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
Vvi17g356 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g357 . . . Bda15g00524 Bpe12g00685 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma08g00070 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g358 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g359 Blo04g00809 . . Bda15g00544 Bpe12g00667 . . . . . Cma10g00300 . Car10g00285 . . . . . . . . . . . . . . . . . . . . Cone13ag0296 . . . . . Blo13g00141 . . . . . . Bma08g00086 . Cmo10g00322 . . . . . . . . . . . . . . . . . . . . . . Csa01g00287 Chy02g02448 .
Vvi17g360 . . Bda06g00488 Bda15g00658 Bpe12g00497 . . . . . Cma10g00245 Cma11g00261 Car10g00232 . . . Cpe04g01413 . . . . . . . Cla06g01481 Cam06g1636 Cec06g1698 Cco06g1694 Clacu06g1602 Cmu06g1551 Cre06g2364 . . Cone13ag0297 Cone19ag0268 . . . . . . . . . . . . . Cmo10g00264 Cmo11g00267 . . . . . Cpe18g00747 . . . . . . . . . . . . . . Lsi06g01345 Csa01g00367 Chy02g02377 Cme02g01760
Vvi17g361 . . Bda06g00489 Bda15g00657 . . . Bma12g00939 . . Cma10g00247 Cma11g00259 Car10g00234 Car11g00237 . . Cpe04g01415 . . . . . . . Cla06g01483 Cam06g1638 . Cco06g1696 Clacu06g1604 Cmu06g1553 . . . Cone13ag0298 Cone19ag0267 . . . . . Blo15g00367 . . Bpe07g00729 . . . . Cmo10g00267 Cmo11g00265 . . . . . Cpe18g00745 . . . . . . . . . . . . . . . Csa01g00365 . Cme02g01763
Vvi17g362 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g363 . . Bda06g00490 Bda15g00656 Bpe12g00498 . . Bma12g00940 . . Cma10g00248 Cma11g00257 Car10g00236 Car11g00236 . . Cpe04g01416 . . . . . . . Cla06g01484 Cam06g1639 Cec06g1699 Cco06g1697 Clacu06g1605 Cmu06g1554 Cre06g2366 . . . . . . . . . Blo15g00366 . . Bpe07g00730 . . . . . Cmo11g00263 . . . . . Cpe18g00744 . . . . . . . . . . . . . . Lsi06g01347 Csa01g00364 Chy02g02379 Cme02g01764
Vvi17g364 . . Bda06g00491 . . . . Bma12g00941 . . Cma10g00249 . Car10g00237 . . . . . . . . . . . Cla06g01486 Cam06g1640 Cec06g1700 Cco06g1698 Clacu06g1606 Cmu06g1555 Cre06g2367 . . . Cone19ag0263 . . . . . Blo15g00365 . . Bpe07g00731 . . . . Cmo10g00269 . . . . . . Cpe18g00743 . . . . . . . . . . . . . . Lsi06g01348 Csa01g00363 Chy02g02380 Cme02g01765
Vvi17g365 . . Bda06g00492 Bda15g00655 Bpe12g00499 . . Bma12g00942 Cmo13g01080 . Cma10g00251 . Car10g00238 . Sed08g0332 Cpe20g00287 . Bhi02g00003 Tan09g1947 Cmetu02g0652 . . . . Cla06g01487 Cam06g1641 Cec06g1701 Cco06g1699 Clacu06g1607 Cmu06g1556 Cre06g2369 . . Cone13ag0300 . Lsi02g00165 . Chy12g01453 Cme12g01893 . Blo15g00364 . . Bpe07g00732 . . . Sed08g2165 Cmo10g00270 . Cma13g01039 . Car13g00871 . . Cpe18g00742 Bhi08g01210 Tan05g2291 Cmetu12g0125 Lac10g0217 Hepe07g2413 . . Cla04g01109 Cam04g1161 Cec01g1672 Cco01g1718 Clacu04g1189 Cmu04g1168 Cre01g1466 Lsi06g01349 Csa01g00361 Chy02g02382 Cme02g01766
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 6900949 6902149 - Bda023733.2 Bda06g00488 488
6 6904699 6907426 - Bda023734.1 Bda06g00489 489
6 6944810 6949662 - Bda023736.1 Bda06g00490 490
6 6951024 6955839 - Bda023737.1 Bda06g00491 491
6 6981959 6983008 + Bda023739.1 Bda06g00492 492
15 8295672 8298128 + Bda012354.1 Bda15g00524 524
15 8497047 8499492 - Bda012377.1 Bda15g00544 544
15 10022440 10023468 - Bda012503.1 Bda15g00655 655
15 10037769 10043311 + Bda012505.1 Bda15g00656 656
15 10049380 10050911 + Bda012507.1 Bda15g00657 657
15 10053616 10054715 + Bda012508.1 Bda15g00658 658
2 92371 94394 + XM_039022888.1 Bhi02g00003 3
8 37639019 37641831 - XM_039039247.1 Bhi08g01210 1210
4 8390921 8393789 - BLOR13721 Blo04g00809 809
13 4441743 4444408 + BLOR05422 Blo13g00141 141
15 4785516 4794542 - BLOR06758 Blo15g00364 364
15 4847530 4853849 + BLOR06759 Blo15g00365 365
15 4879591 4887724 + BLOR06760 Blo15g00366 366
15 4897246 4900665 + BLOR06761 Blo15g00367 367
8 872840 875349 + Bma027069.1 Bma08g00070 70
8 1007157 1009573 - Bma027085.1 Bma08g00086 86
12 41200852 41201879 - Bma030521 Bma12g00939 939
12 41204920 41210059 - Bma030522 Bma12g00940 940
12 41211977 41217933 - Bma030523 Bma12g00941 941
12 41224019 41225113 + Bma008282.1 Bma12g00942 942
7 13824702 13837674 - Bpe021573.1 Bpe07g00729 729
7 13839610 13844576 - Bpe021574.1 Bpe07g00730 730
7 13845882 13850782 - Bpe026077 Bpe07g00731 731
7 13858905 13859954 + Bpe021575.1 Bpe07g00732 732
12 10783517 10784583 - Bpe024895 Bpe12g00497 497
12 10791233 10796763 - Bpe005760.1 Bpe12g00498 498
12 10812478 10813506 + Bpe005761.1 Bpe12g00499 499
12 12329785 12332213 + Bpe005927.1 Bpe12g00667 667
12 12443224 12445506 - Bpe005944.2 Bpe12g00685 685
4 25676918 25678194 + CaPI482276_04g011610.1 Cam04g1161 1161
6 27801158 27802268 - CaPI482276_06g016360.1 Cam06g1636 1636
6 27810158 27815607 - CaPI482276_06g016380.1 Cam06g1638 1638
6 27815723 27825861 - CaPI482276_06g016390.1 Cam06g1639 1639
6 27834212 27845723 - CaPI482276_06g016400.1 Cam06g1640 1640
6 27864311 27865511 - CaPI482276_06g016410.1 Cam06g1641 1641
10 1102053 1103475 - Carg17911-RA Car10g00232 232
10 1105338 1109648 - Carg17909-RA Car10g00234 234
10 1111406 1119762 - Carg17907-RA Car10g00236 236
10 1121558 1130388 - Carg17906-RA Car10g00237 237
10 1134385 1135686 - Carg17905-RA Car10g00238 238
10 1370957 1376756 - Carg15152-RA Car10g00285 285
11 1328627 1334690 + Carg09153-RA Car11g00236 236
11 1335346 1339777 + Carg09152-RA Car11g00237 237
13 9223112 9224384 + Carg04801-RA Car13g00871 871
1 29931639 29932915 + CcPI632755_01g017180.1 Cco01g1718 1718
6 27495723 27496833 - CcPI632755_06g016940.1 Cco06g1694 1694
6 27505264 27510751 - CcPI632755_06g016960.1 Cco06g1696 1696
6 27510914 27520995 - CcPI632755_06g016970.1 Cco06g1697 1697
6 27533081 27540884 - CcPI632755_06g016980.1 Cco06g1698 1698
6 27559643 27560843 - CcPI632755_06g016990.1 Cco06g1699 1699
1 31357332 31358611 + CePI673135_01g016720.1 Cec01g1672 1672
6 30551839 30552949 - CePI673135_06g016980.1 Cec06g1698 1698
6 30560175 30575928 - CePI673135_06g016990.1 Cec06g1699 1699
6 30588094 30595929 - CePI673135_06g017000.1 Cec06g1700 1700
6 30611994 30613197 - CePI673135_06g017010.1 Cec06g1701 1701
2 27593636 27594736 - Chy2G046440.1 Chy02g02377 2377
2 27604048 27618768 - Chy2G046460.1 Chy02g02379 2379
2 27627429 27634298 - Chy2G046470.1 Chy02g02380 2380
2 27643162 27644196 - Chy2G046490.1 Chy02g02382 2382
2 28105040 28112661 - Chy2G047150.1 Chy02g02448 2448
12 18507587 18508824 + Chy12G220530.1 Chy12g01453 1453
4 26065082 26066356 + ClG42_04g0118900.10 Clacu04g1189 1189
6 26853795 26854905 - ClG42_06g0160200.10 Clacu06g1602 1602
6 26862611 26868079 - ClG42_06g0160400.10 Clacu06g1604 1604
6 26868195 26878326 - ClG42_06g0160500.10 Clacu06g1605 1605
6 26889784 26897588 - ClG42_06g0160600.10 Clacu06g1606 1606
6 26916222 26917412 - ClG42_06g0160700.10 Clacu06g1607 1607
4 26285757 26287031 + ClCG04G011270.1 Cla04g01109 1109
6 28370605 28371715 - ClCG06G014980.1 Cla06g01481 1481
6 28378619 28386020 - ClCG06G015000.2 Cla06g01483 1483
6 28387349 28395123 - ClCG06G015010.2 Cla06g01484 1484
6 28409307 28421052 - ClCG06G015030.1 Cla06g01486 1486
6 28442432 28443622 - ClCG06G015040.2 Cla06g01487 1487
10 1092891 1094340 - CmaCh10G002450.1 Cma10g00245 245
10 1096663 1101334 - CmaCh10G002470.1 Cma10g00247 247
10 1102128 1110280 - CmaCh10G002480.1 Cma10g00248 248
10 1112237 1121432 - CmaCh10G002490.1 Cma10g00249 249
10 1125345 1127009 - CmaCh10G002510.1 Cma10g00251 251
10 1356186 1361970 - CmaCh10G003000.1 Cma10g00300 300
11 1304803 1310581 + CmaCh11G002570.1 Cma11g00257 257
11 1312485 1316348 + CmaCh11G002590.1 Cma11g00259 259
11 1319866 1321536 + CmaCh11G002610.1 Cma11g00261 261
13 7930012 7931011 + CmaCh13G010390.1 Cma13g01039 1039
2 24527011 24528989 - MELO3C017292.2.1 Cme02g01760 1760
2 24537353 24543858 - MELO3C017289.2.1 Cme02g01763 1763
2 24545059 24552847 - MELO3C017288.2.1 Cme02g01764 1764
2 24560785 24568263 - MELO3C017287.2.1 Cme02g01765 1765
2 24576035 24577997 - MELO3C017286.2.1 Cme02g01766 1766
12 25077880 25079727 + MELO3C002076.2.1 Cme12g01893 1893
2 22912572 22914567 - PI0009455.1 Cmetu02g0652 652
12 1129461 1130703 - PI0019972.1 Cmetu12g0125 125
10 1173721 1175149 - CmoCh10G002640.1 Cmo10g00264 264
10 1177445 1181163 - CmoCh10G002670.1 Cmo10g00267 267
10 1183016 1202615 - CmoCh10G002690.1 Cmo10g00269 269
10 1207434 1208339 - CmoCh10G002700.1 Cmo10g00270 270
10 1445053 1456482 - CmoCh10G003220.1 Cmo10g00322 322
11 1296730 1302483 + CmoCh11G002630.1 Cmo11g00263 263
11 1303973 1307794 + CmoCh11G002650.1 Cmo11g00265 265
11 1311612 1313014 + CmoCh11G002670.1 Cmo11g00267 267
13 8937938 8939255 + CmoCh13G010800.1 Cmo13g01080 1080
4 26246852 26248126 + CmPI595203_04g011680.1 Cmu04g1168 1168
6 26756520 26757630 - CmPI595203_06g015510.1 Cmu06g1551 1551
6 26765336 26770804 - CmPI595203_06g015530.1 Cmu06g1553 1553
6 26770920 26781056 - CmPI595203_06g015540.1 Cmu06g1554 1554
6 26792488 26800299 - CmPI595203_06g015550.1 Cmu06g1555 1555
6 26818910 26820100 - CmPI595203_06g015560.1 Cmu06g1556 1556
13 2234645 2243209 + Conep13aG0031400.1 Cone13ag0296 296
13 2243550 2244644 - Conep13aG0031500.1 Cone13ag0297 297
13 2255921 2260799 - Conep13aG0031600.1 Cone13ag0298 298
13 2293531 2294340 - Conep13aG0031800.1 Cone13ag0300 300
19 1774553 1781158 - Conep19aG0027300.1 Cone19ag0263 263
19 1832509 1837037 + Conep19aG0027700.1 Cone19ag0267 267
19 1851126 1852631 + Conep19aG0027800.1 Cone19ag0268 268
4 11366690 11367843 - Cp4.1LG04g14100.1 Cpe04g01413 1413
4 11372309 11377219 - Cp4.1LG04g14230.1 Cpe04g01415 1415
4 11377967 11383545 - Cp4.1LG04g14250.1 Cpe04g01416 1416
18 7204557 7206172 + Cp4.1LG18g07440.1 Cpe18g00742 742
18 7209797 7219220 + Cp4.1LG18g07460.1 Cpe18g00743 743
18 7220515 7228944 + Cp4.1LG18g07470.1 Cpe18g00744 744
18 7229960 7234200 + Cp4.1LG18g07480.1 Cpe18g00745 745
18 7237274 7238449 + Cp4.1LG18g07450.1 Cpe18g00747 747
20 1590006 1594223 + Cp4.1LG20g02880.1 Cpe20g00287 287
1 27894508 27895820 + CrPI670011_01g014660.1 Cre01g1466 1466
6 31558739 31559849 - CrPI670011_06g023640.1 Cre06g2364 2364
6 31567665 31583400 - CrPI670011_06g023660.1 Cre06g2366 2366
6 31590010 31602619 - CrPI670011_06g023670.1 Cre06g2367 2367
6 31627886 31629098 - CrPI670011_06g023690.1 Cre06g2369 2369
1 1800473 1806924 + CsaV3_1G002870.1 Csa01g00287 287
1 2248340 2250830 + CsaV3_1G003610.1 Csa01g00361 361
1 2257803 2265303 + CsaV3_1G003630.1 Csa01g00363 363
1 2271371 2280360 + CsaV3_1G003640.1 Csa01g00364 364
1 2281308 2287899 + CsaV3_1G003650.1 Csa01g00365 365
1 2295714 2298516 + CsaV3_1G003670.1 Csa01g00367 367
7 68484568 68485699 + Hsped.07g24130.1 Hepe07g2413 2413
10 1702544 1703647 - Lag0024262.1 Lac10g0217 217
2 1386697 1388257 - Lsi02G001650.1 Lsi02g00165 165
6 24030941 24032987 - Lsi06G013450.1 Lsi06g01345 1345
6 24041140 24058079 - Lsi06G013470.1 Lsi06g01347 1347
6 24071933 24079485 - Lsi06G013480.1 Lsi06g01348 1348
6 24096487 24097515 - Lsi06G013490.1 Lsi06g01349 1349
8 1998727 2000775 + Sed0006307.2 Sed08g0332 332
8 35571545 35573266 - Sed0024758.1 Sed08g2165 2165
5 74232717 74234038 + Tan0015789.1 Tan05g2291 2291
9 70411445 70413263 - Tan0013890.1 Tan09g1947 1947
17 4155404 4159947 + Vvi17g356 Vvi17g356 356
17 4166030 4174318 + Vvi17g357 Vvi17g357 357
17 4191394 4195089 + Vvi17g358 Vvi17g358 358
17 4195886 4225096 + Vvi17g359 Vvi17g359 359
17 4225512 4226967 - Vvi17g360 Vvi17g360 360
17 4232999 4244972 - Vvi17g361 Vvi17g361 361
17 4274452 4277479 + Vvi17g362 Vvi17g362 362
17 4277598 4305670 - Vvi17g363 Vvi17g363 363
17 4309790 4334309 - Vvi17g364 Vvi17g364 364
17 4343549 4345620 + Vvi17g365 Vvi17g365 365
       

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