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
Vvi4g312 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g313 . . . . Bpe02g01177 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda01g00932 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g314 . . . . Bpe02g01176 . . . . . Cma01g01433 . Car09g00566 . . Cpe07g00222 . Bhi04g00833 . . . Hepe10g0350 . Lcy13g1395 . . . . . . . . . Cone17ag1115 Cone20ag0605 Lsi04g02336 Csa03g04557 Chy04g00145 Cme03g01733 Blo17g00076 . Bda01g00931 Bda13g01337 Bpe14g00510 . . . . Cmo01g01482 Cmo09g00622 Cma09g00640 Cma12g00259 . . . Cpe02g00515 Bhi09g02589 Tan01g3941 . . Hepe01g2227 Mch11g0777 . Cla08g01230 Cam08g1689 Cec08g1268 Cco08g1389 Clacu08g1387 . Cre08g1172 Lsi08g01093 . Chy03g01239 Cme04g00171
Vvi4g315 . . . . . . . Bma01g02162 . . . Cma05g00464 . . . . . . . . . . . . . . . . . . . . . . Cone20ag0663 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla08g01314 Cam08g1774 Cec08g1356 Cco08g1476 Clacu08g1470 . Cre08g1257 . . . .
Vvi4g316 . Blo12g00759 . Bda03g00427 . . Bma04g00402 . . . Cma01g01432 . Car09g00568 . . . . . . . . . . . . . . . . . . . . . . Lsi04g02338 Csa03g04559 Chy04g00143 . . . . . . Bpe04g00393 . . Sed04g0534 Cmo01g01481 Cmo09g00625 Cma09g00643 . . . . Cpe02g00516 Bhi09g02595 Tan01g3944 Cmetu04g1421 . Hepe01g2228 Mch11g0778 . . . . . . . . . . . Cme04g00168
Vvi4g317 Blo01g01771 . . Bda03g00426 . Bpe02g00173 . Bma01g02552 Cmo05g00625 Cmo12g00213 . Cma05g00599 . Car12g00244 Sed01g1278 Cpe07g00224 . Bhi04g00831 Tan02g2574 Cmetu03g0651 . Hepe10g0349 . Lcy13g1394 . . . . . . . . . . . . . . Cme03g01732 . . . . . Bpe04g00392 . . . . . . Cma12g00260 . Car05g00542 Cpe11g00523 . . . . . . . . Cla08g01231 . . . . . . Lsi08g01094 . Chy03g01238 .
Vvi4g318 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g319 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g320 Blo01g01770 Blo12g00760 Bda01g00727 Bda03g00425 Bpe02g01190 Bpe02g00174 Bma04g00401 . Cmo05g00626 Cmo12g00214 Cma01g01431 . . Car12g00245 Sed01g1279 Cpe07g00225 . Bhi04g00830 Tan02g2575 Cmetu03g2145 . Hepe10g0348 . Lcy13g1393 . . . . . . . . . Cone17ag1114 Cone20ag0607 Lsi04g02339 Csa03g04560 Chy04g00142 Cme03g01731 . Blo18g00073 Bda01g00944 . . Bpe04g00391 Bma01g01338 . . Cmo01g01480 . . Cma12g00261 . Car05g00543 Cpe11g00524 Cpe02g00517 Bhi09g02597 . . . Hepe01g2229 Mch11g0779 . Cla08g01232 Cam08g1690 Cec08g1269 Cco08g1390 Clacu08g1388 . Cre08g1173 Lsi08g01095 . Chy03g01237 Cme04g00382
Vvi4g321 Blo01g01769 . . . . Bpe02g00175 . Bma01g02551 . . Cma01g01430 . . . . . . . . . . . . . . . . . . . . . . . Cone20ag0608 . Csa03g04561 . . . . . . . . . . Sed12g1405 Cmo01g01479 . . . . . . Cpe02g00518 Bhi09g02599 Tan01g3948 Cmetu04g1371 . Hepe01g2230 Mch11g0780 . . . . . . . . . . . Cme04g00166
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 34575149 34576566 + Bda002764.1 Bda01g00727 727
1 42645049 42650080 + Bda003080.1 Bda01g00931 931
1 42651377 42653304 - Bda003081.1 Bda01g00932 932
1 42879492 42886059 - Bda003096.1 Bda01g00944 944
3 3671051 3672864 + Bda016391.2 Bda03g00425 425
3 3676027 3676974 + Bda016392.1 Bda03g00426 426
3 3677511 3681209 - Bda016393.1 Bda03g00427 427
13 35653625 35658685 - Bda000148.2 Bda13g01337 1337
4 21043838 21050536 + XM_039029133.1 Bhi04g00830 830
4 21052188 21057598 + XM_039030857.1 Bhi04g00831 831
4 21069803 21075087 + XM_039029484.1 Bhi04g00833 833
9 70217877 70225652 - XM_039042698.1 Bhi09g02589 2589
9 70240085 70244195 + XM_039042157.1 Bhi09g02595 2595
9 70244374 70250560 - XM_039042155.1 Bhi09g02597 2597
9 70267537 70270320 - XM_039040877.1 Bhi09g02599 2599
1 57426704 57428373 + BLOR01769 Blo01g01769 1769
1 57430090 57435069 + BLOR01770 Blo01g01770 1770
1 57437038 57438146 + BLOR01771 Blo01g01771 1771
12 25932837 25936718 + BLOR04778 Blo12g00759 759
12 25937278 25949747 - BLOR04779 Blo12g00760 760
17 565527 572104 - BLOR15897 Blo17g00076 76
18 586970 593598 + BLOR08561 Blo18g00073 73
1 18629867 18636427 + Bma001659.1 Bma01g01338 1338
1 78457949 78460080 - Bma003007.1 Bma01g02162 2162
1 83167833 83169006 + Bma003433.1 Bma01g02551 2551
1 83171654 83182222 + Bma003434.1 Bma01g02552 2552
4 3274224 3279215 + Bma018864.1 Bma04g00401 401
4 3282850 3286565 - Bma018865.2 Bma04g00402 402
2 1208484 1210307 - Bpe008025.1 Bpe02g00173 173
2 1211702 1216704 - Bpe008026.1 Bpe02g00174 174
2 1218031 1219201 - Bpe008027.1 Bpe02g00175 175
2 15439150 15444244 + Bpe009037.1 Bpe02g01176 1176
2 15445501 15447428 - Bpe009038.1 Bpe02g01177 1177
2 15588329 15595055 - Bpe009051.1 Bpe02g01190 1190
4 2455695 2460947 + Bpe015077.1 Bpe04g00391 391
4 2463540 2467436 + Bpe015078.1 Bpe04g00392 392
4 2467997 2471586 - Bpe025619 Bpe04g00393 393
14 4510203 4515396 + Bpe007160.1 Bpe14g00510 510
8 23160943 23166896 - CaPI482276_08g016890.1 Cam08g1689 1689
8 23172210 23188398 - CaPI482276_08g016900.1 Cam08g1690 1690
8 23974490 23979776 - CaPI482276_08g017740.1 Cam08g1774 1774
5 3169824 3173069 - Carg08285-RA Car05g00542 542
5 3174810 3179526 - Carg08286-RA Car05g00543 543
9 3204489 3210274 - Carg03049-RA Car09g00566 566
9 3219061 3222705 + Carg03051-RA Car09g00568 568
12 1638485 1643056 - Carg03851-RA Car12g00244 244
12 1643973 1649784 - Carg03852-RA Car12g00245 245
8 25789336 25795344 - CcPI632755_08g013890.1 Cco08g1389 1389
8 25803409 25816228 - CcPI632755_08g013900.1 Cco08g1390 1390
8 26619917 26625101 - CcPI632755_08g014760.1 Cco08g1476 1476
8 24644469 24650399 - CePI673135_08g012680.1 Cec08g1268 1268
8 24660337 24671290 - CePI673135_08g012690.1 Cec08g1269 1269
8 25493608 25498895 - CePI673135_08g013560.1 Cec08g1356 1356
3 15455613 15461711 + Chy3G062170.1 Chy03g01237 1237
3 15463530 15466688 + Chy3G062180.1 Chy03g01238 1238
3 15472380 15477807 + Chy3G062190.1 Chy03g01239 1239
4 1277971 1288679 + Chy4G068600.1 Chy04g00142 142
4 1289652 1293451 - Chy4G068610.1 Chy04g00143 143
4 1309003 1314188 + Chy4G068630.1 Chy04g00145 145
8 23915225 23921183 - ClG42_08g0138700.10 Clacu08g1387 1387
8 23928886 23941803 - ClG42_08g0138800.10 Clacu08g1388 1388
8 24725163 24731081 - ClG42_08g0147000.10 Clacu08g1470 1470
8 25205922 25212698 - ClCG08G012320.2 Cla08g01230 1230
8 25219954 25223476 - ClCG08G012330.2 Cla08g01231 1231
8 25226303 25233449 - ClCG08G012340.2 Cla08g01232 1232
8 26049978 26055291 - ClCG08G013160.2 Cla08g01314 1314
1 10061966 10064296 + CmaCh01G014300.1 Cma01g01430 1430
1 10064395 10071348 + CmaCh01G014310.1 Cma01g01431 1431
1 10072185 10079315 - CmaCh01G014320.1 Cma01g01432 1432
1 10081201 10088990 + CmaCh01G014330.1 Cma01g01433 1433
5 2141128 2145669 + CmaCh05G004640.1 Cma05g00464 464
5 2991315 3001776 - CmaCh05G005990.1 Cma05g00599 599
9 3019569 3027235 - CmaCh09G006400.1 Cma09g00640 640
9 3034442 3039704 + CmaCh09G006430.1 Cma09g00643 643
12 1320931 1325225 - CmaCh12G002590.1 Cma12g00259 259
12 1327402 1331363 - CmaCh12G002600.1 Cma12g00260 260
12 1332575 1338552 - CmaCh12G002610.1 Cma12g00261 261
3 25899216 25905700 + MELO3C011154.2.1 Cme03g01731 1731
3 25906810 25911250 + MELO3C011153.2.1 Cme03g01732 1732
3 25915784 25922584 + MELO3C011152.2.1 Cme03g01733 1733
4 1258468 1261476 + MELO3C003454.2.1 Cme04g00166 166
4 1268506 1274130 - MELO3C003456.2.1 Cme04g00168 168
4 1285674 1293082 + MELO3C003457.2.1 Cme04g00171 171
4 3073360 3077046 + MELO3C003674.2.1 Cme04g00382 382
3 3526425 3531292 - PI0023510.2 Cmetu03g0651 651
3 3532260 3538772 - PI0002316.1 Cmetu03g2145 2145
4 32160041 32163006 - PI0028111.1 Cmetu04g1371 1371
4 32148135 32153963 + PI0014187.1 Cmetu04g1421 1421
1 11475535 11478093 + CmoCh01G014790.1 Cmo01g01479 1479
1 11479229 11484805 + CmoCh01G014800.1 Cmo01g01480 1480
1 11485369 11492424 - CmoCh01G014810.1 Cmo01g01481 1481
1 11494607 11503055 + CmoCh01G014820.1 Cmo01g01482 1482
5 3138899 3142804 - CmoCh05G006250.1 Cmo05g00625 625
5 3143769 3148816 - CmoCh05G006260.1 Cmo05g00626 626
9 3102633 3110827 - CmoCh09G006220.1 Cmo09g00622 622
9 3117826 3123284 + CmoCh09G006250.1 Cmo09g00625 625
12 1404725 1409474 - CmoCh12G002130.1 Cmo12g00213 213
12 1410173 1416175 - CmoCh12G002140.1 Cmo12g00214 214
17 8266401 8271210 + Conep17aG0114300.1 Cone17ag1114 1114
17 8278021 8284748 + Conep17aG0114400.1 Cone17ag1115 1115
20 3550335 3557163 - Conep20aG0062200.1 Cone20ag0605 605
20 3572734 3577343 - Conep20aG0062400.1 Cone20ag0607 607
20 3587827 3589722 - Conep20aG0062500.1 Cone20ag0608 608
20 4043960 4048297 - Conep20aG0068400.1 Cone20ag0663 663
2 3036490 3044032 - Cp4.1LG02g03470.1 Cpe02g00515 515
2 3046266 3053370 + Cp4.1LG02g03580.1 Cpe02g00516 516
2 3054056 3059262 - Cp4.1LG02g03490.1 Cpe02g00517 517
2 3060528 3063215 - Cp4.1LG02g03460.1 Cpe02g00518 518
7 1439138 1443464 - Cp4.1LG07g02250.1 Cpe07g00222 222
7 1445967 1450864 - Cp4.1LG07g02260.1 Cpe07g00224 224
7 1451616 1457162 - Cp4.1LG07g02320.1 Cpe07g00225 225
11 3091237 3096945 - Cp4.1LG11g05270.1 Cpe11g00523 523
11 3098320 3103214 - Cp4.1LG11g05320.1 Cpe11g00524 524
8 24954382 24960335 - CrPI670011_08g011720.1 Cre08g1172 1172
8 24968136 24980953 - CrPI670011_08g011730.1 Cre08g1173 1173
8 25774642 25779931 - CrPI670011_08g012570.1 Cre08g1257 1257
3 39686043 39693296 - CsaV3_3G048630.1 Csa03g04557 4557
3 39707232 39710878 + CsaV3_3G048650.1 Csa03g04559 4559
3 39711423 39718166 - CsaV3_3G048660.1 Csa03g04560 4560
3 39719218 39722464 - CsaV3_3G048670.1 Csa03g04561 4561
1 86936767 86944682 - Hsped.01g22270.1 Hepe01g2227 2227
1 86952989 86964045 + Hsped.01g22280.1 Hepe01g2228 2228
1 86964477 86969279 - Hsped.01g22290.1 Hepe01g2229 2229
1 86972426 86975675 - Hsped.01g22300.1 Hepe01g2230 2230
10 3807381 3814988 + Hsped.10g03480.1 Hepe10g0348 348
10 3816561 3821527 + Hsped.10g03490.1 Hepe10g0349 349
10 3829984 3837455 + Hsped.10g03500.1 Hepe10g0350 350
13 32192674 32204964 + Maker00025724 Lcy13g1393 1393
13 32206822 32212215 + Maker00025746 Lcy13g1394 1394
13 32223725 32230861 + Maker00025657 Lcy13g1395 1395
4 30561162 30568869 - Lsi04G023360.1 Lsi04g02336 2336
4 30583793 30593043 + Lsi04G023380.1 Lsi04g02338 2338
4 30591686 30602281 - Lsi04G023390.1 Lsi04g02339 2339
8 19532460 19539256 - Lsi08G010930.1 Lsi08g01093 1093
8 19545344 19550820 - Lsi08G010940.1 Lsi08g01094 1094
8 19560461 19566636 - Lsi08G010950.1 Lsi08g01095 1095
11 5233563 5237277 - MC11g0654 Mch11g0777 777
11 5248137 5257303 + MC11g0655 Mch11g0778 778
11 5256102 5262102 - MC11g0656 Mch11g0779 779
11 5262998 5266325 - MC11g0657 Mch11g0780 780
1 9529671 9535370 - Sed0027283.3 Sed01g1278 1278
1 9536541 9544146 - Sed0008487.1 Sed01g1279 1279
4 3958871 3965717 - Sed0008402.1 Sed04g0534 534
12 11526038 11530160 - Sed0025370.1 Sed12g1405 1405
1 104290443 104298155 - Tan0008824.1 Tan01g3941 3941
1 104314475 104319585 + Tan0020009.1 Tan01g3944 3944
1 104334099 104337836 - Tan0022465.3 Tan01g3948 3948
2 94320325 94327815 - Tan0006646.1 Tan02g2574 2574
2 94329025 94336733 - Tan0003275.1 Tan02g2575 2575
4 2986003 2987436 - Vvi4g312 Vvi4g312 312
4 2989478 2992239 + Vvi4g313 Vvi4g313 313
4 2998629 3016695 - Vvi4g314 Vvi4g314 314
4 3022801 3030621 + Vvi4g315 Vvi4g315 315
4 3040226 3044954 + Vvi4g316 Vvi4g316 316
4 3045207 3049485 - Vvi4g317 Vvi4g317 317
4 3049488 3050612 - Vvi4g318 Vvi4g318 318
4 3051065 3053938 + Vvi4g319 Vvi4g319 319
4 3054748 3076022 - Vvi4g320 Vvi4g320 320
4 3080418 3083398 - Vvi4g321 Vvi4g321 321
       

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