Table S1. Gene Ontology biological process enrichment analysis of genes with R > 1. # whole Expected Fold Sign GO category # sample P-value Q-value genome in sample enrichment enrichment polyadenylation-dependent snoRNA 3'-end processing 8 6 .92 6.54 + 1.70E-03 4.91E-02 snoRNA 3'-end processing 13 8 1.49 5.37 + 7.35E-04 2.48E-02 ncRNA 3'-end processing 32 18 3.67 4.91 + 1.11E-06 9.95E-05 ncRNA processing 343 139 39.31 3.54 + 2.41E-30 1.78E-27 ncRNA metabolic process 421 147 48.25 3.05 + 1.43E-26 7.71E-24 RNA metabolic process 3039 593 348.30 1.70 + 2.77E-33 3.28E-30 nucleic acid metabolic process 3438 682 394.03 1.73 + 8.10E-41 2.39E-37 nucleobase-containing compound metabolic 3878 724 444.46 1.63 + 6.42E-36 9.49E-33 _______________process organic cyclic compound metabolic process 4493 770 514.94 1.50 + 7.00E-28 4.14E-25 organic substance metabolic process 9935 1270 1138.65 1.12 + 4.87E-06 3.60E-04 metabolic process 11121 1384 1274.58 1.09 + 1.90E-04 7.50E-03 cellular nitrogen compound metabolic 4767 825 546.35 1.51 + 1.77E-31 1.50E-28 _____________ ____process nitrogen compound metabolic process 8015 1122 918.60 1.22 + 1.47E-13 3.63E-11 cellular metabolic process 9524 1230 1091.54 1.13 + 1.24E-06 1.08E-04 cellular process 12555 1589 1438.93 1.10 + 4.25E-07 4.41E-05 heterocycle metabolic process 4196 753 480.90 1.57 + 1.20E-32 1.18E-29 cellular aromatic compound metabolic 4370 761 500.85 1.52 + 2.59E-29 1.70E-26 _________________process primary metabolic process 9223 1201 1057.05 1.14 + 3.70E-07 4.05E-05 macromolecule metabolic process 7271 1052 833.33 1.26 + 4.19E-16 1.18E-13 RNA processing 819 269 93.87 2.87 + 5.49E-44 3.24E-40 gene expression 3289 556 376.95 1.47 + 2.75E-18 1.02E-15 RNA 3'-end processing 65 29 7.45 3.89 + 3.59E-08 5.45E-06 snoRNA processing 18 11 2.06 5.33 + 7.93E-05 3.61E-03 snoRNA metabolic process 20 12 2.29 5.24 + 4.30E-05 2.08E-03 protein refolding 26 17 2.98 5.70 + 4.68E-07 4.78E-05 protein folding 266 90 30.49 2.95 + 4.22E-16 1.13E-13 U4 snRNA 3'-end processing 11 7 1.26 5.55 + 1.38E-03 4.18E-02 snRNA 3'-end processing 15 11 1.72 6.40 + 2.37E-05 1.32E-03 snRNA processing 16 11 1.83 6.00 + 3.63E-05 1.82E-03 snRNA metabolic process 23 17 2.64 6.45 + 1.34E-07 1.72E-05 chiasma assembly 16 10 1.83 5.45 + 1.46E-04 5.93E-03 synapsis 28 14 3.21 4.36 + 4.66E-05 2.24E-03 chromosome organization involved in meiotic cell cycle 49 20 5.62 3.56 + 1.30E-05 7.79E-04 chromosome organization 544 113 62.35 1.81 + 5.38E-08 7.95E-06 organelle organization 1645 297 188.53 1.58 + 1.26E-12 2.86E-10 cellular component organization 2799 423 320.79 1.32 + 5.44E-08 7.84E-06 cellular component organization or biogenesis 3161 528 362.28 1.46 + 1.79E-16 5.28E-14 meiotic cell cycle process 145 36 16.62 2.17 + 1.08E-04 4.67E-03 meiotic cell cycle 173 43 19.83 2.17 + 2.32E-05 1.30E-03 reproductive process 1756 251 201.25 1.25 + 9.32E-04 3.05E-02 reproduction 1766 253 202.40 1.25 + 8.38E-04 2.77E-02 cell cycle 568 95 65.10 1.46 + 9.41E-04 3.06E-02 homologous chromosome segregation 35 15 4.01 3.74 + 9.98E-05 4.34E-03 meiotic chromosome segregation 58 19 6.65 2.86 + 2.31E-04 8.85E-03 meiotic nuclear division 100 29 11.46 2.53 + 5.29E-05 2.50E-03 nuclear division 156 40 17.88 2.24 + 2.53E-05 1.40E-03 organelle fission 201 48 23.04 2.08 + 2.07E-05 1.19E-03 nuclear chromosome segregation 100 29 11.46 2.53 + 5.29E-05 2.48E-03 chromosome segregation 124 36 14.21 2.53 + 5.47E-06 3.85E-04 meiosis I 72 24 8.25 2.91 + 2.94E-05 1.58E-03 meiosis I cell cycle process 77 26 8.82 2.95 + 1.16E-05 6.99E-04 reciprocal meiotic recombination 58 21 6.65 3.16 + 3.41E-05 1.75E-03 homologous recombination 58 21 6.65 3.16 + 3.41E-05 1.74E-03 DNA recombination 155 47 17.76 2.65 + 7.31E-08 9.83E-06 DNA metabolic process 537 111 61.55 1.80 + 6.76E-08 9.29E-06 cellular component assembly 788 146 90.31 1.62 + 3.11E-07 3.61E-05 cellular component biogenesis 1309 270 150.02 1.80 + 1.93E-17 6.02E-15 RNA phosphodiester bond hydrolysis, endonucleolytic 22 12 2.52 4.76 + 8.58E-05 3.84E-03 RNA phosphodiester bond hydrolysis 59 26 6.76 3.85 + 2.17E-07 2.68E-05 nucleic acid phosphodiester bond hydrolysis 86 33 9.86 3.35 + 7.65E-08 1.00E-05 spliceosomal snRNP assembly 28 15 3.21 4.67 + 1.35E-05 7.89E-04 mRNA splicing, via spliceosome 184 59 21.09 2.80 + 3.50E-10 6.67E-08 mRNA processing 393 109 45.04 2.42 + 3.54E-14 9.10E-12 mRNA metabolic process 523 143 59.94 2.39 + 9.97E-18 3.27E-15 RNA splicing, via transesterification reactions with bulged 201 67 23.04 2.91 + 4.16E-12 9.11E-10 adenosine as nucleophile RNA splicing, via transesterification reactions 201 67 23.04 2.91 + 4.16E-12 8.79E-10 RNA splicing 285 86 32.66 2.63 + 4.04E-13 9.55E-11 ribonucleoprotein complex assembly 212 54 24.30 2.22 + 1.19E-06 1.05E-04 ribonucleoprotein complex subunit organization 221 57 25.33 2.25 + 4.23E-07 4.47E-05 protein-containing complex subunit organization 645 132 73.92 1.79 + 7.06E-09 1.19E-06 ribonucleoprotein complex biogenesis 532 167 60.97 2.74 + 9.26E-26 4.56E-23 cellular protein-containing complex assembly 508 110 58.22 1.89 + 9.52E-09 1.56E-06 protein-containing complex assembly 554 115 63.49 1.81 + 3.47E-08 5.39E-06 endoplasmic reticulum unfolded protein response 19 10 2.18 4.59 + 4.14E-04 1.49E-02 signal transduction 1944 155 222.80 .70 - 2.63E-06 2.10E-04 signaling 1973 155 226.13 .69 - 9.92E-07 9.32E-05 cell communication 2207 174 252.94 .69 - 2.74E-07 3.24E-05 cellular response to unfolded protein 33 18 3.78 4.76 + 1.55E-06 1.27E-04 response to unfolded protein 36 20 4.13 4.85 + 3.30E-07 3.76E-05 response to topologically incorrect protein 55 22 6.30 3.49 + 6.35E-06 4.27E-04 cellular response to topologically incorrect protein 48 20 5.50 3.64 + 1.02E-05 6.25E-04 cellular response to stress 967 162 110.83 1.46 + 1.31E-05 7.75E-04 maturation of LSU-rRNA 40 21 4.58 4.58 + 3.45E-07 3.85E-05 ribosomal large subunit biogenesis 104 37 11.92 3.10 + 6.25E-08 8.80E-06 ribosome biogenesis 440 138 50.43 2.74 + 1.89E-21 7.46E-19 rRNA processing 228 99 26.13 3.79 + 1.03E-23 4.37E-21 rRNA metabolic process 241 102 27.62 3.69 + 1.01E-23 4.58E-21 RNA secondary structure unwinding 27 14 3.09 4.52 + 3.43E-05 1.73E-03 Group II intron splicing 18 9 2.06 4.36 + 1.06E-03 3.39E-02 cleavage involved in rRNA processing 24 12 2.75 4.36 + 1.61E-04 6.48E-03 rRNA catabolic process 19 9 2.18 4.13 + 1.42E-03 4.29E-02 ncRNA catabolic process 22 10 2.52 3.97 + 9.99E-04 3.23E-02 RNA catabolic process 119 29 13.64 2.13 + 5.96E-04 2.09E-02 RNA surveillance 19 9 2.18 4.13 + 1.42E-03 4.27E-02 mitochondrial mRNA modification 45 20 5.16 3.88 + 4.79E-06 3.59E-04 mRNA modification 62 25 7.11 3.52 + 1.36E-06 1.13E-04 RNA modification 441 176 50.54 3.48 + 1.75E-37 3.46E-34 macromolecule modification 2842 406 325.72 1.25 + 1.85E-05 1.07E-03 mitochondrial RNA modification 48 22 5.50 4.00 + 1.09E-06 1.01E-04 mitochondrial RNA metabolic process 65 31 7.45 4.16 + 3.61E-09 6.27E-07 chaperone cofactor-dependent protein refolding 34 15 3.90 3.85 + 7.71E-05 3.59E-03 chaperone-mediated protein folding 60 25 6.88 3.64 + 8.41E-07 8.16E-05 'de novo' posttranslational protein folding 35 16 4.01 3.99 + 3.20E-05 1.69E-03 'de novo' protein folding 46 23 5.27 4.36 + 1.90E-07 2.39E-05 maturation of 5.8S rRNA 32 14 3.67 3.82 + 1.42E-04 5.80E-03 rRNA modification 40 17 4.58 3.71 + 3.81E-05 1.89E-03 protein import into mitochondrial matrix 29 12 3.32 3.61 + 6.24E-04 2.16E-02 protein targeting to mitochondrion 52 21 5.96 3.52 + 9.11E-06 5.79E-04 establishment of protein localization to mitochondrion 52 21 5.96 3.52 + 9.11E-06 5.67E-04 protein localization to mitochondrion 52 21 5.96 3.52 + 9.11E-06 5.73E-04 mitochondrial transport 128 30 14.67 2.04 + 8.85E-04 2.91E-02 mitochondrion organization 171 60 19.60 3.06 + 9.40E-12 1.92E-09 intracellular protein transmembrane transport 85 23 9.74 2.36 + 6.56E-04 2.23E-02 protein transmembrane transport 88 23 10.09 2.28 + 1.36E-03 4.16E-02 protein transmembrane import into intracellular organelle 53 17 6.07 2.80 + 5.88E-04 2.07E-02 protein import 133 33 15.24 2.16 + 2.57E-04 9.79E-03 mitochondrial transmembrane transport 56 17 6.42 2.65 + 1.34E-03 4.12E-02 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU- 44 18 5.04 3.57 + 3.40E-05 1.76E-03 rRNA, 5.8S rRNA, LSU-rRNA) maturation of SSU-rRNA 59 24 6.76 3.55 + 1.94E-06 1.57E-04 ribosomal small subunit biogenesis 95 32 10.89 2.94 + 1.25E-06 1.07E-04 nuclear-transcribed mRNA catabolic process, exonucleolytic 30 12 3.44 3.49 + 7.93E-04 2.65E-02 nuclear-transcribed mRNA catabolic process 90 23 10.31 2.23 + 1.51E-03 4.47E-02 cellular response to heat 65 26 7.45 3.49 + 9.49E-07 9.05E-05 response to heat 213 83 24.41 3.40 + 7.73E-18 2.69E-15 response to temperature stimulus 601 133 68.88 1.93 + 9.78E-11 1.93E-08 heat acclimation 43 17 4.93 3.45 + 7.83E-05 3.59E-03 mitochondrial gene expression 41 16 4.70 3.40 + 1.42E-04 5.84E-03 RNA methylation 64 22 7.34 3.00 + 4.26E-05 2.08E-03 macromolecule methylation 167 42 19.14 2.19 + 2.77E-05 1.52E-03 megagametogenesis 67 23 7.68 3.00 + 2.93E-05 1.59E-03 embryo sac development 136 45 15.59 2.89 + 1.79E-08 2.86E-06 gametophyte development 423 83 48.48 1.71 + 2.25E-05 1.28E-03 regulation of mRNA splicing, via spliceosome 38 13 4.36 2.98 + 1.57E-03 4.61E-02 regulation of RNA splicing 43 15 4.93 3.04 + 5.98E-04 2.08E-02 tRNA modification 72 24 8.25 2.91 + 2.94E-05 1.57E-03 tRNA processing 104 34 11.92 2.85 + 1.34E-06 1.13E-04 tRNA metabolic process 176 41 20.17 2.03 + 1.15E-04 4.94E-03 ribonucleoprotein complex export from nucleus 59 19 6.76 2.81 + 2.76E-04 1.04E-02 protein export from nucleus 64 19 7.34