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
Vvi3g296 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g297 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g298 . . . . . . . . Cmo19g00819 Cmo11g01788 . . . . Sed05g2162 Cpe04g00633 Cpe15g00643 Bhi05g01580 Tan02g0572 Cmetu01g1669 Lac12g0474 . . . Cla02g00345 Cam02g0354 Cec02g0355 Cco02g0361 Clacu02g0346 Cmu02g0343 Cre02g0675 Cone12ag1298 Cone8ag1333 . . . Csa07g00188 . Cme01g01145 Blo04g00607 Blo13g00472 . Bda14g00649 Bpe15g00782 . Bma03g00639 Bma08g00716 . . . Cma11g01331 Cma19g00799 Car11g01415 Car19g00615 . . . . . . . . . . . . . . . . Lsi11g01287 . Chy01g00592 .
Vvi3g299 . . . . . . . . Cmo19g00820 . Cma02g00302 Cma20g00712 Car02g00182 Car20g00612 Sed01g0628 . Cpe15g00644 Bhi05g01578 Tan02g0571 Cmetu11g0730 Lac12g0472 . . . Cla02g00344 Cam02g0353 Cec02g0354 Cco02g0360 Clacu02g0345 Cmu02g0342 Cre02g0674 Cone12ag1297 Cone8ag1334 . . . Csa07g00190 . Cme01g01144 . . . . Bpe15g00781 . . . . Cmo02g00296 Cmo20g00708 . Cma19g00800 . Car19g00616 Cpe16g00354 Cpe05g01335 . . . . . . . . . . . . . . Lsi11g01288 . Chy01g00591 Cme11g01046
Vvi3g300 . . . . . Bpe12g00152 . . Cmo19g00823 Cmo11g01791 . . . . . Cpe04g00635 Cpe15g00647 Bhi05g01561 Tan02g0564 . Lac12g0465 Hepe02g0361 . . Cla02g00340 Cam02g0349 Cec02g0350 Cco02g0355 Clacu02g0340 Cmu02g0338 Cre02g0670 Cone12ag1294 . Cone3ag1177 Cone10ag1211 . Csa07g00194 . Cme01g01140 . Blo13g00469 . . . . . Bma08g00714 . . . Cma11g01329 Cma19g00801 Car11g01418 Car19g00619 . . . . . . . . . . . . . . . . Lsi11g01292 Csa02g01292 Chy01g00586 .
Vvi3g301 . Blo15g00418 Bda06g00445 . Bpe07g00677 Bpe12g00153 . Bma12g00884 . . . Cma20g00711 . Car20g00611 . . . . . . . . . . . . . . . . . Cone12ag1292 Cone8ag1338 Cone3ag1252 . . . . . . Blo13g00468 . . . . . Bma08g00713 . . Cmo20g00707 . . . . Cpe16g00355 . . . . . . . . . . . . . . . . . . Cme11g01036
Vvi3g302 . . . . . Bpe12g00155 . . . Cmo11g01793 . . . . Sed08g1540 Cpe04g00636 . Bhi05g01557 Tan02g0561 Cmetu06g1238 Lac12g0462 Hepe02g0359 . . Cla02g00337 Cam02g0346 Cec02g0347 Cco02g0352 Clacu02g0337 Cmu02g0335 Cre02g0667 . . . Cone10ag1210 . Csa07g00198 . . . Blo13g00467 . . . . . Bma08g00712 . . . Cma11g01327 . Car11g01419 . . . . . . . . . . . . . . . . . Lsi11g01295 . . .
Vvi3g303 . Blo15g00417 Bda06g00446 . Bpe07g00679 Bpe12g00156 . Bma12g00885 Cmo19g00826 Cmo11g01794 . . . . . Cpe04g00637 Cpe15g00649 Bhi05g01556 . . . . . . Cla02g00336 . . . . Cmu02g0334 . Cone12ag1291 Cone8ag1339 . . . Csa07g00199 . . . . . . . . . Bma08g00711 . . . Cma11g01326 Cma19g00804 Car11g01420 Car19g00622 . . . . . . . . . . . . . . . . Lsi11g01296 . Chy01g00583 .
Vvi3g304 . Blo15g00416 Bda06g00447 . Bpe07g00680 . . . Cmo19g00827 Cmo11g01795 Cma02g00303 Cma20g00710 . Car20g00610 Sed05g2144 Cpe04g00638 . Bhi05g01555 Tan02g0555 Cmetu01g1370 Lac12g0460 Hepe02g0357 . . Cla02g00335 Cam02g0344 Cec02g0345 Cco02g0350 Clacu02g0335 Cmu02g0333 Cre02g0665 . . . . . Csa07g00202 . . Blo04g00609 . . Bda14g00651 Bpe15g00778 . Bma03g00641 . . . Cmo20g00705 Cma11g01325 Cma19g00805 Car11g01422 Car19g00623 . . . . . . . . . . . . . . . . Lsi11g01299 . Chy01g00577 Cme11g01035
Vvi3g305 . Blo15g00415 Bda06g00448 . . . . Bma12g00886 . . Cma02g00304 . Car02g00183 . . . . . . . . . . . . . . . . . . Cone12ag1289 Cone8ag1341 . . . . . . . . . . . . . . . Cmo02g00297 . . . . . . Cpe05g01334 . . . . . . . Cla02g01058 Cam02g1130 Cec02g1134 Cco02g1174 Clacu02g1118 Cmu02g1081 Cre02g1385 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 6524301 6527936 - Bda023690.1 Bda06g00445 445
6 6532400 6535574 + Bda023691.1 Bda06g00446 446
6 6537169 6537651 - Bda023692.1 Bda06g00447 447
6 6538752 6542288 + Bda023693.1 Bda06g00448 448
14 4859279 4868511 + Bda027406.1 Bda14g00649 649
14 4879315 4880711 - Bda027408.1 Bda14g00651 651
5 52433098 52436068 + XM_039032997.1 Bhi05g01555 1555
5 52436371 52442386 - XM_039032996.1 Bhi05g01556 1556
5 52447495 52455950 - XM_039031331.1 Bhi05g01557 1557
5 52478220 52488273 - XM_039032791.1 Bhi05g01561 1561
5 52556340 52558135 + XM_039032553.1 Bhi05g01578 1578
5 52563181 52572835 - XM_039031594.1 Bhi05g01580 1580
4 5259295 5268506 + BLOR13519 Blo04g00607 607
4 5277660 5279468 - BLOR13521 Blo04g00609 609
13 25413152 25418974 - BLOR05748 Blo13g00467 467
13 25420387 25422925 + BLOR05749 Blo13g00468 468
13 25423504 25432541 - BLOR05750 Blo13g00469 469
13 25547165 25554334 - BLOR05753 Blo13g00472 472
15 5904600 5912950 - BLOR06809 Blo15g00415 415
15 5912997 5913479 + BLOR06810 Blo15g00416 416
15 5915181 5918435 - BLOR06811 Blo15g00417 417
15 5976229 5979825 + BLOR06812 Blo15g00418 418
3 5278670 5289307 + Bma016932.2 Bma03g00639 639
3 5300985 5302997 - Bma016934.1 Bma03g00641 641
8 42909003 42911805 - Bma028073.2 Bma08g00711 711
8 42913636 42915459 - Bma028074.1 Bma08g00712 712
8 42926157 42928664 + Bma028075.1 Bma08g00713 713
8 42929176 42933553 - Bma028076.1 Bma08g00714 714
8 42944460 42966323 - Bma028078.2 Bma08g00716 716
12 40065070 40068598 - Bma008210.1 Bma12g00884 884
12 40074291 40079078 + Bma008211.1 Bma12g00885 885
12 40093687 40097248 + Bma008212.1 Bma12g00886 886
7 13467735 13471164 - Bpe021526.1 Bpe07g00677 677
7 13482730 13486161 + Bpe021527.2 Bpe07g00679 679
7 13488903 13489385 - Bpe021528.1 Bpe07g00680 680
12 1122423 1126867 + Bpe005389.2 Bpe12g00152 152
12 1127715 1130224 - Bpe005390.1 Bpe12g00153 153
12 1135908 1137808 + Bpe005392.1 Bpe12g00155 155
12 1139477 1142279 + Bpe005393.1 Bpe12g00156 156
15 18069281 18069763 + Bpe001705.1 Bpe15g00778 778
15 18081406 18082695 + Bpe001708.1 Bpe15g00781 781
15 18083913 18093086 - Bpe001709.2 Bpe15g00782 782
2 4192266 4195179 + CaPI482276_02g003440.1 Cam02g0344 344
2 4207829 4213360 - CaPI482276_02g003460.1 Cam02g0346 346
2 4228270 4238075 - CaPI482276_02g003490.1 Cam02g0349 349
2 4275799 4277100 + CaPI482276_02g003530.1 Cam02g0353 353
2 4280804 4289695 - CaPI482276_02g003540.1 Cam02g0354 354
2 21237240 21244053 - CaPI482276_02g011300.1 Cam02g1130 1130
2 1091400 1092683 - Carg19771-RA Car02g00182 182
2 1097431 1103076 + Carg19772-RA Car02g00183 183
11 11580206 11588353 + Carg18116-RA Car11g01415 1415
11 11594571 11599217 + Carg18113-RA Car11g01418 1418
11 11599927 11604744 + Carg18112-RA Car11g01419 1419
11 11607534 11612646 + Carg18110-RA Car11g01420 1420
11 11618243 11618704 - Carg18108-RA Car11g01422 1422
19 7611354 7619452 + Carg04096-RA Car19g00615 615
19 7621098 7622378 - Carg04097-RA Car19g00616 616
19 7642635 7651241 + Carg04100-RA Car19g00619 619
19 7660111 7665375 + Carg04103-RA Car19g00622 622
19 7665784 7673285 - Carg04104-RA Car19g00623 623
20 3429846 3430322 + Carg16130-RA Car20g00610 610
20 3433857 3438203 + Carg16131-RA Car20g00611 611
20 3438942 3440225 + Carg16132-RA Car20g00612 612
2 3192079 3194943 + CcPI632755_02g003500.1 Cco02g0350 350
2 3207823 3213303 - CcPI632755_02g003520.1 Cco02g0352 352
2 3228266 3234051 - CcPI632755_02g003550.1 Cco02g0355 355
2 3274747 3276048 + CcPI632755_02g003600.1 Cco02g0360 360
2 3279737 3288273 - CcPI632755_02g003610.1 Cco02g0361 361
2 20600074 20607032 - CcPI632755_02g011740.1 Cco02g1174 1174
2 3200568 3203479 + CePI673135_02g003450.1 Cec02g0345 345
2 3216267 3221811 - CePI673135_02g003470.1 Cec02g0347 347
2 3236449 3242187 - CePI673135_02g003500.1 Cec02g0350 350
2 3283764 3285065 + CePI673135_02g003540.1 Cec02g0354 354
2 3288665 3297441 - CePI673135_02g003550.1 Cec02g0355 355
2 25354454 25361509 - CePI673135_02g011340.1 Cec02g1134 1134
1 4138310 4138762 + Chy1G005770.1 Chy01g00577 577
1 4169105 4174177 + Chy1G005830.1 Chy01g00583 583
1 4180344 4185748 - Chy1G005860.1 Chy01g00586 586
1 4223269 4224732 + Chy1G005910.1 Chy01g00591 591
1 4228094 4236629 - Chy1G005920.1 Chy01g00592 592
2 3069050 3071962 + ClG42_02g0033500.10 Clacu02g0335 335
2 3084510 3090015 - ClG42_02g0033700.10 Clacu02g0337 337
2 3105105 3110751 - ClG42_02g0034000.10 Clacu02g0340 340
2 3152095 3153396 + ClG42_02g0034500.10 Clacu02g0345 345
2 3156918 3165759 - ClG42_02g0034600.10 Clacu02g0346 346
2 21250771 21257539 - ClG42_02g0111800.10 Clacu02g1118 1118
2 3274592 3277505 + ClCG02G003330.2 Cla02g00335 335
2 3278395 3284314 - ClCG02G003340.1 Cla02g00336 336
2 3289846 3297195 - ClCG02G003350.1 Cla02g00337 337
2 3312003 3317650 - ClCG02G003380.2 Cla02g00340 340
2 3358998 3360299 + ClCG02G003420.1 Cla02g00344 344
2 3365890 3377882 - ClCG02G003430.2 Cla02g00345 345
2 22037288 22044174 - ClCG02G010830.2 Cla02g01058 1058
2 1420207 1421490 - CmaCh02G003020.1 Cma02g00302 302
2 1424658 1425508 - CmaCh02G003030.1 Cma02g00303 303
2 1426164 1430954 + CmaCh02G003040.1 Cma02g00304 304
11 8792165 8792626 + CmaCh11G013250.1 Cma11g01325 1325
11 8795971 8801773 - CmaCh11G013260.1 Cma11g01326 1326
11 8803788 8808728 - CmaCh11G013270.1 Cma11g01327 1327
11 8810190 8814623 - CmaCh11G013290.1 Cma11g01329 1329
11 8820271 8828571 - CmaCh11G013310.1 Cma11g01331 1331
19 7720970 7729382 + CmaCh19G007990.1 Cma19g00799 799
19 7730758 7732038 - CmaCh19G008000.1 Cma19g00800 800
19 7732635 7760787 + CmaCh19G008010.1 Cma19g00801 801
19 7768659 7772921 + CmaCh19G008040.1 Cma19g00804 804
19 7774374 7776449 - CmaCh19G008050.1 Cma19g00805 805
20 3287099 3287575 + CmaCh20G007100.1 Cma20g00710 710
20 3290867 3295436 + CmaCh20G007110.1 Cma20g00711 711
20 3295989 3297272 + CmaCh20G007120.1 Cma20g00712 712
1 14678459 14684734 - MELO3C013246.2.1 Cme01g01140 1140
1 14725090 14726920 + MELO3C013250.2.1 Cme01g01144 1144
1 14729689 14738845 - MELO3C013251.2.1 Cme01g01145 1145
11 14990819 14991845 + MELO3C013487.2.1 Cme11g01035 1035
11 15046855 15051565 + MELO3C013489.2.1 Cme11g01036 1036
11 15178818 15180101 - MELO3C013498.2.1 Cme11g01046 1046
1 4433804 4436735 + PI0028648.1 Cmetu01g1370 1370
1 4517263 4526734 - PI0015983.1 Cmetu01g1669 1669
6 19490050 19497180 + PI0026436.1 Cmetu06g1238 1238
11 17439815 17441757 - PI0008487.1 Cmetu11g0730 730
2 1482924 1484207 - CmoCh02G002960.1 Cmo02g00296 296
2 1489024 1493510 + CmoCh02G002970.1 Cmo02g00297 297
11 12574035 12583011 + CmoCh11G017880.1 Cmo11g01788 1788
11 12588834 12593199 + CmoCh11G017910.1 Cmo11g01791 1791
11 12593842 12599246 + CmoCh11G017930.1 Cmo11g01793 1793
11 12601263 12606316 + CmoCh11G017940.1 Cmo11g01794 1794
11 12613301 12613762 - CmoCh11G017950.1 Cmo11g01795 1795
19 8073698 8081882 + CmoCh19G008190.1 Cmo19g00819 819
19 8083540 8084820 - CmoCh19G008200.1 Cmo19g00820 820
19 8110181 8115155 + CmoCh19G008230.1 Cmo19g00823 823
19 8124042 8128802 + CmoCh19G008260.1 Cmo19g00826 826
19 8130469 8138124 - CmoCh19G008270.1 Cmo19g00827 827
20 3485986 3486462 + CmoCh20G007050.1 Cmo20g00705 705
20 3491198 3494493 + CmoCh20G007070.1 Cmo20g00707 707
20 3495163 3496446 + CmoCh20G007080.1 Cmo20g00708 708
2 3062493 3065405 + CmPI595203_02g003330.1 Cmu02g0333 333
2 3066532 3071672 - CmPI595203_02g003340.1 Cmu02g0334 334
2 3078105 3083628 - CmPI595203_02g003350.1 Cmu02g0335 335
2 3098302 3109090 - CmPI595203_02g003380.1 Cmu02g0338 338
2 3145296 3146597 + CmPI595203_02g003420.1 Cmu02g0342 342
2 3150228 3159067 - CmPI595203_02g003430.1 Cmu02g0343 343
2 21123184 21130088 - CmPI595203_02g010810.1 Cmu02g1081 1081
3 30447805 30450806 - Conep03aG0168300.1 Cone3ag1177 1177
3 31357402 31361244 - Conep03aG0175900.1 Cone3ag1252 1252
8 10758146 10764511 + Conep08aG0137200.1 Cone8ag1333 1333
8 10765166 10766458 - Conep08aG0137300.1 Cone8ag1334 1334
8 10779735 10782282 - Conep08aG0137700.1 Cone8ag1338 1338
8 10784065 10787487 + Conep08aG0137800.1 Cone8ag1339 1339
8 10789216 10792722 + Conep08aG0138000.1 Cone8ag1341 1341
10 8978939 8981460 - Conep10aG0124500.1 Cone10ag1210 1210
10 8985690 8990770 - Conep10aG0124600.1 Cone10ag1211 1211
12 9835877 9839468 - Conep12aG0133000.1 Cone12ag1289 1289
12 9841439 9844610 - Conep12aG0133200.1 Cone12ag1291 1291
12 9849138 9851689 + Conep12aG0133300.1 Cone12ag1292 1292
12 9853275 9857307 - Conep12aG0133500.1 Cone12ag1294 1294
12 9864604 9866173 + Conep12aG0133800.1 Cone12ag1297 1297
12 9866620 9872836 - Conep12aG0133900.1 Cone12ag1298 1298
4 6545891 6554458 + Cp4.1LG04g04580.1 Cpe04g00633 633
4 6560466 6565342 + Cp4.1LG04g04570.1 Cpe04g00635 635
4 6566803 6572495 + Cp4.1LG04g04590.1 Cpe04g00636 636
4 6575487 6580844 + Cp4.1LG04g04450.1 Cpe04g00637 637
4 6584293 6584754 - Cp4.1LG04g04340.1 Cpe04g00638 638
5 9385774 9391220 - Cp4.1LG05g13440.1 Cpe05g01334 1334
5 9396900 9398183 + Cp4.1LG05g13320.1 Cpe05g01335 1335
15 7137748 7146682 + Cp4.1LG15g06350.1 Cpe15g00643 643
15 7148644 7149924 - Cp4.1LG15g06400.1 Cpe15g00644 644
15 7172461 7181548 + Cp4.1LG15g06550.1 Cpe15g00647 647
15 7187208 7192146 + Cp4.1LG15g06540.1 Cpe15g00649 649
16 5273073 5274356 - Cp4.1LG16g03540.1 Cpe16g00354 354
16 5275044 5279492 - Cp4.1LG16g03570.1 Cpe16g00355 355
2 3609197 3612104 + CrPI670011_02g006650.1 Cre02g0665 665
2 3624754 3630360 - CrPI670011_02g006670.1 Cre02g0667 667
2 3645098 3650843 - CrPI670011_02g006700.1 Cre02g0670 670
2 3690580 3691881 + CrPI670011_02g006740.1 Cre02g0674 674
2 3695273 3704140 - CrPI670011_02g006750.1 Cre02g0675 675
2 22684285 22691039 - CrPI670011_02g013850.1 Cre02g1385 1385
2 12571370 12574220 - CsaV3_2G015080.1 Csa02g01292 1292
7 1532787 1542134 + CsaV3_7G001880.1 Csa07g00188 188
7 1547250 1549227 - CsaV3_7G001900.1 Csa07g00190 190
7 1584463 1590436 + CsaV3_7G001940.1 Csa07g00194 194
7 1604053 1610763 + CsaV3_7G001980.1 Csa07g00198 198
7 1613530 1620409 + CsaV3_7G001990.1 Csa07g00199 199
7 1628342 1632298 - CsaV3_7G002020.1 Csa07g00202 202
2 3353179 3356352 + Hsped.02g03570.1 Hepe02g0357 357
2 3367072 3371897 - Hsped.02g03590.1 Hepe02g0359 359
2 3381094 3385954 - Hsped.02g03610.1 Hepe02g0361 361
12 5071836 5074681 + Lag0014832.1 Lac12g0460 460
12 5088383 5093744 - Lag0014834.1 Lac12g0462 462
12 5104674 5110704 - Lag0014837.1 Lac12g0465 465
12 5172010 5172819 + Lag0014844.1 Lac12g0472 472
12 5176682 5185253 - Lag0014846.1 Lac12g0474 474
11 21498193 21507906 + Lsi11G012870.1 Lsi11g01287 1287
11 21513120 21514421 - Lsi11G012880.1 Lsi11g01288 1288
11 21564679 21571434 + Lsi11G012920.1 Lsi11g01292 1292
11 21591833 21595948 + Lsi11G012950.1 Lsi11g01295 1295
11 21605345 21611741 + Lsi11G012960.1 Lsi11g01296 1296
11 21622167 21622628 - Lsi11G012990.1 Lsi11g01299 1299
1 4504507 4506288 + Sed0009088.1 Sed01g0628 628
5 34459883 34463019 + Sed0028195.1 Sed05g2144 2144
5 34536328 34546727 - Sed0023090.1 Sed05g2162 2162
8 30270133 30274926 - Sed0001999.1 Sed08g1540 1540
2 4941501 4945291 + Tan0020404.1 Tan02g0555 555
2 4968090 4976131 - Tan0021388.1 Tan02g0561 561
2 4991829 5000643 - Tan0011263.2 Tan02g0564 564
2 5039984 5041862 + Tan0018657.1 Tan02g0571 571
2 5043252 5053115 - Tan0009225.1 Tan02g0572 572
3 2814402 2814940 - Vvi3g296 Vvi3g296 296
3 2822231 2823699 - Vvi3g297 Vvi3g297 297
3 2833609 2847123 + Vvi3g298 Vvi3g298 298
3 2857243 2858851 - Vvi3g299 Vvi3g299 299
3 2864533 2872609 + Vvi3g300 Vvi3g300 300
3 2875913 2881812 - Vvi3g301 Vvi3g301 301
3 2885252 2887990 + Vvi3g302 Vvi3g302 302
3 2890431 2895797 + Vvi3g303 Vvi3g303 303
3 2896410 2902779 - Vvi3g304 Vvi3g304 304
3 2903440 2909631 + Vvi3g305 Vvi3g305 305
       

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