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
Vvi6g4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi6g5 . Blo03g01398 . . . . Bma14g00742 Bma07g01371 Cmo10g00829 Cmo11g00777 Cma10g00802 . . . . . Cpe18g00278 Bhi02g01439 Tan09g0742 . . . . . . . . . . . . . Cone5ag1410 . . Lsi06g00378 . . . . . Bda07g00772 Bda09g00340 . Bpe11g00947 Bma07g00328 . . . . Cma11g00768 . . . . Cpe04g00992 . . . . . . . Cla03g01411 Cam03g1491 Cec03g1529 Cco03g1523 Clacu03g1514 Cmu03g2071 Cre03g1743 . Csa01g03033 Chy02g01313 Cme02g00345
Vvi6g6 . . . . . . . . Cmo10g01101 . Cma10g01045 . . . . . Cpe18g00084 . . . . . . . . . . . . . . . . . . . . . . . Blo14g00340 . . Bpe08g00334 . Bma07g00328 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi6g7 . . . . Bpe01g00364 . . . . . . . . . . Cpe05g00570 . . . . . . . . . . . . . . . . . Cone18ag0002 Cone11ag1591 . . . . Blo08g00159 Blo14g00332 . . . . . Bma11g00347 . Cmo02g01192 . Cma02g01158 . Car02g00958 . . . . . . . . . . . . . . . . . . . . .
Vvi6g8 . . . . . . . . . . . . . . . . . . . . . . . . Cla02g02369 Cam02g2520 Cec02g2568 Cco02g2597 Clacu02g2494 Cmu02g2425 Cre02g2744 . . . . . . . . . . . . . . . . . . . . . . . Cpe16g00943 . . . . . . . . . . . . . . . . . . .
Vvi6g9 . . . . . . Bma14g00740 . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag0376 . . . . . . . . . Bda07g00774 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi6g10 . Blo03g01399 . . . . . Bma07g01368 Cmo10g00831 . Cma10g00804 . . . Sed12g1675 . Cpe18g00276 Bhi02g01729 Tan09g1016 Cmetu02g1283 . Hepe09g0974 . . . . . . . . . . . Cone18ag0004 Cone11ag1589 Lsi06g00380 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla03g01409 Cam03g1489 Cec03g1526 Cco03g1521 Clacu03g1511 Cmu03g2068 Cre03g1741 . Csa01g03035 Chy02g01315 Cme02g00347
Vvi6g11 . . . . Bpe01g00363 . . . . . . . . . . Cpe05g00569 . . . . . . . . Cla02g02369 Cam02g2520 Cec02g2568 Cco02g2597 Clacu02g2494 Cmu02g2425 Cre02g2744 . . Cone18ag0005 Cone11ag1588 . . Chy05g00001 Cme05g00001 . . . . Bpe08g00327 . Bma07g00318 Bma11g00346 Sed01g3430 Cmo02g01193 Cmo20g00003 Cma02g01159 Cma20g00003 Car02g00959 Car20g00001 . . Bhi10g00491 Tan07g0561 Cmetu05g1769 . Hepe08g0006 . . . . . . . . . . . . .
Vvi6g12 . . . . Bpe01g00362 . . . . . . . . . . Cpe05g00568 . . . . . . . . Cla02g02368 Cam02g2519 Cec02g2566 Cco02g2595 Clacu02g2493 Cmu02g2424 Cre02g2742 . . . . . . Chy05g00006 Cme05g00008 Blo08g00158 Blo14g00331 . . . . Bma07g00317 Bma11g00345 . Cmo02g01194 Cmo20g00005 Cma02g01160 Cma20g00005 Car02g00960 Car20g00003 Cpe16g00943 . Bhi10g00490 Tan07g0562 . . . . . . . . . . . . . . . .
Vvi6g13 . . . . . . Bma14g00739 Bma07g01367 . . . . . . . Cpe05g00567 . . . . . . . . Cla02g02367 Cam02g2518 Cec02g2565 Cco02g2594 Clacu02g2492 Cmu02g2423 Cre02g2741 . Cone5ag1304 Cone18ag0007 Cone11ag1586 . . Chy05g00007 Cme05g00009 . . Bda07g00775 Bda09g00342 . Bpe11g00949 . . Sed01g3428 Cmo02g01195 Cmo20g00006 Cma02g01161 Cma20g00006 Car02g00961 Car20g00004 Cpe16g00942 . Bhi10g00488 Tan07g0564 Cmetu05g1641 . Hepe08g0007 . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 9156089 9160861 + Bda025910.1 Bda07g00772 772
7 9195141 9213328 + Bda025912.1 Bda07g00774 774
7 9284622 9286504 + Bda025914.1 Bda07g00775 775
9 4350457 4352245 + Bda030910.1 Bda09g00340 340
9 4381595 4383743 - Bda030915.1 Bda09g00342 342
2 38561411 38565573 + XM_039024285.1 Bhi02g01439 1439
2 47566653 47579495 + XM_039024044.1 Bhi02g01729 1729
10 10996629 11001098 + XM_039045458.1 Bhi10g00488 488
10 11003784 11005645 - XM_039045834.1 Bhi10g00490 490
10 11056258 11095895 + XM_039045881.1 Bhi10g00491 491
3 40477939 40485215 + BLOR12579 Blo03g01398 1398
3 40490217 40494204 - BLOR12580 Blo03g01399 1399
8 1629110 1630171 - BLOR20328 Blo08g00158 158
8 1630313 1639121 - BLOR20329 Blo08g00159 159
14 3401341 3402354 - BLOR14649 Blo14g00331 331
14 3406564 3413813 - BLOR14650 Blo14g00332 332
14 3639275 3645521 - BLOR14658 Blo14g00340 340
7 3806447 3809337 - Bma025096.1 Bma07g00317 317
7 3813864 3815662 - Bma025097.1 Bma07g00318 318
7 4274710 4282003 - Bma025109.1 Bma07g00328 328
7 49299899 49302071 + Bma026648.1 Bma07g01367 1367
7 49303412 49307534 + Bma026649.1 Bma07g01368 1368
7 49344022 49345269 - Bma026654.1 Bma07g01371 1371
11 3389968 3390978 - Bma005802.1 Bma11g00345 345
11 3394703 3396402 - Bma005803.1 Bma11g00346 346
11 3397761 3401376 - Bma005804.1 Bma11g00347 347
14 8190402 8192451 + Bma030679 Bma14g00739 739
14 8194854 8212770 - Bma011209.1 Bma14g00740 740
14 8218743 8221836 - Bma011210.1 Bma14g00742 742
1 2276471 2277487 - Bpe000351.1 Bpe01g00362 362
1 2282252 2283855 - Bpe000352.1 Bpe01g00363 363
1 2285039 2288605 - Bpe000353.1 Bpe01g00364 364
8 1937815 1939600 - Bpe022422.1 Bpe08g00327 327
8 1980252 1985220 - Bpe022428.1 Bpe08g00334 334
11 7038616 7041720 + Bpe004284.1 Bpe11g00947 947
11 7065574 7067579 - Bpe004287.1 Bpe11g00949 949
2 37533455 37537176 + CaPI482276_02g025180.1 Cam02g2518 2518
2 37538877 37539923 - CaPI482276_02g025190.1 Cam02g2519 2519
2 37544255 37551516 + CaPI482276_02g025200.1 Cam02g2520 2520
3 29804776 29812129 + CaPI482276_03g014890.1 Cam03g1489 1489
3 29827888 29832801 + CaPI482276_03g014910.1 Cam03g1491 1491
2 6749732 6753809 - Carg13983-RA Car02g00958 958
2 6755384 6761124 + Carg13982-RA Car02g00959 959
2 6762800 6764602 + Carg13981-RA Car02g00960 960
2 6765991 6769606 - Carg13980-RA Car02g00961 961
20 14021 16758 - Carg28115-RA Car20g00001 1
20 17580 18680 + Carg28117-RA Car20g00003 3
20 19024 21460 - Carg28118-RA Car20g00004 4
2 38204725 38208439 + CcPI632755_02g025940.1 Cco02g2594 2594
2 38210171 38211214 - CcPI632755_02g025950.1 Cco02g2595 2595
2 38221395 38233456 + CcPI632755_02g025970.1 Cco02g2597 2597
3 29810645 29818006 + CcPI632755_03g015210.1 Cco03g1521 1521
3 29836722 29841525 + CcPI632755_03g015230.1 Cco03g1523 1523
2 42647892 42651617 + CePI673135_02g025650.1 Cec02g2565 2565
2 42653266 42654312 - CePI673135_02g025660.1 Cec02g2566 2566
2 42658765 42669289 + CePI673135_02g025680.1 Cec02g2568 2568
3 33359743 33367100 + CePI673135_03g015260.1 Cec03g1526 1526
3 33382807 33387722 + CePI673135_03g015290.1 Cec03g1529 1529
2 9700961 9705281 - Chy2G035800.1 Chy02g01313 1313
2 9717328 9723902 - Chy2G035820.1 Chy02g01315 1315
5 2698 15253 + Chy5G090470.1 Chy05g00001 1
5 45088 50587 + Chy5G090520.1 Chy05g00006 6
5 51841 55369 - Chy5G090530.1 Chy05g00007 7
2 37778018 37781738 + ClG42_02g0249200.10 Clacu02g2492 2492
2 37783449 37784498 - ClG42_02g0249300.10 Clacu02g2493 2493
2 37788829 37806058 + ClG42_02g0249400.10 Clacu02g2494 2494
3 28683363 28690714 + ClG42_03g0151100.10 Clacu03g1511 1511
3 28706465 28711363 + ClG42_03g0151400.10 Clacu03g1514 1514
2 38726985 38731244 + ClCG02G024460.1 Cla02g02367 2367
2 38732677 38733762 - ClCG02G024470.1 Cla02g02368 2368
2 38737975 38749078 + ClCG02G024480.1 Cla02g02369 2369
3 29593287 29601052 + ClCG03G014660.2 Cla03g01409 1409
3 29616560 29622549 + ClCG03G014680.2 Cla03g01411 1411
2 6825853 6828177 - CmaCh02G011580.1 Cma02g01158 1158
2 6830174 6837639 + CmaCh02G011590.1 Cma02g01159 1159
2 6840315 6841723 + CmaCh02G011600.1 Cma02g01160 1160
2 6842627 6846241 - CmaCh02G011610.1 Cma02g01161 1161
10 3701802 3705888 - CmaCh10G008020.1 Cma10g00802 802
10 3712691 3720114 - CmaCh10G008040.1 Cma10g00804 804
10 5812571 5821848 - CmaCh10G010450.1 Cma10g01045 1045
11 3737784 3741456 - CmaCh11G007680.1 Cma11g00768 768
20 8559 13831 - CmaCh20G000030.1 Cma20g00003 3
20 13841 14968 + CmaCh20G000050.1 Cma20g00005 5
20 15272 17680 - CmaCh20G000060.1 Cma20g00006 6
2 2843340 2848609 - MELO3C015560.2.1 Cme02g00345 345
2 2858824 2866012 - MELO3C015562.2.1 Cme02g00347 347
5 394 6369 + MELO3C031044.2.1 Cme05g00001 1
5 72377 74152 + MELO3C014733.2.1 Cme05g00008 8
5 74897 79026 - MELO3C014732.2.1 Cme05g00009 9
2 2974047 2981911 - PI0014333.1 Cmetu02g1283 1283
5 23044724 23049082 + PI0006791.1 Cmetu05g1641 1641
5 23055057 23074331 + PI0013592.2 Cmetu05g1769 1769
2 7133585 7137548 - CmoCh02G011920.1 Cmo02g01192 1192
2 7138907 7146010 + CmoCh02G011930.1 Cmo02g01193 1193
2 7148547 7150021 + CmoCh02G011940.1 Cmo02g01194 1194
2 7151090 7154480 - CmoCh02G011950.1 Cmo02g01195 1195
10 3898070 3901733 - CmoCh10G008290.1 Cmo10g00829 829
10 3908720 3916466 - CmoCh10G008310.1 Cmo10g00831 831
10 6248032 6254201 - CmoCh10G011010.1 Cmo10g01101 1101
11 3801726 3806317 - CmoCh11G007770.1 Cmo11g00777 777
20 94471 97972 - CmoCh20G000030.1 Cmo20g00003 3
20 97838 98947 + CmoCh20G000050.1 Cmo20g00005 5
20 99289 101734 - CmoCh20G000060.1 Cmo20g00006 6
2 37641732 37645452 + CmPI595203_02g024230.1 Cmu02g2423 2423
2 37647164 37648213 - CmPI595203_02g024240.1 Cmu02g2424 2424
2 37652804 37669419 + CmPI595203_02g024250.1 Cmu02g2425 2425
3 29078286 29085637 + CmPI595203_03g020680.1 Cmu03g2068 2068
3 29101357 29106257 + CmPI595203_03g020710.1 Cmu03g2071 2071
1 3166766 3197283 + Conep01aG0039600.1 Cone1ag0376 376
5 7389395 7394663 - Conep05aG0134600.1 Cone5ag1304 1304
5 8813213 8817478 - Conep05aG0145500.1 Cone5ag1410 1410
11 11006216 11008330 + Conep11aG0163900.1 Cone11ag1586 1586
11 11036178 11040091 - Conep11aG0164100.1 Cone11ag1588 1588
11 11040391 11043887 + Conep11aG0164200.1 Cone11ag1589 1589
11 11045240 11049270 + Conep11aG0164400.1 Cone11ag1591 1591
18 16180 24691 - Conep18aG0000200.1 Cone18ag0002 2
18 25965 30194 - Conep18aG0000400.1 Cone18ag0004 4
18 29631 34096 + Conep18aG0000500.1 Cone18ag0005 5
18 61771 63859 + Conep18aG0000700.1 Cone18ag0007 7
4 8926106 8930850 + Cp4.1LG04g11370.1 Cpe04g00992 992
5 3427347 3431420 + Cp4.1LG05g05680.1 Cpe05g00567 567
5 3428728 3434369 - Cp4.1LG05g05790.1 Cpe05g00568 568
5 3436297 3445282 - Cp4.1LG05g05780.1 Cpe05g00569 569
5 3447560 3450451 + Cp4.1LG05g05700.1 Cpe05g00570 570
16 8677035 8685761 + Cp4.1LG16g09220.1 Cpe16g00942 942
16 8679463 8680784 - Cp4.1LG16g09430.1 Cpe16g00943 943
18 2267632 2270966 + Cp4.1LG18g00840.1 Cpe18g00084 84
18 4360194 4367515 + Cp4.1LG18g02830.1 Cpe18g00276 276
18 4374657 4378484 + Cp4.1LG18g02760.1 Cpe18g00278 278
2 40559024 40562744 + CrPI670011_02g027410.1 Cre02g2741 2741
2 40564465 40565508 - CrPI670011_02g027420.1 Cre02g2742 2742
2 40571449 40578777 + CrPI670011_02g027440.1 Cre02g2744 2744
3 34209116 34216464 + CrPI670011_03g017410.1 Cre03g1741 1741
3 34232829 34237734 + CrPI670011_03g017430.1 Cre03g1743 1743
1 26435396 26440440 - CsaV3_1G041490.1 Csa01g03033 3033
1 26449411 26456913 - CsaV3_1G041510.1 Csa01g03035 3035
8 91376 105630 + Hsped.08g00060.1 Hepe08g0006 6
8 106224 108986 - Hsped.08g00070.1 Hepe08g0007 7
9 9940293 9951926 - Hsped.09g09740.1 Hepe09g0974 974
6 4179434 4184337 - Lsi06G003780.1 Lsi06g00378 378
6 4199568 4205371 - Lsi06G003800.1 Lsi06g00380 380
1 63349384 63352990 + Sed0013259.1 Sed01g3428 3428
1 63355970 63363618 - Sed0012812.2 Sed01g3430 3430
12 27968193 27983100 + Sed0004485.1 Sed12g1675 1675
7 9199713 9220446 + Tan0018817.3 Tan07g0561 561
7 9225862 9227856 + Tan0011910.2 Tan07g0562 562
7 9229351 9233416 - Tan0011753.1 Tan07g0564 564
9 57461889 57464108 + Tan0015410.2 Tan09g0742 742
9 62266713 62300582 + Tan0015749.1 Tan09g1016 1016
6 106475 108096 - Vvi6g4 Vvi6g4 4
6 111925 120245 - Vvi6g5 Vvi6g5 5
6 129469 138528 - Vvi6g6 Vvi6g6 6
6 148815 156557 - Vvi6g7 Vvi6g7 7
6 173001 174251 + Vvi6g8 Vvi6g8 8
6 183244 227075 + Vvi6g9 Vvi6g9 9
6 227873 247289 - Vvi6g10 Vvi6g10 10
6 247697 255256 + Vvi6g11 Vvi6g11 11
6 257194 259488 + Vvi6g12 Vvi6g12 12
6 260300 263555 - Vvi6g13 Vvi6g13 13
       

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