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Table 2 Genes encoding carotenoid biosynthetic enzymes, chlorophyll binding proteins and photosystem proteins

From: Transcriptome analysis of ectopic chloroplast development in green curd cauliflower (Brassica oleracea L. var. botrytis)

  RPKM green/white   Top hit  
unigene ID white green ratio p value ID description* e value
Carotenoid biosynthesis        
PP038070 0.3 7 23.3333 0 AT4G25700.1 CAROTENE BETA-RING HYDROXYLASE 8e-093
PP043130 0.3 4.2 14 0 AT4G25700.1 CAROTENE BETA-RING HYDROXYLASE 6e-036
PP013262 0.7 3.5 5 5.64E-06 AT3G21500.2 1-DEOXY-D-XYLULOSE-5-PHOSPHATE SYNTHASE 1e-032
PP011276 1.1 4.3 3.90909 2.88E-06 AT5G67030.1 ZEAXANTHIN EPOXIDASE 1e-034
PP088927 5.4 18.9 3.5 0 AT4G15560.1 1-DEOXY-D-XYLULOSE-5-PHOSPHATE SYNTHASE 1e-054
Chlorophyll binding        
PP019996 0.2 36.9 184.5 0 AT1G15820.1 LHCB6 8e-042
PP013404 1.1 100.8 91.6364 0 AT2G34430.1 LHCB1.4 4e-042
PP042072 0.2 12.1 60.5 0 AT1G29930.1 LHCB1.5 4e-047
PP032956 2.5 140.7 56.28 0 AT2G34430.1 LHCB1.4 5e-112
PP036244 0.5 15.5 31 0 AT3G54890.1 LHCA1 1e-131
PP026927 1 26.9 26.9 0 AT3G27690.1 LHCB2.3 4e-059
PP032648 0.5 12 24 0 AT2G34430.1 LHCB1.4 3e-144
PP034454 1.2 25.7 21.4167 0 AT3G27690.1 LHCB2.3 3e-096
PP014055 4.5 90.2 20.0444 0 AT1G29930.1 LHCB1.5 5e-120
PP022096 1.8 34.9 19.3889 0 AT3G54890.1 LHCA1 3e-043
PP016518 5.2 80.2 15.4231 0 AT1G61520.1 LHCA3 1e-096
PP036291 5.6 85.6 15.2857 0 AT3G61470.1 LHCA2 6e-103
PP002791 0.7 10.4 14.8571 0 AT1G15820.1 LHCB6 6e-026
PP060891 0 13.8 13.8 0 AT3G54890.1 LHCA1 3e-037
PP032891 0.7 9.4 13.4286 0 AT5G01530.1 LHCB4.1 2e-039
PP033574 1.4 18.1 12.9286 0 AT3G54890.1 LHCA1 9e-121
PP043522 2.1 25.6 12.1905 0 AT1G61520.1 LHCA3 5e-036
PP004292 6.9 83.9 12.1594 0 AT3G61470.1 LHCA2 4e-132
PP041756 1.1 13.3 12.0909 0 AT2G34430.1 LHCB1.4 6e-023
PP004529 21.5 259.4 12.0651 0 AT1G15820.1 LHCB6 1e-128
PP003367 14.8 176.1 11.8986 0 AT3G61470.1 LHCA2 7e-125
PP019899 28.5 328.4 11.5228 0 AT1G29930.1 LHCB1.5 2e-146
PP020291 40.5 445.8 11.0074 0 AT2G34430.1 LHCB1.4 1e-143
PP055138 0.7 7.6 10.8571 0 AT3G27690.1 LHCB2.3 9e-048
PP005460 2.1 21.5 10.2381 0 AT3G54890.2 LHCA1 9e-066
PP020373 0 9.9 9.9 0 AT3G08940.2 LHCB4.2 3e-025
PP021872 12.4 115 9.27419 0 AT3G08940.2 LHCB4.2 1e-144
PP034445 0.9 8.3 9.22222 0 AT3G27690.1 LHCB2.3 3e-099
PP003971 13.1 117.1 8.93893 0 AT3G54890.1 LHCA1 1e-135
PP034046 1.1 9.2 8.36364 0 AT5G54270.1 LHCB3 4e-153
PP033656 4 31.3 7.825 0 AT5G54270.1 LHCB3 1e-028
PP029126 6 46.1 7.68333 0 AT1G61520.1 LHCA3 3e-077
PP005284 6.7 47.7 7.1194 0 AT1G29930.1 LHCB1.5 2e-105
PP021031 36.8 258.7 7.02989 0 AT2G34430.1 LHCB1.4 1e-061
PP016372 2.4 16.7 6.95833 0 AT2G34430.1 LHCB1.4 7e-020
PP022981 6.9 47 6.81159 0 AT2G34430.1 LHCB1.4 6e-060
PP021682 14.1 91.5 6.48936 0 AT1G61520.1 LHCA3 2e-130
PP003968 50.6 320 6.32411 0 AT1G29930.1 LHCB1.5 9e-151
PP020586 22.7 135.7 5.97797 0 AT1G61520.1 LHCA3 3e-129
PP005425 5.4 26.2 4.85185 0 AT1G29910.1 LHCB1.5 1e-051
PP010147 48.6 226.7 4.66461 0 AT1G15820.1 LHCB6 5e-123
PP003504 66.3 305.1 4.60181 0 AT3G47470.1 LHCA4 8e-131
PP004840 40.6 181.7 4.47537 0 AT2G34430.1 LHCB1.4 4e-115
PP020865 14.6 61.6 4.21918 0 AT2G34430.1 LHCB1.4 2e-019
PP032222 8.6 34.2 3.97674 0 AT4G10340.1 LHCB5 7e-098
PP021166 104.1 391.8 3.76369 0 AT2G34430.1 LHCB1.4 6e-150
PP005062 24.4 90.1 3.69262 0 AT4G10340.1 LHCB5 2e-128
PP033260 4.3 15.8 3.67442 0 AT3G27690.1 LHCB2.3 3e-140
PP032950 102.9 376.3 3.65695 0 AT2G34430.1 LHCB1.4 5e-150
PP022979 10 33 3.3 0 AT1G44575.1 NPQ4 6e-068
PP001298 3.7 12 3.24324 0 AT5G01530.1 LHCB4.1 3e-031
PP021716 24.4 78.8 3.22951 0 AT4G10340.1 LHCB5 1e-133
PP003549 24.1 74.3 3.08299 0 AT1G44575.1 NPQ4 1e-107
Photosystem proteins        
PP008642 0.2 25.8 129 0 AT3G21055.1 PSBTN (PHOTOSYSTEM II SUBUNIT T) 5e-027
PP000591 0.5 54.9 109.8 0 AT1G03130.1 PSAD-2 (PHOTOSYSTEM I SUBUNIT D-2) 1e-053
PP006879 0.1 4.7 47 0 P11594 OXYGEN-EVOLVING ENHANCER PROTEIN 2 2e-012
PP004388 1.1 45.3 41.1818 0 AT1G55670.1 PSAG (PHOTOSYSTEM I SUBUNIT G) 1e-066
PP016988 0.2 4.9 24.5 0 AT2G30570.1 PSBW (PHOTOSYSTEM II REACTION CENTER W) 5e-025
PP018045 7.8 174.6 22.3846 0 AT1G08380.1 PSAO (PHOTOSYSTEM I SUBUNIT O) 8e-070
PP036218 0.3 5 16.6667 0 ATCG00280.1 CP43 SUBUNIT OF THE PHOTOSYSTEM II REACTION CENTER 2.00E-171
PP032734 1.1 17.4 15.8182 0 AT1G08380.1 PSAO (PHOTOSYSTEM I SUBUNIT O) 1e-065
PP020420 14.5 221.7 15.2897 0 AT1G06680.1 PSBP-1 (PHOTOSYSTEM II SUBUNIT P-1) 9e-122
PP018042 0 14.7 14.7 0 AT1G52230.1 PSAH2 (PHOTOSYSTEM I SUBUNIT H2) 2e-019
PP004848 3.4 49.6 14.5882 0 AT1G06680.1 PSBP-1 (PHOTOSYSTEM II SUBUNIT P-1) 3e-118
PP014192 7.3 103.1 14.1233 0 AT3G21055.1 PSBTN (PHOTOSYSTEM II SUBUNIT T) 6e-036
PP021663 4.9 63.5 12.9592 0 AT2G06520.1 PSBX (PHOTOSYSTEM II SUBUNIT X) 1e-038
PP069357 0.7 8.2 11.7143 0 AT3G21055.1 PSBTN (PHOTOSYSTEM II SUBUNIT T) 1e-035
PP005143 6.3 68.6 10.8889 0 AT4G12800.1 PSAL (PHOTOSYSTEM I SUBUNIT L) 5e-096
PP016409 7.1 60.7 8.5493 0 AT1G08380.1 PSAO (PHOTOSYSTEM I SUBUNIT O) 2e-065
PP033894 5.6 44.7 7.98214 0 AT1G03600.1 PHOTOSYSTEM II FAMILY PROTEIN 2e-051
PP014928 10.7 84 7.85047 0 AT1G30380.1 PSAK (PHOTOSYSTEM I SUBUNIT K) 5e-057
PP017397 10.6 76.7 7.23585 0 AT2G06520.1 PSBX (PHOTOSYSTEM II SUBUNIT X) 2e-018
PP060944 0 7.1 7.1 0 AT1G52230.1 PSAH2 (PHOTOSYSTEM I SUBUNIT H2) 4e-016
PP017005 0 6.6 6.6 0 AT1G79040.1 PSBR (PHOTOSYSTEM II SUBUNIT R) 2e-034
PP021626 0 6.5 6.5 0 AT1G52230.1 PSAH2 (PHOTOSYSTEM I SUBUNIT H2) 1e-035
PP000042 7.8 48.3 6.19231 0 AT1G52230.1 PSAH2 (PHOTOSYSTEM I SUBUNIT H2) 2e-056
PP022192 25.2 130.2 5.16667 0 AT3G50820.1 PSBO2 (PHOTOSYSTEM II SUBUNIT O-2) 4e-176
PP032949 6.7 33.7 5.02985 0 AT1G79040.1 PSBR (PHOTOSYSTEM II SUBUNIT R) 2e-060
PP032493 5.2 25.1 4.82692 0 AT1G52230.1 PSAH2 (PHOTOSYSTEM I SUBUNIT H2) 2e-056
PP033323 21.5 100.9 4.69302 0 AT1G79040.1 PSBR (PHOTOSYSTEM II SUBUNIT R) 4e-061
PP033241 6 27.1 4.51667 0 AT4G03280.1 PETC (PHOTOSYNTHETIC ELECTRON TRANSFER C) 3e-107
PP033302 7.4 32.5 4.39189 0 AT1G79040.1 PSBR (PHOTOSYSTEM II SUBUNIT R) 3e-064
PP005186 48.6 205.7 4.23251 0 AT1G06680.1 PSBP-1 (PHOTOSYSTEM II SUBUNIT P-1) 7e-116
PP016053 22.9 96.6 4.21834 0 AT2G30570.1 PSBW (PHOTOSYSTEM II REACTION CENTER W) 3e-042
PP022547 5.8 23.8 4.10345 0 AT2G06520.1 PSBX (PHOTOSYSTEM II SUBUNIT X) 3e-018
PP012172 7.3 29.7 4.06849 0 AT1G03600.1 PHOTOSYSTEM II FAMILY PROTEIN 6e-066
PP000003 17 68.8 4.04706 0 AT1G55670.1 PSAG (PHOTOSYSTEM I SUBUNIT G) 8e-067
PP033216 12.2 47.9 3.92623 0 AT1G79040.1 PSBR (PHOTOSYSTEM II SUBUNIT R) 2e-054
PP041363 2 7.7 3.85 0 NP_174418 PSAF (PHOTOSYSTEM I SUBUNIT F) 4e-009
PP012010 26.9 95.3 3.54275 0 AT4G12800.1 PSAL (PHOTOSYSTEM I SUBUNIT L) 5e-101
PP033278 11.6 40.2 3.46552 0 AT1G79040.1 PSBR (PHOTOSYSTEM II SUBUNIT R) 6e-044
PP033227 10.1 33.6 3.32673 0 AT1G52220.1 PSI-P (PHOTOSYSTEM I P SUBUNIT) 4e-042
PP005055 24 76.9 3.20417 0 AT1G30380.1 PSAK (PHOTOSYSTEM I SUBUNIT K) 3e-055
PP039593 2.1 6.5 3.09524 0 AT1G31330.1 PSAF (PHOTOSYSTEM I SUBUNIT F) 9e-036
PP013176 7 21.5 3.07143 0 AT2G46820.1 PSI-P (PHOTOSYSTEM I P SUBUNIT) 2e-044
  1. *That the top hits of several cauliflower unigenes correspond to one gene in Arabidopsis could be due to paralogs or alternative splicing of genes in cauliflower.