Supplemental Figure 1. Comparisons of GC3 distribution computed with raw EST data, bi-beta fits and complete genome sequences for 6 species.

Transcription

1 Supplemental Figure 1. Comparisons of GC3 distribution computed with raw EST data, bi-beta fits and complete genome sequences for 6 species. Filled distributions: GC3 computed with raw EST data. Dashed distribution: GC3 bi-beta distribution fitted with raw EST data. Unfilled distributions: GC3 computed with complete genome sequences. Eudicots (in cadet blue): Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera. Monocots (in gold): Brachypodium distachyon, Oryza sativa, Sorghum bicolor, Zea mays. 1

2 Supplemental Figure 2: Comparison of the means and standard deviations estimated from the raw data and from the bi-beta distributions. The colors correspond to the groups used in the main text: violet red: gymnosperms, turquoise: basal angiosperms, brown: non-commelinids monocots; orange: non-poaceae commelinids; gold: Poaceae; cadet blue: eudicots. Black lines correspond to the bissectrices. 2

3 Supplemental Figure 3: Relationship between the residuals of the regression of GC3 standard deviation against mean GC3 (bi-beta estimates) and the number of EST sequences and unigenes. The colors correspond to the groups used in the main text: violet red: gymnosperms, turquoise: basal angiosperms, brown: non-commelinids monocots; orange: non-poaceae commelinids; gold: Poaceae; cadet blue: eudicots. 3

4 Supplemental Figure 4: Box plots of mean GC3 by Super Order and Order. The colors correspond to the groups used in the main text: violet red: gymnosperms, turquoise: basal angiosperms, brown: non-commelinids monocots; orange: non-poaceae commelinids; gold: Poaceae; cadet blue: eudicots. On each box plot the dark midline is the median, the bottom and top of the box are the lower and upper quartiles, respectively, and the ends of the whiskers are the lowest, respectively highest, data still within 1.5 times the inter-quartile range of the lower, respectively higher, quartile. 4

5 Supplemental Figure 5: Box plots of GC3 standard deviation by Super Order and Order. The colors correspond to the groups used in the main text: violet red: gymnosperms, turquoise: basal angiosperms, brown: non commelinids monocots; orange: non Poaceae commelinids; gold: Poaceae; cadet blue: eudicots. On each box plot the dark midline is the median, the bottom and top of the box are the lower and upper quartiles, respectively, and the ends of the whiskers are the lowest, respectively highest, data still within 1.5 times the inter-quartile range of the lower, respectively higher, quartile. 5

6 Supplemental Figure 6: Relationship between local recombination rate and GC1, GC2, and GCUTR in three grass species Genes have been grouped into 20 bins according to their local recombination rate. Dots correspond to the mean GC-content of each bin and bars to the standard error. Black dots: Brachypodium distachyon, grey dots: maize, white dots: rice. 6

7 Supplemental Figure 7: Correlation between mean GC3 and GC3 standard variation averaged by taxonomic level 7

8 Supplemental Figure 8: Correlation between mean GC3 and the two means of the bi-beta distribution averaged by taxonomic level 8

9 Supplemental Table 1: mean GC-content by taxonomic group and Kruskal-Wallis test for differences between groups. GC mean GC1 GC2 GC3 GC5UTR GC3UTR Means per group gymnos 49.1% 40.6% 42.4% 40.1% 35.7% basal angios 49.3% 40.4% 44.4% 40.4% 36.9% monocots 53.9% 43.6% 55.8% 49.6% 40.4% non commelinids monocots 50.6% 41.1% 48.1% 43.3% 36.5% commelinids 55.0% 44.4% 58.2% 51.5% 41.6% non Poaceae commelinids 53.0% 42.6% 53.1% 47.2% 38.3% Poaceae 55.4% 44.8% 59.2% 52.3% 42.2% eudicots 49.9% 41.2% 43.9% 40.3% 35.4% Kruskal-Wallis tests Gym, Bas, Eud NS NS NS NS * Gym, Mon *** *** *** *** *** Bas, Mon ** ** *** ** ** Eud, Mon *** *** *** *** *** nocom Mon, Com *** *** *** *** *** nopoa Com, Poa * ** * ** *** NS: p-value>0.05; *: p-value<0.05; **: p-value<0.01; ***: p-value< Gym: Gymnosperms; Bas: basal angiosperms; Mon: all monocots; nocom Mon: non-commelinids monocots; Com: all commelinids; nopoa Com: non-poaceae commelinids; Poa: Poaceae; Eud: eudicots. Unbiased mean GC for GC1, GC2, GC3. Raw mean GC for GC5UTR and GC3UTR. 9

10 Supplemental Table 2: GC-content standard deviations by taxonomic group and Kruskal-Wallis tests for differences between groups. GC standard-deviation GC1 GC2 GC3 GC5UTR GC3UTR Means per group gymnos basal angios monocots Non-commelinids monocots commelinids Non-Poaceae commelinids Poaceae eudicots Kruskal-Wallis tests Gym, Bas, Eud NS NS NS ** *** Gym, Mon NS *** *** *** *** Bas, Mon NS ** *** *** *** Eud, Mon *** *** *** *** *** nocom Mon, Com * *** *** *** NS nopoa Com, Poa * ** ** *** * NS: p-value>0.05; *: p-value<0.05; **: p-value<0.01; ***: p-value< Gym: Gymnosperms; Bas: basal angiosperms; Mon: all monocots; nocom Mon: non-commelinids monocots; Com: all commelinids; nopoa Com: non-poaceae commelinids; Poa: Poaceae; Eud: eudicots. Unbiased standard deviation GC for GC1, GC2, GC3. Raw standard deviation GC for GC5UTR and GC3UTR. 10

11 Supplemental Table 3: Non-parametric Spearman correlation coefficient (rho) and p-value of the correlation between local recombination rate and GC1, GC2, and GCUTR in three grass species. The correlations are computed using every gene as a data point. For O. sativa and Z.mays results are given for the total dataset including all annotated genes or only protein coding genes (excluding pseudogenes, transposable elements, and mirna). Species dataset GC1 GC2 GC3 GC5UTR GC3UTR O. sativa protein-coding rho p-value <10e <10e E-05 total rho p-value <10e-15 <10e-15 <10e E-04 Z. mays protein-coding rho p-value 5.04E <10e-15 <10e-15 <10e-15 total rho p-value <10e-15 <10e-15 <10e-15 <10e-15 <10e-15 B. distachyon unfiltered rho p-value 7.34E E-11 <10e E-07 <10e-16 11

12 Supplemental Table 4: Taxonomy levels used in the analyses. Group Infra group Super order Gymnosperms Coniferopsida Coniferopsida Cycadopsida Cycadopsida Ginkgoopsida Ginkgoopsida Gnetopsida Gnetopsida basal angiosperms basal angiosperms basal angiosperms Monocots+Magnoliids Magnoliids Magnoliids Monocots basal monocots Commelinids Eudicots basal eudictos stem eudicots basal core eudicots Rosids basal rosids Fabids Malvids Asterids basal asterids Lamiids Campanulids Upper case (lower case) is used for monophyletic (paraphyletic) groups, respectively. 12

13 Supplemental Table 5: Correlation between mean GC3 and GC3 standard variation by taxonomic group Group Infra Group Super Order Order Family Genus # species Spearman's rho p-value Gymnosperms Coniferopsida Coniferales Pinaceae Pinus basal angiosperms Magnoliids Magnoliales Monocots basal monocots Asparagales Commelinids Zingiberales Poales Poaceae Eudicots basal eudicots stem eudicots basal core eudicots Caryophyllales Rosids basal rosids Myrtales Myrtaceae Fabids Malpighiales Euphorbiaceae Salicacecae Populus Fabales Fabaceae Rosales Rosaceae Fagales Fagaceae Malvids Brassicales Brassicaceae Malvales Malvaceae Sapindales Rutaceae Citrus Asterids basal asterids Ericales Lamiids Gentianales Rubiaceae Lamiales Solanales Solanaceae Solanum Campanulids Asterales Asteraceae Helianthus Lactuca