Doc-Alignment

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Cucurbitales genomes. We used V.vinifera as a reference, and by comparing homologous gene locus maps and Ks values between V.vinifera and other Cucurbitales, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We created a hierarchical lists of homologous genes using V.vinifera as a reference.
  The relevant gene ids can be obtained from the Cucurbitales blast and match under the Tools module. This link is Cucurbitales blast and match.

Orthogroup analysis platform
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Select Vvi1 Blo1 Blo2 Bda1 Bda2 Bpe1 Bpe2 Bma1 Bma2 Cmo1 Cmo2 Cma1 Cma2 Car1 Car2 Sed1 Cpe1 Cpe2 Bhi1 Tan1 Cmetu1 Lac1 Hepe1 Mch1 Lcy1 Cla1 Cam1 Cec1 Cco1 Clacu1 Cmu1 Cre1 Cone1 Cone2 Cone3 Cone4 Lsi1 Csa1 Chy1 Cme1 Blo3 Blo4 Bda3 Bda4 Bpe3 Bpe4 Bma3 Bma4 Sed2 Cmo3 Cmo4 Cma3 Cma4 Car3 Car4 Cpe3 Cpe4 Bhi2 Tan2 Cmetu2 Lac2 Hepe2 Mch2 Lcy2 Cla2 Cam2 Cec2 Cco2 Clacu2 Cmu2 Cre2 Lsi2 Csa2 Chy2 Cme2
Vvi2g32 . . . . . . . Bma14g00601 . . Cma02g01429 Cma15g01248 Car02g01197 Car15g01126 . . Cpe05g00357 . . . . . . . . . . . . . . . . . . . Csa05g00251 Chy09g01256 . . . . . . Bpe11g00667 . . . Cmo02g01463 Cmo15g01314 . . . . . Cpe13g00136 Bhi12g00300 . . . . . Lcy12g1620 Cla01g00234 Cam01g0240 Cec01g0232 Cco01g0247 Clacu01g0238 Cmu01g0230 Cre09g2280 Lsi09g00226 . . Cme09g01791
Vvi2g33 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g34 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g35 Blo02g01118 Blo03g00220 Bda06g00117 Bda08g00506 Bpe05g00656 Bpe07g00101 . Bma14g00600 . Cmo16g00634 Cma02g01428 Cma15g01250 Car02g01196 Car15g01127 . Cpe14g00495 Cpe05g00358 . . . . . . . Cla07g00759 Cam07g0815 Cec07g0875 Cco07g0850 Clacu07g0793 Cmu07g0801 Cre07g1155 Cone8ag0280 Cone12ag0286 Cone6ag0806 Cone9ag0803 . Csa05g00250 . Cme07g01619 . . . . . Bpe11g00668 Bma05g00828 Bma12g00070 . Cmo02g01462 Cmo15g01315 . Cma16g00584 . . . Cpe13g00135 Bhi12g00301 . . . . . Lcy12g1619 Cla01g00233 Cam01g0239 Cec01g0231 Cco01g0246 Clacu01g0237 Cmu01g0229 Cre09g2281 Lsi09g00225 Csa04g00606 Chy07g01206 Cme09g01792
Vvi2g36 . . . . . . . . . . Cma02g01427 . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00249 Chy09g01258 . . . . . . . . . . Cmo02g01461 . . . . . . . Bhi12g00303 . . . . . Lcy12g1618 Cla01g00232 . . . . . . Lsi09g00224 . . Cme09g01793
Vvi2g37 Blo02g01119 Blo03g00221 Bda06g00118 . Bpe05g00657 Bpe07g00100 . . . Cmo16g00633 . . . . . Cpe14g00494 . . . . . . . . Cla07g00758 Cam07g0813 Cec07g0871 Cco07g0848 Clacu07g0791 Cmu07g0798 Cre07g1154 Cone8ag0279 Cone12ag0285 . Cone9ag0804 . . . Cme07g01618 . . . . . . Bma05g00830 . . . . . Cma16g00583 . . . . . . . . . . . . . . . . . . . Csa04g00607 Chy07g01205 .
Vvi2g38 . . . . . . . Bma14g00599 . . . Cma15g01251 . Car15g01128 . . . . . . . . . . . . . . . . . . . Cone6ag0808 Cone9ag0805 . Csa05g00247 Chy09g01259 . . . . . . Bpe11g00669 . . . . Cmo15g01316 . . . . . Cpe13g00134 Bhi12g00305 . . . . . . Cla01g00231 . Cec01g0229 Cco01g0243 Clacu01g0234 Cmu01g0227 Cre09g2283 Lsi09g00223 . . Cme09g01794
Vvi2g39 . . . . . . . . . . . Cma15g01252 . Car15g01129 . . . . . . . . . . Cla07g00757 Cam07g0809 Cec07g0870 Cco07g0847 Clacu07g0790 Cmu07g0797 Cre07g1153 . . Cone6ag0809 . . Csa05g00244 Chy09g01260 Cme07g01617 . . . . . . . . . . Cmo15g01127 Cma06g01085 . . . . Cpe13g00133 Bhi12g00309 . . . Hepe06g1514 . Lcy12g1614 Cla01g00230 Cam01g0236 Cec01g0228 Cco01g0242 Clacu01g0233 Cmu01g0226 Cre09g2284 Lsi09g00219 Csa04g00608 Chy07g01204 Cme09g01797
Vvi2g40 Blo02g01120 Blo03g00222 Bda06g00119 . . Bpe07g00098 . . . Cmo16g00632 . . . . . Cpe14g00493 . . . . . . . . Cla07g00752 Cam07g0805 Cec07g0867 Cco07g0843 Clacu07g0787 Cmu07g0794 Cre07g1146 . . . Cone9ag0808 . . . Cme07g01616 . . . . . . . Bma12g00069 . . . . Cma16g00582 . . . . . . . . . . . . . . . . . . . Csa04g00609 Chy07g01202 .
Vvi2g41 Blo02g01121 . . Bda08g00505 Bpe05g00658 . . . . . . . . . . . . . . . . . . . Cla07g00750 Cam07g0804 Cec07g0866 Cco07g0841 Clacu07g0784 Cmu07g0792 Cre07g1144 . . Cone6ag0810 Cone9ag0809 . . . Cme07g01615 . . . . . . Bma05g00831 . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00610 Chy07g01201 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 1857534 1858650 - Bda023312.2 Bda06g00117 117
6 1862145 1863308 + Bda023313.1 Bda06g00118 118
6 1865671 1867070 - Bda023314.1 Bda06g00119 119
8 5126206 5127992 + Bda024956.1 Bda08g00505 505
8 5141854 5143021 + Bda024958.1 Bda08g00506 506
12 8633444 8638168 - XM_039051223.1 Bhi12g00300 300
12 8641042 8642779 - XM_039051227.1 Bhi12g00301 301
12 8776981 8779210 - XM_039020193.1 Bhi12g00303 303
12 8877099 8884263 + XM_039020051.1 Bhi12g00305 305
12 8986907 8987762 + XM_039019813.1 Bhi12g00309 309
2 42355535 42359104 - BLOR10848 Blo02g01118 1118
2 42359206 42360363 + BLOR10849 Blo02g01119 1119
2 42421193 42422825 - BLOR10850 Blo02g01120 1120
2 42433588 42435351 - BLOR10851 Blo02g01121 1121
3 4974121 4974992 - BLOR11401 Blo03g00220 220
3 4977070 4978425 + BLOR11402 Blo03g00221 221
3 5036384 5042946 - BLOR11403 Blo03g00222 222
5 45657172 45658316 - Bma021937.1 Bma05g00828 828
5 45688591 45689751 + Bma021940.1 Bma05g00830 830
5 45691622 45693396 - Bma021941.1 Bma05g00831 831
12 1254281 1256055 + Bma030490 Bma12g00069 69
12 1262723 1263749 + Bma006940.1 Bma12g00070 70
14 6499290 6505021 - Bma011036.1 Bma14g00599 599
14 6516049 6517299 + Bma011037.1 Bma14g00600 600
14 6518582 6523974 + Bma011038.1 Bma14g00601 601
5 20319273 20320251 - Bpe025821 Bpe05g00656 656
5 20323573 20324733 + Bpe018071.2 Bpe05g00657 657
5 20326822 20328580 - Bpe025822 Bpe05g00658 658
7 718823 720891 + Bpe020912.1 Bpe07g00098 98
7 725636 726799 - Bpe020914.1 Bpe07g00100 100
7 730312 731241 + Bpe020915.1 Bpe07g00101 101
11 5124719 5127554 - Bpe004024.1 Bpe11g00667 667
11 5128830 5130223 - Bpe004025.1 Bpe11g00668 668
11 5134809 5140316 + Bpe004026.1 Bpe11g00669 669
1 2652091 2678690 - CaPI482276_01g002360.1 Cam01g0236 236
1 2709826 2711263 + CaPI482276_01g002390.1 Cam01g0239 239
1 2714680 2718746 + CaPI482276_01g002400.1 Cam01g0240 240
7 20243171 20247586 + CaPI482276_07g008040.1 Cam07g0804 804
7 20310370 20312780 + CaPI482276_07g008050.1 Cam07g0805 805
7 20425585 20426397 - CaPI482276_07g008090.1 Cam07g0809 809
7 20452200 20453405 - CaPI482276_07g008130.1 Cam07g0813 813
7 20513179 20515075 + CaPI482276_07g008150.1 Cam07g0815 815
2 8142255 8146091 + Carg02552-RA Car02g01196 1196
2 8146811 8150426 + Carg02551-RA Car02g01197 1197
15 8878926 8883868 - Carg16616-RA Car15g01126 1126
15 8885711 8887657 - Carg16615-RA Car15g01127 1127
15 8888612 8895104 + Carg16614-RA Car15g01128 1128
15 8897582 8898050 + Carg16613-RA Car15g01129 1129
1 2286355 2287298 - CcPI632755_01g002420.1 Cco01g0242 242
1 2291879 2302384 - CcPI632755_01g002430.1 Cco01g0243 243
1 2333853 2335310 + CcPI632755_01g002460.1 Cco01g0246 246
1 2338710 2342804 + CcPI632755_01g002470.1 Cco01g0247 247
7 19470905 19475330 + CcPI632755_07g008410.1 Cco07g0841 841
7 19535584 19537962 + CcPI632755_07g008430.1 Cco07g0843 843
7 19686963 19687797 - CcPI632755_07g008470.1 Cco07g0847 847
7 19715351 19716556 - CcPI632755_07g008480.1 Cco07g0848 848
7 19777234 19779079 + CcPI632755_07g008500.1 Cco07g0850 850
1 2254104 2263210 - CePI673135_01g002280.1 Cec01g0228 228
1 2269734 2276281 - CePI673135_01g002290.1 Cec01g0229 229
1 2311728 2313175 + CePI673135_01g002310.1 Cec01g0231 231
1 2316600 2320699 + CePI673135_01g002320.1 Cec01g0232 232
7 21345329 21349726 + CePI673135_07g008660.1 Cec07g0866 866
7 21439709 21442104 + CePI673135_07g008670.1 Cec07g0867 867
7 21602326 21603107 - CePI673135_07g008700.1 Cec07g0870 870
7 21615813 21617018 - CePI673135_07g008710.1 Cec07g0871 871
7 21680997 21682859 + CePI673135_07g008750.1 Cec07g0875 875
7 16861531 16865854 + Chy7G140310.1 Chy07g01201 1201
7 16877750 16879734 + Chy7G140320.1 Chy07g01202 1202
7 16884910 16885666 - Chy7G140340.1 Chy07g01204 1204
7 16890098 16891315 - Chy7G140350.1 Chy07g01205 1205
7 16897095 16898980 + Chy7G140360.1 Chy07g01206 1206
9 14581312 14584697 + Chy9G169720.1 Chy09g01256 1256
9 14601526 14603727 - Chy9G169740.1 Chy09g01258 1258
9 14615969 14628231 + Chy9G169750.1 Chy09g01259 1259
9 14631817 14636395 + Chy9G169760.1 Chy09g01260 1260
1 2282745 2283691 - ClG42_01g0023300.10 Clacu01g0233 233
1 2289843 2296899 - ClG42_01g0023400.10 Clacu01g0234 234
1 2326805 2328251 + ClG42_01g0023700.10 Clacu01g0237 237
1 2331653 2335729 + ClG42_01g0023800.10 Clacu01g0238 238
7 19894648 19899050 + ClG42_07g0078400.10 Clacu07g0784 784
7 19975587 19977958 + ClG42_07g0078700.10 Clacu07g0787 787
7 20144440 20145223 - ClG42_07g0079000.10 Clacu07g0790 790
7 20162535 20163740 - ClG42_07g0079100.10 Clacu07g0791 791
7 20227890 20229787 + ClG42_07g0079300.10 Clacu07g0793 793
1 2302272 2320796 - ClCG01G002360.1 Cla01g00230 230
1 2327120 2334098 - ClCG01G002370.1 Cla01g00231 231
1 2357995 2360794 + ClCG01G002380.2 Cla01g00232 232
1 2366429 2368338 + ClCG01G002390.2 Cla01g00233 233
1 2370951 2375937 + ClCG01G002400.2 Cla01g00234 234
7 20996082 21000768 + ClCG07G007880.1 Cla07g00750 750
7 21080969 21083340 + ClCG07G007900.1 Cla07g00752 752
7 21250422 21251205 - ClCG07G007940.2 Cla07g00757 757
7 21268520 21269725 - ClCG07G007950.1 Cla07g00758 758
7 21330981 21340047 + ClCG07G007960.1 Cla07g00759 759
2 8234485 8235888 + CmaCh02G014270.1 Cma02g01427 1427
2 8236190 8237921 + CmaCh02G014280.1 Cma02g01428 1428
2 8238896 8243079 + CmaCh02G014290.1 Cma02g01429 1429
6 7304618 7305817 + CmaCh06G010850.1 Cma06g01085 1085
15 7927658 7932191 - CmaCh15G012480.1 Cma15g01248 1248
15 7933995 7936197 - CmaCh15G012500.1 Cma15g01250 1250
15 7936689 7943346 + CmaCh15G012510.1 Cma15g01251 1251
15 7945963 7946742 + CmaCh15G012520.1 Cma15g01252 1252
16 3012078 3013989 + CmaCh16G005820.1 Cma16g00582 582
16 3017620 3018825 - CmaCh16G005830.1 Cma16g00583 583
16 3021734 3024306 + CmaCh16G005840.1 Cma16g00584 584
7 21940894 21945494 + MELO3C016339.2.1 Cme07g01615 1615
7 21959762 21962446 + MELO3C016340.2.1 Cme07g01616 1616
7 21968929 21969978 - MELO3C016341.2.1 Cme07g01617 1617
7 21979839 21981079 - MELO3C016342.2.1 Cme07g01618 1618
7 21985730 21988142 + MELO3C016343.2.1 Cme07g01619 1619
9 22327506 22331911 - MELO3C005705.2.1 Cme09g01791 1791
9 22334035 22335823 - MELO3C005706.2.1 Cme09g01792 1792
9 22338534 22340684 - MELO3C005707.2.1 Cme09g01793 1793
9 22351439 22357312 + MELO3C005708.2.1 Cme09g01794 1794
9 22365640 22366688 + MELO3C005711.2.1 Cme09g01797 1797
2 8594220 8595392 + CmoCh02G014610.1 Cmo02g01461 1461
2 8595893 8597551 + CmoCh02G014620.1 Cmo02g01462 1462
2 8598641 8602744 + CmoCh02G014630.1 Cmo02g01463 1463
15 7830368 7832201 - CmoCh15G011270.1 Cmo15g01127 1127
15 9024086 9029073 - CmoCh15G013140.1 Cmo15g01314 1314
15 9030753 9032783 - CmoCh15G013150.1 Cmo15g01315 1315
15 9033880 9040674 + CmoCh15G013160.1 Cmo15g01316 1316
16 3113635 3115672 + CmoCh16G006320.1 Cmo16g00632 632
16 3120108 3121313 - CmoCh16G006330.1 Cmo16g00633 633
16 3124484 3126915 + CmoCh16G006340.1 Cmo16g00634 634
1 2235839 2236795 - CmPI595203_01g002260.1 Cmu01g0226 226
1 2243241 2249971 - CmPI595203_01g002270.1 Cmu01g0227 227
1 2279834 2281280 + CmPI595203_01g002290.1 Cmu01g0229 229
1 2284686 2288762 + CmPI595203_01g002300.1 Cmu01g0230 230
7 20108607 20113010 + CmPI595203_07g007920.1 Cmu07g0792 792
7 20189605 20191981 + CmPI595203_07g007940.1 Cmu07g0794 794
7 20358161 20358944 - CmPI595203_07g007970.1 Cmu07g0797 797
7 20376266 20377471 - CmPI595203_07g007980.1 Cmu07g0798 798
7 20441655 20443552 + CmPI595203_07g008010.1 Cmu07g0801 801
6 4089429 4090920 - Conep06aG0083000.1 Cone6ag0806 806
6 4099019 4104578 + Conep06aG0083200.1 Cone6ag0808 808
6 4105694 4106667 + Conep06aG0083300.1 Cone6ag0809 809
6 4117892 4119229 - Conep06aG0083400.1 Cone6ag0810 810
8 1614860 1615981 - Conep08aG0029400.1 Cone8ag0279 279
8 1621527 1624308 + Conep08aG0029500.1 Cone8ag0280 280
9 3850318 3851732 - Conep09aG0082100.1 Cone9ag0803 803
9 3861698 3862931 + Conep09aG0082200.1 Cone9ag0804 804
9 3866289 3869973 + Conep09aG0082300.1 Cone9ag0805 805
9 3883100 3885543 - Conep09aG0082600.1 Cone9ag0808 808
9 3887697 3889141 - Conep09aG0082700.1 Cone9ag0809 809
12 1541854 1542417 - Conep12aG0029700.1 Cone12ag0285 285
12 1546475 1549199 + Conep12aG0029800.1 Cone12ag0286 286
5 1990847 1994800 - Cp4.1LG05g03130.1 Cpe05g00357 357
5 1995209 1997495 - Cp4.1LG05g03120.1 Cpe05g00358 358
13 969699 970661 - Cp4.1LG13g01320.1 Cpe13g00133 133
13 972757 979516 - Cp4.1LG13g01300.1 Cpe13g00134 134
13 980603 982387 + Cp4.1LG13g01260.1 Cpe13g00135 135
13 984706 991670 + Cp4.1LG13g01390.1 Cpe13g00136 136
14 3131590 3133673 + Cp4.1LG14g02300.1 Cpe14g00493 493
14 3138517 3139722 - Cp4.1LG14g02240.1 Cpe14g00494 494
14 3142327 3144867 + Cp4.1LG14g02270.1 Cpe14g00495 495
7 23458339 23462855 + CrPI670011_07g011440.1 Cre07g1144 1144
7 23523669 23526050 + CrPI670011_07g011460.1 Cre07g1146 1146
7 23657081 23657916 - CrPI670011_07g011530.1 Cre07g1153 1153
7 23671647 23672852 - CrPI670011_07g011540.1 Cre07g1154 1154
7 23760544 23762886 + CrPI670011_07g011550.1 Cre07g1155 1155
9 42001456 42005561 - CrPI670011_09g022800.1 Cre09g2280 2280
9 42008932 42010381 - CrPI670011_09g022810.1 Cre09g2281 2281
9 42039964 42052921 + CrPI670011_09g022830.1 Cre09g2283 2283
9 42057014 42057805 + CrPI670011_09g022840.1 Cre09g2284 2284
4 3995725 3998200 - CsaV3_4G006060.1 Csa04g00606 606
4 4002800 4005391 + CsaV3_4G006070.1 Csa04g00607 607
4 4008731 4009898 + CsaV3_4G006080.1 Csa04g00608 608
4 4014277 4017001 - CsaV3_4G006090.1 Csa04g00609 609
4 4027360 4032209 - CsaV3_4G006100.1 Csa04g00610 610
5 1487722 1489069 - CsaV3_5G002440.1 Csa05g00244 244
5 1496763 1502564 - CsaV3_5G002470.1 Csa05g00247 247
5 1514532 1516861 + CsaV3_5G002490.1 Csa05g00249 249
5 1519517 1521503 + CsaV3_5G002500.1 Csa05g00250 250
5 1523550 1527973 + CsaV3_5G002510.1 Csa05g00251 251
6 65769728 65770435 - Hsped.06g15140.1 Hepe06g1514 1514
12 36378676 36379504 - Maker00029399 Lcy12g1614 1614
12 36474236 36476438 + Maker00029417 Lcy12g1618 1618
12 36491021 36492874 + Maker00029426 Lcy12g1619 1619
12 36495400 36500267 + Maker00029284 Lcy12g1620 1620
9 2288322 2289232 - Lsi09G002190.1 Lsi09g00219 219
9 2309862 2316731 - Lsi09G002230.1 Lsi09g00223 223
9 2333611 2339155 + Lsi09G002240.1 Lsi09g00224 224
9 2344666 2365683 + Lsi09G002250.1 Lsi09g00225 225
9 2368024 2373033 + Lsi09G002260.1 Lsi09g00226 226
2 380309 386888 - Vvi2g32 Vvi2g32 32
2 412567 416019 + Vvi2g33 Vvi2g33 33
2 422316 424434 + Vvi2g34 Vvi2g34 34
2 424466 429608 - Vvi2g35 Vvi2g35 35
2 433947 435565 - Vvi2g36 Vvi2g36 36
2 447131 448304 + Vvi2g37 Vvi2g37 37
2 450004 457491 + Vvi2g38 Vvi2g38 38
2 459803 461157 + Vvi2g39 Vvi2g39 39
2 470206 475234 - Vvi2g40 Vvi2g40 40
2 479435 487361 - Vvi2g41 Vvi2g41 41
       

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