A to S, although scenarios with multiple recent mutations cannot be ruled out.
Expression evolution of numit rps13
To compare expression patterns of numit rps13 to other nuclear encoded ribosomal protein genes, we analyzed expression data for three other nuclear encoded mitochondrial ribosomal protein genes: rps9, rps10, and rps11 . The expression levels and patterns of all four genes were highly similar (R = 0.73–0.94, P < 0.0001), although rps11 expression levels were lower in some organs (P < 0.05; Figure 5B). Thus numit rps13 has evolved an expression pattern similar to that of other nuclear-encoded genes for mitochondrial ribosomal proteins, and its expression has diverged from that of nucp rps13.
Malus contains an expressed and RNA-edited copy of rps13 in the mitochondrion
Having studied the sequence and expression evolution of numit rps13 we next consider the fate of mt rps13 in rosids. A large number of rosids, including Arabidopsis, Gossypium, Glycine, and Citrus have lost mt rps13, as judged by DNA gel blot hybridization  (see Additional file 1), but some rosids retain rps13 in mitochondrial DNA. We identified a transcribed copy of rps13 in Malus domestica (apple) from BLAST searches of the NCBI EST database that is 90–92% identical with the rps13 gene in the mitochondrion of several eudicots. The sequence was derived from a study of ESTs in Malus . A similar gene (97% identical) was found in Prunus persica, another member of the Rosaceae family. We evaluated the rps13 sequence from Malus for sites of C-to-U RNA editing by PCR amplifying and sequencing rps13 from genomic DNA and comparing the gDNA sequence to the EST sequences. C-to-U RNA editing plays an important role in the expression of plant mitochondrial genes to restore certain amino acids to those that are evolutionarily conserved . Among angiosperm rps13 genes, nine possible edited sites have been identified (see Additional file 4). Four of those sites are already T's instead of C's in the genomic DNA sequence of mt rps13 from Malus, and thus RNA editing might be expected at five sites in the Malus cDNAs. No editing was observed in the two ESTs from Malus, and the EST from Prunus had editing at only one site (the 100th base). To verify the lack of RNA editing, we amplified and directly sequenced mt rps13 cDNAs from leaves and petals of Malus. Unexpectedly five RNA editing sites were discovered in both leaves and petals at five sites (see Additional file 4). After transcription, RNA editing converts codons from serine to leucine (the 26th, 56th, and 287th bases) and from arginine to cysteine (the 100th and 256th bases). The changes made by RNA editing would restore an evolutionarily conserved amino acid sequence and make the resulting protein likely to be functional, should the transcripts be translated.
Co-expression of numit rps13 and mt rps13 in 14 different organ types and under five different stress conditions
Although both copies of rps13 are expressed in many organ types it is possible that there might be partitioning of expression between the two genes under stress conditions. We tested the hypothesis by examining the expression patterns of numit rps13 and mt rps13 under five different stresses including cold, dark, heat, salt, and water submersion treatments to determine if expression partitioning occurs under different environmental stresses. Apple seedlings were independently subjected to each of these five stresses (see Materials and Methods). Four organ types, including roots, hypocotyls, cotyledons, and leaves were examined for expression of numit rps13 and mt rps13. Based on RT-PCR results, transcripts of numit rps13 and mt rps13 were observed under each of the five stress conditions: cold, dark, heat, salt, and water submersion treatments. Sequencing of RT-PCR products showed that the transcripts were RNA edited at 5 sites, although in some cases there was partial editing at one or more sites.
Purifying selection acting on numit rps13, nucp rps13, and mt rps13 in Malus
LRT statistics of branch specific model for Malus branch.
Parameters from MAtest1
Selected positive sites
p0 = 0.6485, p1 = 0.2817, (p2 + p3 = 0.0698)
ω0 = 0.12, ω1 = 1, ω2 = 112.98
31H, 32Q, 117R (0.5 <P < 0.8)
p0 = 0.9005, p1 = 0.0733, (p2 + p3 = 0.0262)
ω0 = 0.04, ω1 = 1, ω2 = 96.7
p0 = 0.6646, p1 = 0.3354, (p2 + p3 = 0) ω0 = 0, ω1 = 1, ω2 = 1
Selection on numit RPS13 in seven rosid species.
Purifying Selection (%, Ka/Ks < 1)a
Neutral Evolution (%, Ka/Ks = 1)a
Positive Selection (%, Ka/Ks > 1)a
Selected positive sites
31H, 32Q, 117R
39I, 88S, 102S
18G, 36H, 60G, 83D
Continuous accelerated evolution and molecular adaptation of numit rps13 among rosids
After gene duplication some retained duplicated genes undergo asymmetric rate divergence and the faster evolving copy experiences relaxed constraint or positive selection [34, 35]. The increased Ka rate, Ka/Ks ratio, and positively selected sites detected in numit rps13, compared with nucp rps13, across different rosid species show there has been accelerated sequence evolution of numit rps13. The increased Ka rate is likely to be correlated with the modified function of numit rps13 – from encoding a chloroplast ribosomal protein to a mitochondrial ribosomal protein. Some amino acid sequence changes were probably necessary for numit RPS13 to interact well with other proteins in the mitochondrial ribosome. The increased rate of non-synonymous substitutions is a continuing process instead of there being a burst of sequence change upon formation of numit rps13 followed by a prolonged period of lower rates of non-synonymous substitutions. The continued higher Ka rate, and the two positively selected codons in numit rps13 near the positions where RPS13 interacts with 16S RNA domain, show that the sequence, and suggest that the function, of numit RPS13 in mitochondria is continuing to be refined. Site-specific positive selection has been detected in other duplicated genes [36–38]. For example, in duplicated AP3 and PI genes there has been functional diversification driven by positive selection acting on different sites within a functional domain involved in heterodimerization .
The sixteen amino acids in one or more rosid species that have changed to the amino acid present in mt RPS13 (Figure 4) indicate that numit RPS13 is becoming more like mt RPS13. We propose that this is a type of convergent sequence evolution of numit rps13 that possibly improves the function of numit RPS13 in the ribosome. The amino acid changes appear to have been taking place continuously during rosid evolution (Figure 4B), with the largest number (five) having occurred on the branch leading to the legumes Glycine and Medicago. We speculate that some of the amino acid changes that have taken place along the terminal or subterminal branches of the tree might have allowed numit rps13 to be selected for, over mt rps13, and allowed multiple independent losses of mt rps13 in different lineages (see Additional file 1). In species where mt rps13 has been lost the product of numit rps13 presumably functions as well as, or perhaps better than, mt rps13 or else there would have been selection for retention of mt rps13. Overall the adaptive and convergent evolutionary forces that seem to be acting on numit rps13 have continued during rosid evolution instead of being factors only soon after gene duplication in a common ancestor of most rosids.
Expression evolution of numit rps13 and nucp rps13 in Arabidopsis
Expression patterns of some duplicated genes have been shown to evolve in a divergent and sometimes asymmetric manner [40–42]. For example, many of the genes derived by an ancient polyploidy event in the Arabidopsis lineage have undergone considerable expression divergence [43–45], some of which may have been asymmetric between the two duplicates. Considering that numit rps13 and nucp rps13 show asymmetric divergence in sequence, and different subcellular locations of their protein products, we predicted that they also would show asymmetric divergence in expression, with the expression pattern of numit rps13 being similar to that of other nuclear-encoded genes for mitochondrial ribosomal proteins. Numit rps13 and nucp rps13 did show some differences in expression patterns although the differences were only dramatic in roots, senescing leaves, and pollen. Numit rps13 has evolved a similar expression pattern to three other genes for mitochondrial ribosomal proteins, perhaps by gaining regulatory elements from another gene for a mitochondrial protein, as have several mitochondrial genes that have been transferred to the nucleus . Alternatively there may have been mutations in the regulatory elements of numit rps13 soon after gene duplication that produced an expression pattern similar to that of other genes for mitochondrial ribosomal proteins. Considering that numit rps13 was formed in a common ancestor of most rosids, distinguishing between the above possibilities about the origin of its regulatory elements is impossible. Overall numit rps13 and nucp rps13 add to the growing number of duplicated genes reported in Arabidopsis thaliana that have experienced divergence in expression patterns.
Co-expression of numit rps13 and mt rps13 in Malus
We have shown that numit rps13 and mt rps13 in Malus are both transcribed in 14 different organ types and under five abiotic stress conditions, mt rps13 is RNA edited at sites to make the transcripts contain an evolutionarily conserved sequence, and abundant steady-state transcripts from both genes are present in a variety of organs. Both genes are experiencing purifying selection. Taken together, the data obtained in this study indicate that it is likely that both numit rps13 and mt rps13 in Malus are functional genes and not pseudogenes. However there is the possibility, albeit unlikely, that transcripts from one gene (particularly mt rps13) might not be translated. Even if both proteins are present, there is the possibility that only one is assembled into mitochondrial ribosomes, and that process could vary among organs and environmental conditions. Showing that both numit RPS13 and mt RPS13 proteins are assembled into mitochondrial ribosomes, especially in a variety of organ types and under various environmental conditions, is beyond the scope of the current evolutionary study.
Although we have provided evidence for the functionality of the gene products from numit rps13 and mt rps13 in Malus, might numit rps13 have experienced functional reversion to encode a chloroplast protein? Several lines of evidence do not support that possibility. The mitochondrial targeting presequence of numit RPS13 is similar to those of numit RPS13 in Arabidopsis, Gossypium, and Glycine (Figure 1), each of which was experimentally determined to be imported into mitochondria but not chloroplasts [11, 12]. Numit rps13 in Malus does not have a greatly accelerated rate of sequence evolution or show more sites under positive selection, compared with numit rps13 in other rosids, as might be expected if its product now functions in the chloroplast. Instead purifying selection is operating on numit rps13 in Malus. Finally, there is no evidence to suggest that nucp rps13 in Malus is a pseudogene and indeed the gene is experiencing strong purifying selection.
Co-expression of numit rps13 and mt rps13 genes in Malus contrasts with the atp9 genes in Neurospora crassa where the nuclear and mitochondrial copies are expressed during different stages of the life cycle  and expression has been partitioned between the two genes. Presumably the nuclear copy of atp9 was derived from transfer of the mitochondrial gene to the nucleus in an ancestor of Neurospora, and the current availability of several ascomycete genome sequences could shed light on the evolutionary timing of the gene transfer. Only three other cases of co-expression of nuclear and mitochondrial genes have been reported, to our knowledge, including cox2 genes in multiple legume species within the Phaseoleae tribe , rpl5 genes in wheat (Triticum aestivum) , and sdh4 genes in Populus . Those genes contrast to rps13 in rosids because the nuclear copies were derived by transfer of the mitochondrial gene to the nucleus.
Considering that numit rps13 was created by gene duplication in the common ancestor of most rosids, co-expression of mt rps13 and numit rps13 in Malus has presumably occurred for a long period of evolutionary time. Other cases of co-expression of nuclear and mitochondrial genes in plants represent evolutionarily recent gene transfers to the nucleus. Indeed following transfer of a mitochondrial gene to the nucleus the mitochondrial copy is often lost in a relatively short amount of time . Thus it was unexpected that numit rps13 and mt rps13 have been preserved without partitioning of expression patterns. Why would both copies continue to be retained and expressed? One possibility is that there is partitioning of expression in organs, tissues, or cell types, or under environmental conditions that were not examined in this study. Another possibility is that, despite the considerable level of sequence divergence between numit rps13 and mt rps13 (about 42% identity), the product of either gene functions well in the mitochondrial ribosomes of Malus. That possibility is supported by the fact that some rosids (such as Arabidopsis, Gossypium, Glycine, and Citrus) have only the numit rps13 and non-rosid angiosperms have only mt rps13. Another possibility is that mutations have not occurred in numit rps13 from Malus that cause it to be selected for over mt rps13, as presumably occurred in other lineages of rosids that have lost mt rps13. In this regard it is notable that there are no amino acid changes in numit RPS13 to the residue present in mt RPS13 that occurred along the terminal branch leading to Malus (Figure 4B), unlike all of the other terminal branches on the tree leading to species that have lost mt rps13.
The accelerated rate of amino acid evolution, positive selection on specific sites, and amino acid changes to the residue present in mt RPS13 provide evidence that numit rps13 genes in rosids have experienced adaptive evolution and convergent sequence evolution with mt rps13. Numit rps13 provides an example of a gene that has experienced site-specific positive selection while the gene as a whole has been under purifying selection. Expression patterns of numit rps13 have diverged to become similar to those of other genes for mitochondrial ribosomal proteins. Malus contains intact genes for both numit rps13 and mt rps13 that are transcribed in a range of organs and under several abiotic stresses. Abundant levels of steady state transcripts from both numit rps13 and mt rps13 in Malus in a variety of organ types, as well as purifying selection acting on both genes, suggest that both genes are functional and not pseudogenes. The three organellar rps13 genes in rosids provide a distinctive case of gene duplication involving the co-evolution of the nuclear and cytoplasmic genomes.
The following expressed sequence tags (EST) for numit rps13 were obtained from GenBank by BLAST searches using numit rps13 from Arabidopsis thaliana (DR380621) as a query: Citrus sinensis (CX672493), Malus domestica (DR995890, CN494589, CN925904, and CX023021), Populus trichocarpa (DT496554), Medicago truncatula (BI272420), Glycine max (BM188020), and Gossypium hirsutum (DW488419). The following ESTs for nucp rps13 were obtained from GenBank by BLAST searches using nucp rps13 from Arabidopsis thaliana (DR367899) as a query: Citrus sinensis (CX053776), Glycine max (EH261685), Gossypium hirsutum (DW226103), Malus domestica (DT000985), Medicago truncatula (BI265445) and Populus trichocarpa (DT486949). Mt rps13 ESTs from Malus (CN871057 and CN875489) and Prunus persica (AJ873687) were identified by BLAST searches of GenBank using mt rps13 from Beta vulgaris as a query. Mt rps13 genes used in this study include: Triticum aestivum (Y00520), Zea mays (AF079549), Magnolia spp. (Z49799), Helianthus annuus (AJ243789), Daucus carota (X54417), Oenothera berteriana (X54416), Beta vulgaris (DQ381464) and Marchantia polymorpha (M68929).
Sequence alignment/analysis and phylogenetic analysis
Sequence alignment was done using transAlign, which aligns protein-coding DNA sequence based on the alignment of amino acids . Aligned sequences were refined with BioEdit  for further phylogenetic and codon substitution analysis (see Additional file 5). For phylogenetic analysis, maximum likelihood (ML) analysis was conducted with MultiPhyl v1.0.6  with SPR (subtree pruning and regrafting) branch swapping. The optimal evolutionary model selected for ML was K81uf+I+G (Kimura three parameter with unequal base frequencies + proportion of sites + gamma distribution) using the following parameters: assumed nucleotide frequencies A = 0.36736, C = 0.20950, G = 0.27698, T = 0.14616; expected transition/transversion ratio = 0.94; expected pyrimidine transition/purine transition ratio = 0.30; proportion sites assumed to be invariable = 0.29; rates for variable sites assumed to follow the gamma distribution with shape parameter = 4.28. Bootstrapping was performed using MultiPhyl v1.0.6 with neighbor-joining algorithm and 100 replicates .
Ka/Ks analyses and likelihood ratio tests (LRT) for positive selection
Nonsynonymous (Ka) and synonymous (Ks) nucleotide substitution rates were calculated by using program yn00 in PAML v3.15  (see Additional file 2). The t-test was used for testing for significant differences of Ka, Ks, and Ka/Ks ratios between the nucp rps13 and numit rps13 cDNA sequences. The statistically significant level was set at 95%. The statistical analysis in this study was implemented by using the statistical package R .
For detection of positive selection, codon-based analysis was implemented using codeml in PAML v3.15 . The mature coding region, without the mitochondrial targeting presequences, was included in our analysis. Site specific models were used for testing positive selection on numit rps13 and nucp rps13 . Two LRTs were used for the detection of positive selection: M7-M8 and M8a-M8 [22, 25, 26]. Because comparison of M7 and M8 provides a more powerful test of positive selection and has less sensitivity to large evolutionary distances and G+C content than comparison of M1 and M2 [55, 56], only comparison of M7 and M8 was used for the detection of positive selection in this study. M7 and M8a models are the null models without positive selection (no codon with Ka/Ks > 1) and the M8 model is the alternative model with positive selection. Branch specific model was used to test if there has been positive selection for Malus branch in numit rps13, nucp rps13, and mt rps13 . For this analysis, the branch which we are interested in testing positive selection was assigned as foreground lineage. Therefore, Malus branch in numit rps13, nucp rps13, and mt rps13 were set as foreground lineage and the rest of other rosid species were designated as background lineage. For branch specific model, two LRTs were used for detection of positive selection as follows: M1-Model A test1 (MAtest1) and Model A test2 (MAtest2)-MAtest1 [25, 26]. M1 and MAtest2 models are the null hypothesis without positive selection (no codon with Ka/Ks > 1) and the MAtest1 model is the alternative selection with positive selection. For site-specific and branch-specific models used for detection of positive selection, M8a is more stringent than M7 and MAtest2 is more stringent than M1 because their ω2 (Ka/Ks) is fixed at 1. For all LRTs, the first model is simpler than the second one, with fewer parameters and poor fit to the data. Therefore, the first model has a lower maximum likelihood index. To test if there is statistically better maximum likelihood for the second model, twice difference of log maximum likelihood values between the two compared models [2δL = 2(Ln2-Ln1), where Ln1 and Ln2 represent for log of maximum likelihood value in the first model and the second model] was compared against χ2 distribution. The degrees of freedom (d.f.) equals to the additional parameters used in more complex model. The d.f. is 2 for M7-M8 and M1-MAtest1, while the d.f. is 1 for M8a-M8 and MAtest2-MAtest1. However, it was argued that the appropriate model comparison for M8a-M8 would be to use 50:50 mixture of d.f. = 0 and d.f. = 1 . In this study, the calculation of P value for M8a-M8 was followed as described in Kapralov and Filatov . P value was first obtained using d.f. = 1 and then divided by 2. Bayes empirical bayes (BEB) approach was used to determine positive selected sites in M8 model and MAtest1 model. In BEB analysis, the posterior probabilities were calculated to select the codon with Ka/Ks greater than 1. Because BEB analysis is more powerful to detect positive selection than naive empirical Bayes (NEB) analysis , only BEB analysis was considered in this study.
Structural analysis of RPS13
Using first approach mode in SWISS-MODEL , nucp, numit, and mt RPS13 amino acid sequences in Malus were selected to search for a suitable template for further structural analysis. Based on the results, RPS13 of Escherichia coli and Thermus thermophilus were chosen for the following structural analysis. RPS13 structural data file for E. coli (PDB ID: 2gy9M)  and T. thermophilus (PDB ID: 1fjgM)  were obtained from RCSB Protein Data Bank . Location and property of each amino acid in E. coli and T. thermophilus RPS13 was analyzed using DeepView-Swiss-PdbViewer v.3.7 . Selected positive sites obtained by BEB analysis and sites shared with similarity between numit RPS13 and mt RPS13 were plotted in the relative position of RPS13 in E. coli and T. thermophilus according to amino acid alignment (Figure 4).
Microarray data analysis
Raw Affymetrix ATH1 microarray data  were downloaded from the TAIR website (TAIR accession number: ME00319). Raw data were processed and normalized based on the GC-RMA method . The expression values were converted into log2 numbers by only considering values of perfect-match probes . Normalization and analysis of the microarray data were implemented using Bioconductor. Pearson correlation analysis was conducted to statistically compare the similarity of expression profile among rps9, rps10, rps11, and numit rps13, and between numit rps13 and nucp rps13. The correlation coefficient (R) values correspond to the similarity of the expression profile between two genes. A one-way ANOVA with Bonferroni post hoc tests was used to test if there is a significant expression difference between two different genes or any two different organ types. All statistical analyses were implemented using statistical package R . The statistically significant level was set at 95%.
Plant materials and abiotic stress treatments
Several organ types, including stems, leaves, peduncles, sepals, petals, stamens, stigmas+styles, and young fruit of apple (Malus domestica Borkh.) were collected from the University of British Columbia's Botanical Garden. Seedlings were used for abiotic stress experiments. Prior to sowing, apple seeds were soaked in distilled water at 4°C for 6 weeks for vernalization. Seedlings were cultivated in a peat-vermiculite soil mixture under fixed day/night (16 h day/8 h night) and temperature of 20–23°C. After germination and emergence from the soil for 7 days, the plants were subjected to five different abiotic stresses: 4°C for 7 days (cold treatment), 37–40°C for 12 hours (heat stress), 100 mM NaCl solution for 7 days (salt treatment), submerged in distilled water for 4 days (water submersion treatment), and dark for 7 days (dark treatment). After stress treatments, roots, hypocotyls, cotyledons, and leaves were collected and immediately frozen in liquid nitrogen and stored at -80°C until nucleic acid extraction.
Nucleic acid extraction, gene amplification, and sequencing
Genomic DNA extraction was done using the DNeasy Plant Mini Kit (Qiagen) following the manufacturer's protocol. Total RNA extraction was performed as described previously . The extracted nucleic acid concentrations and purities were determined by using a NanoDrop spectrophotometer. The quality was checked by running on 1.5% agarose gels. Before reverse transcription, 3 μg of RNA (500 μg/μl) was treated with 1 unit of DNaseI (New England Biolabs) and incubated at 37°C for 30 min twice. Then 4 μg of DNase-treated RNA was reverse-transcribed by using M-MLV reverse transcriptase (Invitrogen). The reverse transcription conditions were 25°C for 10 min, 37°C for 60 min, and 70°C for 15 min. Finally, the reverse-transcribed samples were treated with RNase (Invitrogen) at 37°C for 20 min.
The rps13 genes were amplified from genomic DNA and cDNA by polymerase chain reaction (PCR) using gene-specific primers (see Additional file 6). The PCR was performed in a reaction mixture (10 μl) consisting of 4.88 μl of ddH2O, 1 μl of genomic DNA/cDNA solution, 1 μl of PCR buffer, 1 μl of 2.5 mM MgCl2 solution, 1 μl of 0.2 mM dNTPs, 0.5 μl of 0.4 μM each primer, and 0.12 units of Taq DNA Polymerase (Sigma). The PCR conditions were 96°C for 4 min, and 30 cycles of 96°C for 40 s, 60°C for 40 s, 72°C for 1 min, and 72°C for 10 min. The PCR products were run on a 1.5% agarose gel and extracted from the gel using QIAquick Gel Extraction Kit (Qiagen). PCR products amplified from genomic DNA and cDNA were sequenced directly. The sequencing was performed in a reaction mixture containing 0.4 μl of ABI BigDye Version 3.1 (Applied Biosystems), 3.6 μl of BigDye buffer, 5.5 μl of 50 ng template, and 0.5 μl of 0.4 μM forward or reverse primer. The sequencing reaction was carried out with the following program: 1 min at 96°C, and 25 cycle of 10 s at 96°C, 5 s at 50°C, and 4 min at 60°C. The sequencing products were run on an ABI 377 DNA Sequencer (Applied Biosystems) at the UBC Centre for Plant Research, or on an ABI 3730 Sequencer at the Nucleic Acids Protein Service unit at UBC. The GenBank accession number for mt rps13 in Malus, including information about RNA editing sites, is [GenBank: EU084692].
Quantitative real-time RT-PCR was performed with a BioRad iQ5 system using SYBR green master mix (BioRad) following the manufacturer's instructions, except that 25μl total reaction volumes were used. The PCR conditions were 96°C for 3 min, and then 35 cycles of 96°C for 10 s, 58°C for 30 s, and 72°C for 30 s. Gene-specific primers are listed in Additional file 6. For each sample, two technical replicates were performed. Reactions for a standard curve were run with each set of experimental reactions. After the completion of PCR, the melting curves were analyzed to distinguish the true product from artifacts such as primer dimers. The iQ5 software and Microsoft Excel were used for data analysis. Normalization was done using the actin gene ACT2. GenBank accession numbers for sequences used to design primers are: Malus ACT2: CN903171, CN902302, and N917499; Malus cob: CN872477, CN856986, CN856316; Malus rps10: CV882925.
Bayes Empirical Bayes analysis
expressed sequence tag
likelihood ratio test
National Center for Biotechnology Information
quantitative real-time polymerase chain reaction
reverse transcription-polymerase chain reaction
We thank Nolan Kane and Michael Barker for advice on the Ka/Ks analysis and LRTs, two anonymous reviewers for helpful comments on an earlier version of the manuscript, and the UBC Botanical Garden for providing tissue from their apple trees. This study was funded by a grant from the National Science and Engineering Research Council of Canada, by start-up funds from the Faculty of Land and Food Systems at the University of British Columbia, and by infrastructure funds from the Canadian Foundation for Innovation.
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