Region-specific, wavelike dynamics of the nidovirus genome expansions.

<p>Relative contributions of the genome regions ORF1a, ORF1b, 3′ORFs, 5′UTR and 3′UTR to the increase in genome size are calculated according to the splines regression and plotted on top of each other and against their sum = 1. Solid horizontal lines and vertical bars on top: genome size ranges and samplings for nidovirus lineages indicated by names. Dotted lines: topology of major nidovirus branches. Selected domains gained (ExoN, OMT, NMT, RsD and ADRP, circles) and lost (NendoU and NMT, diamonds) are colored according to ORF in which they are encoded. See also <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003500#ppat-1003500-g003" target="_blank">Fig. 3</a>, <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003500#ppat.1003500.s002" target="_blank">Fig. S2</a> and the main text.</p

Hierarchy and cooperation in the nidovirus genome expansions.

<p>Functional and evolutionary relations between the three major coding regions of the nidovirus genome are depicted. For a brief description on the relationship between these three coding regions and the processes they dominate in the nidovirus life cycle, see text.</p

Relationship of sizes of three major coding regions and genome size in the nidovirus evolution.

<p>For 28 nidoviruses representing species diversity, absolute sizes of 3′ORFs (A), ORF1a (B), and ORF1b (C) are plotted against the size of the genome. Different symbols were used to group the viruses into five major phylogenetic lineages (see inlet in A). Results of weighted linear, double-logistic and 3rd order monotone splines <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003500#ppat.1003500-Ramsay1" target="_blank">[111]</a> regression analyses are depicted. The three regression models (see inlet in C) fit the data with weighted r² values of 0.908 (linear), 0.949 (double-logistic) and 0.960 (splines) for ORF1a, 0.758, 0.898 and 0.929 for ORF1b, and 0.835, 0.950 and 0.954 for 3′ORFs. For fit comparison of regression models see <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003500#ppat-1003500-t001" target="_blank">Table 1</a>.</p

Comparison of regression models.

a<p>linear regression model (linear); double-logistic regression model (dlog); 3^rd order monotone splines regression model (splines).</p>b<p>standard weighted F test (F); permutation F test (F_perm); a weighted version of a test to compare non-nested regression models (LV) as described in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003500#ppat.1003500-Lavergne1" target="_blank">[112]</a>.</p>c<p>shown is the probability that model A (null hypothesis) fits the data better than model B (alternative hypothesis); asterisks (*) highlight significant values to reject the null in favor of the alternative hypothesis using a confidence level of 0.05; probabilities are calculated separately for ORF1a, ORF1b, 3′ORFs as well as the complete model combining the three coding plus the two UTR regions (total).</p>d<p>none of the 1 million permutations resulted in an F larger than that of the non-permuted dataset.</p

Phylogeny of nidoviruses in comparison to the Tree of life (ToL).

<p>Bayesian phylogenies of nidoviruses (A) and ToL (B) are drawn to a common scale of 0.1 amino acid substitutions per position. Major lineages are indicated by vertical bars and names; arteri: <i>Arteriviridae</i>, mesoni: <i>Mesoniviridae</i>, roni: <i>Roniviridae</i>, toro: <i>Torovirinae</i>, corona: <i>Coronavirinae</i>. Rooting was according to either (A) domain-specific outgroups <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003500#ppat.1003500-Nga1" target="_blank">[10]</a> or (B) as described <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003500#ppat.1003500-Boussau1" target="_blank">[66]</a>. Posterior probability support values and fixed basal branch points (*) are indicated. The nidovirus and ToL alignments include, respectively, three enzymes and 56 single-gene protein families, 604 and 3336 columns, 2.95% and 2.8% gaps. For further details on the nidovirus tree see <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003500#ppat.1003500-Nga1" target="_blank">[10]</a>.</p

Relationship of evolutionary distance to genome size change in nidoviruses.

<p>Evolutionary distance (average number of substitutions per amino acid position in the conserved proteins) in relation to difference in genome size is shown for each pair (n = 378) of the 28 nidovirus species. Points are colored according to pairs of major clades shown in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003500#ppat-1003500-g001" target="_blank">Fig. 1A</a>. The number of comparisons for each pair of clades is indicated by numbers in brackets. Points were grouped into clusters I (intra-lineage comparisons), II (large- vs. large-sized inter-lineage comparisons), III (intermediate-sized vs. others) and IV (small- vs. large-sized).</p

Nidovirus genome and region size differences.

<p>Shown are size distributions of genomes (left part) and the three genome coding parts ORF1b, ORF1a and 3′ORFs (right part) for five small-sized arterivirus species (small), 22 large-sized nidovirus species (large) and one intermediate-sized mesonivirus species (interm.). The distributions are represented by box-and-whisker graphs, where the box spans from the first to the third quartile and includes the median (bold line). The whiskers extend (dashed lines) to the extreme values.</p