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tpj12073-sup-0001-FigS1.pdfapplication/PDF136KFigure S1. Numbers of genes in low-copy-number families (LF; 3–10 copies) in different phylogenic groups.
tpj12073-sup-0002-FigS2.pdfapplication/PDF129KFigure S2. Numbers of genes in high-copy-number families (HF; >10 copies) among different phylogenetic groups.
tpj12073-sup-0003-FigS3.pdfapplication/PDF139KFigure S3. The non-synonymous to synonymous substitution (Ka/Ks) ratio for the coding region of paralogous genes generated from segmental duplications.
tpj12073-sup-0004-FigS4.pdfapplication/PDF181KFigure S4. The top 15 biological processes of genes classified as non-family genes (NF; 1–2 copies per genome) in Arabidopsis.
tpj12073-sup-0005-FigS5.pdfapplication/PDF340KFigure S5. K-means clustering of expression pattern of Arabidopsis for genes classified as non-family genes in NF1 group (i.e. Viridiplantae wide; defined in Figure 3).
tpj12073-sup-0006-FigS6.pdfapplication/PDF595KFigure S6. K-means clustering of expression pattern of Arabidopsis for genes classified as non-family genes in NF5 group (i.e. species-specific; defined in Figure 3).
tpj12073-sup-0007-FigS7.pdfapplication/PDF197KFigure S7. A network analysis of an Arabidopsis non-family (NF; 1–2 copies) gene involved in heat response.
tpj12073-sup-0008-FigS8.pdfapplication/PDF126KFigure S8. Co-expression conservation of NF, LF and HF genes between A. thaliana and O. sativa.
tpj12073-sup-0009-FigS9.pdfapplication/PDF125KFigure S9. Proportion of coding regions in the shorter sequences of duplicated gene pairs were aligned for Ka/Ks analysis in 200 randomly selected gene pairs.
tpj12073-sup-0010-TableS1.xlsxapplication/msexcel69KTable S1. Biological processes over-represented (< 0.05) in conserved (i.e. shared by at least two species) non-family genes as compared with conserved high-copy-number family genes.
tpj12073-sup-0011-TableS2.xlsapplication/msexcel19KTable S2. Biological processes over-represented (< 0.05) in species-specific non-family genes (i.e. gene group NF5 as defined in Figure 3) as compared with species-specific high-copy-number family genes (i.e. gene group HF5 as defined in Figure S2).
tpj12073-sup-0012-TableS3.xlsapplication/msexcel110KTable S3. Biological processes over-represented (< 0.05) in conserved (i.e. shared by at least two species) non-family genes as compared with conserved low-copy-number family genes.
tpj12073-sup-0013-TableS4.xlsapplication/msexcel220KTable S4. Biological processes over-represented (< 0.05) in conserved (i.e. shared by at least two species) low-copy-number family genes as compared with conserved high-copy-number family genes.
tpj12073-sup-0014-TableS5.xlsapplication/msexcel26KTable S5. Biological processes over-represented (< 0.05) in species-specific low-copy-number family genes (i.e. gene group LF5 defined in Figure S1) as compared with species-specific high-copy-number family genes (i.e. gene group HF5 defined in Figure S2).
tpj12073-sup-0015-TableS6.xlsapplication/msexcel20KTable S6. Biological processes over-represented (< 0.05) in species-specific non-family genes as compared with conserved (i.e. shared by at least two species) non-family genes.
tpj12073-sup-0016-TableS7.xlsapplication/msexcel19KTable S7. Number of non-family (NF; 1–2 copies per genome), low-copy-number family (LF; 3–10 copies) and high-copy-number family (HF; >10 copies) genes related to stress responses and cell wall biosynthesis in Arabidopsis.
tpj12073-sup-0017-TableS8.xlsapplication/msexcel54KTable S8. List of Arabidopsis non-family (NF; 1–2 copies per genome) genes related to stress responses and cell wall biosynthesis based on GO annotation and NF genes that were co-expressed with genes involved in stress responses and cell wall biosynthesis.
tpj12073-sup-0018-TableS9.xlsapplication/msexcel20KTable S9. Biological processes over-represented (< 0.001) in the gene cluster in Figure 6 as compared with the Arabidopsis genome.
tpj12073-sup-0019-TableS10.xlsapplication/msexcel20KTable S10. Biological processes over-represented (< 0.001) in the gene cluster in Figure S7A as compared with Arabidopsis genome.
tpj12073-sup-0020-TableS11.xlsapplication/msexcel19KTable S11. Biological processes over-represented (< 0.05) in the gene cluster in Figure 7a as compared with Arabidopsis genome.
tpj12073-sup-0021-TableS12.xlsapplication/msexcel45KTable S12. Non-family hub genes in an Arabidopsis protein-protein interaction network (http://bioinfo.esalq.usp.br/atpin/atpin.pl).
tpj12073-sup-0022-Supplementary Legend.docxWord document28K 

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