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How was synteny identified:

Additional file 9: Figure S2. Syntenic relationships between the pearl millet ( Pennisetum glaucum ) linkage groups and the chromosomes of 5 other sequenced grasses. How was synteny identified:

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How was synteny identified:

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  1. Additional file 9: Figure S2. Syntenicrelationships between the pearl millet (Pennisetumglaucum) linkage groups and the chromosomes of 5 other sequenced grasses • How was synteny identified: • BLASTnsearch of the full length EST sequences of the pearl millet EST-SSR (Xipes and Xicmp) markers was done on the 5 sequenced cereal genomes. • Top hits with evalue <=E-10 were selected and their locus positions were used to identify synteny between these cereals. Notations used for marker names: Bold, underline and italic = If the pearl millet marker had BLAST hits on 4 or 5 other grass genomes Bold, underline = If the pearl millet marker had hits on 3 other grass genomes Bold = If the pearl millet marker had hits on 1 or 2 other grass genomes Normal = If the marker had no hits on other cereal genomes

  2. Oryza sativa Setariaitalica Pennisetumglaucum Sorghum bicolor Zea mays Brachypodiumdistachyon SBI-04 Bd_2 Pg_1 (inverted) SBI-05 Zm_06 Bd_3 Bd_4 SBI-09 Zm_10 Xipes0139 Xipes0098 Xipes0139 Xipes0192 Xipes0127 Xipes0098 Xipes0004 Xipes0004 Xipes0101 Xipes0101 Xicmp4010 Xipes0079 Xicmp4010 Xicmp4010 Xipes0045 Xipes0004 Xipes0101 Xicmp4010 20.4 32.7 2.8 0.7 31.1 130.3 37.3 3.7 0.8 34.5 221.5 55.1 16.5 0.0 51.2 20.8 3.1 35.2 2.0 SBI-08 Xipes0004 Xipes0127 Xipes0004 Xipes0203 Xipes0146 Xipes0045 Xipes0197 Xipes0045 6.7 15.9 41.7 33.0 Os_12 20.1 3.4 2.4 36.3 Zm_08 Si_7 Xicmp4010 9.5 Xipes0226 Xipes0226 Xipes0226 Xipes0098 36.3 Xipes0103 150.6 Xicmp3080 Xicmp3080 Xicmp3080 Xicmp3080 Xipes0017 46.0 Xctm27 16.6 87.2 4.3 3.3 Xipes0146 153.1 Xicmp3032 Xicmp3032 Xicmp3032 Xicmp3032 37.1 Os_10 Xctm12 21.4 Xicmp3017 Xicmp3017 Xicmp3017 Xicmp3017 Xipes0192 29.3 Xipes0216 Xipes0126 4.7 45.6 Xipes0226 47.0 Xipes0229 29.9 Xipes0146 Xipes0103 18.9 50.9 Xipes0103 Xipes0146 22.0 52.7 Xipes0045 59.2 Xicmp3088 44.0 Xipes0009 27.3 Xipes0126 28.5 Xipes0004 70.8 Si_3 Xipes0216 87.3 Si_1 Xipes0139 87.4 Os_05 Xipes0101 93.6 Xipes0045 94.2 Xipes0045 1.4 Xicmp3017 95.8 Xicmp3080 Xicmp3032 96.9 Xicmp3032 2.2 Xicmp3080 Xicmp3017 Xipes0226 97.2 Xipes0146 23.2 Xipes0103 100.6 Xpsmp2080 100.8 Xipes0146 102.2 Xipes0009 103.4 Xipes0126 Si_6 112.1 Xipes0197 116.2 Xipes0079 117.2 Xipes0203 118.4 Xpsmp2273 120.8 Si_8 Xipes0098 121.6 Zm_02 Xicmp4010 Xpsmp2069 122.4 Xipes0042 137.9 Xipes0017 146.6

  3. Oryza sativa Setariaitalica Pennisetumglaucum Sorghum bicolor Zea mays Brachypodiumdistachyon Pg_2 Zm_01 SBI-01 Bd_1 SBI-04 Zm_05 Bd_3 Zm_06 Bd_5 Os_02 Zm_09 Os_03 Os_10 SBI-10 Xipes0123 0.0 Xipes0152.1 Xicmp3063 Xicmp3063 Xipes0221 Xipes0221 Xipes0221 Xipes0181 Xipes0102 Xipes0003 Xipes0162 Xipes0003 Xipes0003 Xipes0221 Xipes0162 Xipes0123 Xipes0152.1 Xicmp3056 74.0 1.8 1.7 0.2 0.3 0.4 15.7 0.2 5.4 19.5 17.6 11.5 0.1 3.2 6.3 74.0 0.5 Xipes0152.1 Xipes0163 Xipes0181 Xipes0027.2 Xipes0118 Xipes0210 Xipes0210 Xicmp3063 228.0 13.0 19.0 9.3 3.5 1.3 25.8 7.2 Xicmp3056 29.4 Xipes0162 40.6 Xicmp3056 Xipes0163 Xipes0218 Xipes0218 Xipes0221 Xipes0181 234.2 19.3 66.4 10.2 2.4 9.5 Xipes0210 31.5 Xicmp3063 18.5 Xicmp3063 Xipes0210 Xipes0118 295.1 Xipes0118 Xipes0007 19.6 70.0 11.7 15.9 Xipes0163 Xipes0162 Xicmp3063 31.7 54.5 36.0 Xicmp3056 21.9 Xipes0163 19.4 Xipes0152.1 55.0 Xipes0210 19.7 Si_9 Xctm03 44.5 Xipes0117 20.8 Xpsmp(sts)322 47.7 Xicmp3056 22.3 Xpsmp2237 48.6 Xipes0160 30.4 Xipes0181 52.1 Xipes0152.1 46.5 Xipes0007 56.2 Xpsmp2088 58.9 Xpsmp2072 61.9 Xipes0162 69.4 Xipes0163 77.0 Xipes0117 85.3 Xicmp3056 86.8 Xipes0003 100.1 Si_4 Xipes0160 102.1 Xpsmp2013 104.9 Xpsmp2231 Xpsmp2206 106.4 Xpsmp2232.1 107.5 Xipes0027.2 109.3 Xctm21 110.9 Xpsmp2059 121.1 Si_1 Xipes0236 124.3 Xipes0152.1 130.6 Xipes0210 136.0 Xipes0218 137.9 Xipes0118 155.1 Xpsmp2089 173.4 Xipes0221 Si_3 175.3 Xipes0102 192.6

  4. Oryza sativa Setariaitalica Pennisetumglaucum Sorghum bicolor Zea mays Brachypodiumdistachyon Pg_A (previously unassigned group) Pg_3 (inverted) Zm_05 Zm_03 SBI-04 Os_01 Os_02 SBI-03 Bd_1 Bd_1 Zm_04 Os_02 SBI-04 Bd_2 Si_1 Zm_05 Bd_3 Xipes0220.1 Xipes0185 Xipes0185 Xipes0185 Xicmp3035 Xipes0110 Xipes0110 Xipes0110 Xipes0110 Xipes0014 Xicmp3035 Xicmp3035 Xicmp3035 Xipes0180 Xipes0185 Xipes0095 Xipes0110 Xicmp4014 Xicmp3035 Xipes0185 5.8 2.2 67.7 2.6 5.2 215.8 36.5 0.0 74.8 0.0 29.2 165.1 1.1 50.4 4.9 38.3 55.4 167.2 33.9 1.5 Xipes0161 Xipes0180 Xipes0180 59.0 56.7 171.9 Xipes0180 42.3 Xipes0180 31.3 Xipes0161 66.3 Xipes0110 Xipes0161 1.7 46.7 Xipes0180 Xicmp4014 18.9 35.7 Xicmp4014 66.6 Xicmp4014 47.0 Xipes0142 22.6 Xipes0213 25.7 Si_1 Xicmp3035 29.0 Xpsmp2249 32.2 Xipes0166 41.2 Xpsmp2070 44.5 Xpsmp2227 45.6 Xipes0233 47.7 Xctm10 51.0 Xipes0185 56.1 Si_7 Xpsmp2229.3 58.4 Xpsmp2214 60.1 Xipes0095 70.8 Si_3 Xipes0161 82.6 Xicmp4014 94.4

  5. Oryza sativa Setariaitalica Pennisetumglaucum Sorghum bicolor Zea mays Brachypodiumdistachyon Si_5 Os_01 SBI-05 Zm_01 Pg_4 Bd_2 Os_08 SBI-07 Bd_3 Zm_02 SBI-08 Zm_06 SBI-09 Zm_10 Xipes0208 Xipes0208 Xipes0066 Xpsmp2086 Xipes0174 Xipes0174 Xipes0225 Xipes0225 Xipes0225 Xipes0066 Xipes0208 Xipes0174 Xipes0225 Xipes0129 Xipes0208 Xipes0186 Xipes0066 44.3 39.7 0.0 1.3 0.7 12.1 55.0 3.3 0.5 25.9 170.2 52.0 217.7 51.6 0.3 44.5 12.3 Xipes0186 Xipes0076 Xipes0076 Xicmp3029 Xipes0186 17.7 13.3 5.4 190.6 3.8 Xipes0208 8.8 Xipes0076 Xipes0225 9.2 10.8 Xipes0208 Xicmp3029 Xicmp3029 294.9 42.7 62.2 Xicmp3029 Xipes0076 26.0 12.9 Xipes0219 39.6 Xicmp3029 Xipes0174 40.4 32.7 Xpsmp2081.1 40.3 Si_3 Xpsmp2076 42.1 Xipes0129 46.5 Xipes0225 48.8 Xpsmp2085 52.8 Xipes0186 58.3 Si_6 Xipes0076 62.5 Xpsmp(sts)305) 69.4 Xicmp3029 70.4 Xipes0066 71.4 Xipes0219 72.8 Xipes0114 75.8 Xpsmp2084 77.4 Xpsmp2008 87.4 Si_9

  6. Oryza sativa Setariaitalica Pennisetumglaucum Sorghum bicolor Zea mays Brachypodiumdistachyon Si_3 Si_4 Si_9 Xipes0191 Xipes0157 Xipes0152.2 46.5 0.6 34.4 Xipes0214 50.8 Xicmp3027 43.4 Xipes0175 52.4 Xipes0093 44.5 Xipes0089 63.1 Xipes0223 65.5 Zm_01 Os_03 SBI-01 Pg_5 Bd_1 Zm_09 Xipes0152.2 Xipes0152.2 Xipes0220.2 Xipes0223 Xipes0175 Xipes0214 0.6 55.0 13.0 52.7 0.0 124.6 Xipes0089 Xipes0214 2.1 58.8 Xipes0191 8.9 Xipes0175 Xipes0175 11.8 60.3 Xipes0214 27.5 Xipes0089 Xipes0214 70.9 13.3 Xipes0152.2 Xipes0223 19.5 72.9 Xipes0152.2 74.0 Xipes0089 147.5 Xpsmp2274 28.9 Xipes0157 42.1 Xicmp3027 43.7 Xipes0230 58.0 Xipes0175 63.0 Xipes0093 62.2 Xpsmp2219 66.8 Xipes0089 72.7 Xipes0152.2 73.5 Xipes0223 74.0 Xpsmp2064 77.0 Xipes0214 80.1 Xipes0175 81.8 Xipes0217 84.1 Xpsmp2078 87.1 Xpsmp2229.1 96.1 Xpsmp2261 99.4 Xpsmp2233 102.4 Xpsmp2276 102.9 Xpsmp2277 104.0 Xpsmp2208 104.5 Xipes0089 113.5 Xipes0223 134.5

  7. Pg_6 (inverted) Xipes0224 0.0 Xipes0019 15.1 Xipes0156 21.2 Xipes0151 23.8 Xipes0141 34.5 Xipes0144 35.0 Xipes0109 36.2 Oryza sativa Setariaitalica Pennisetumglaucum Sorghum bicolor Zea mays Brachypodiumdistachyon Si_1 Si_7 Xipes0027.2 Xipes0224 21.7 3.5 Xipes0011 38.7 Xipes0189 43.2 SBI-02 Os_01 Bd_2 Zm_03 Os_04 SBI-03 Bd_4 Si_5 Os_11 SBI-05 Bd_5 Zm_04 SBI-06 Zm_06 Xipes0052 47.4 Xpsmp2213 65.7 Xipes0087 Xipes0176 Xicmp3058 Xicmp3058 Xipes0224 Xipes0227 Xipes0144 Xipes0144 Xipes0144 Xipes0176 Xipes0227 Xipes0227 Xipes0227 Xipes0224 Xipes0224 98.0 1.2 1.1 22.2 20.7 31.7 17.6 3.2 20.6 44.5 76.5 74.5 0.1 1.2 0.2 Xpsmp2270.1 66.6 Xicmp3058 Xipes0011 Xipes0087 8.2 0.4 36.0 Xicmp3050 10.7 Xipes0224 24.6 Xipes0147 67.5 Xicmp3050 Xicmp3086 13.6 2.1 Xicmp3058 67.9 Xipes0227 Xipes0085 51.5 Xpsmp2081.2 70.1 Xicmp3050 2.5 Xipes0085 35.0 Xipes0207 73.5 Xipes0167 4.8 Xipes0071 59.3 Xipes0176 38.0 Xicmp3002 Xipes0227 169.1 75.4 Xipes0087 5.1 Xipes0085 64.7 Xpsmp2275 Xipes0085 75.8 188.6 Xicmp3058 7.3 Xipes0176 67.3 Xpsmp2255 Xipes0071 77.2 207.6 Xipes0147 11.1 Xicmp3002 69.4 Xpsmp2248 80.8 Xipes0071 38.0 Xicmp3050 83.8 Xipes0085 44.9 Xipes0027.2 85.2 Xipes0176 47.9 Xipes0087 86.1 Xicmp3002 50.3 Xipes0167 86.5 Xipes0200 52.2 Xicmp3086 87.1 Xipes0035 87.9 Xipes0071 88.2 Xipes0085 89.0 Xipes0176 89.6 Xicmp3002 91.2 Xipes0200 96.1 Xicmp3038 113.7 Zm_02

  8. Oryza sativa Setariaitalica Pennisetumglaucum Sorghum bicolor Zea mays Brachypodiumdistachyon Pg_7 (inverted) Zm_02 Os_07 Bd_1 Si_2 Os_09 Bd_4 Zm_07 Si_9 SBI-02 SBI-09 Xipes0206 Xipes0206 Xipes0198 Xipes0082 Xctm08 Xipes0198 Xipes0198 Xipes0082 Xipes0026 Xipes0082 Xipes0026 162.0 14.4 29.4 0.0 6.4 43.5 23.6 13.1 66.4 5.6 14.5 Xpsmp2236 Xipes0097 Xipes0198 4.6 13.1 20.9 Xpsmp2203 Xipes0198 6.6 19.0 Xipes0154 8.1 Xipes0145 Xipes0145 Xipes0145 59.1 107.5 34.7 Xpsmp2087 10.4 Xipes0195 Xipes0195 71.4 49.7 Xipes0082 12.5 Xipes0206 76.6 Xipes0179 52.9 Xipes0082 Xipes0206 53.5 167.2 Xpsmp2266 15.0 Xicmp3092 77.1 Xipes0105 54.7 Xpsmp2210 15.5 Xipes0206 55.0 Xipes0198 16.1 Xicmp3092 55.5 Xipes0026 17.0 Xpsmp2263.1 17.4 Xipes0097 21.9 Xipes0145 23.1 Xpsmp2063 24.5 Xipes0195 25.5 Xpsmp2074 36.4 Xipes0179 40.1 Xipes0024 48.9 Xpsmp2224 54.3 Xipes0205 64.8 Xpsmp2040 85.0 Xipes0153 99.7 Xipes0105 101.0 Xipes0015 108.1 Xipes0206 108.8 Xicmp3092 121.5 Xipes0096 130.0

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