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
Vvi18g1350 . . . . . . . . . Cmo15g00592 . . . . . . Cpe13g00691 Bhi04g02172 . . . . . . Cla08g00276 Cam08g0717 Cec08g0271 Cco08g0364 Clacu08g0427 . Cre08g0252 Cone4ag1482 Cone7ag1462 . . . . . Cme03g00914 Blo17g00138 Blo18g00149 . Bda13g01422 Bpe02g01102 Bpe14g00435 Bma01g01434 Bma02g00157 . . . . . . Car15g00544 . . . . . . . . . . . . . . . . Lsi08g00248 . Chy03g00271 .
Vvi18g1351 Blo01g01736 Blo12g00779 Bda01g00864 Bda03g00400 Bpe02g00207 Bpe04g00363 Bma04g00381 Bma01g02513 Cmo04g02571 Cmo15g00593 . . . . . . . Bhi04g02173 . . . . . . Cla08g00268 Cam08g0708 Cec08g0269 Cco08g0355 Clacu08g0418 . Cre08g0246 Cone4ag1483 Cone7ag1461 Cone17ag0776 Cone20ag0368 . . . Cme03g00299 Blo17g00139 Blo18g00150 Bda11g00867 Bda13g01423 Bpe02g01101 Bpe14g00434 . Bma02g00158 . . Cmo09g01245 . . Car04g02363 Car09g01066 . . . . . . . . . . . . . . . . Lsi08g00564 . Chy03g00496 .
Vvi18g1352 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1353 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1354 . . . . . . . . . Cmo15g00594 . . . . Sed11g1366 . Cpe13g00688 Bhi04g01760 Tan11g1122 Cmetu03g1405 . Hepe02g2802 . Lcy10g1360 Cla08g00721 Cam08g1149 Cec08g0739 Cco08g0845 Clacu08g0857 . Cre08g0657 . . Cone17ag0777 . . . . Cme03g00300 Blo17g00140 . . Bda13g01424 . Bpe14g00433 . Bma02g00159 . . . . . . Car15g00546 . . . . . . . . . . . . . . . . Lsi08g00563 . Chy03g00497 .
Vvi18g1355 . . Bda01g00863 . . . . . . . Cma01g00928 . . . . Cpe06g00967 . Bhi04g02176 . . . . . . Cla08g00080 Cam08g0077 Cec08g0174 Cco08g0134 Clacu08g0090 Cmu08g0089 Cre08g0078 . . . . . . . Cme03g00918 Blo17g00141 Blo18g00151 . Bda13g01425 Bpe02g01100 . Bma01g01436 Bma02g00160 . . . . . . . . . . . . . . . . . . . . . . . Lsi08g00243 . Chy03g00268 .
Vvi18g1356 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo18g00153 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1357 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1358 Blo01g01734 Blo12g00780 . Bda03g00399 Bpe02g00209 Bpe04g00362 Bma04g00380 Bma01g02511 . . . Cma09g01182 . . . . . . . . . . . . . . . . . . . Cone4ag1485 Cone7ag1459 . . . . . Cme03g00962 . . Bda11g00869 . . . . . . Cmo01g00942 Cmo09g01186 . . . Car09g01057 . Cpe02g00947 . . . . . . . Cla11g00791 Cam11g0824 Cec11g0806 Cco11g0812 Clacu11g1033 Cmu11g0894 Cre11g1268 . . Chy03g00247 .
Vvi18g1359 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 41345413 41350470 + Bda002994.2 Bda01g00863 863
1 41353324 41354674 + Bda002995.1 Bda01g00864 864
3 3333551 3340578 + Bda033485 Bda03g00399 399
3 3344833 3346008 + Bda016364.1 Bda03g00400 400
11 8557044 8558360 - Bda005620.1 Bda11g00867 867
11 8567888 8570349 - Bda005622.1 Bda11g00869 869
13 36922003 36925414 + Bda000249.1 Bda13g01422 1422
13 36931278 36932679 - Bda000250.1 Bda13g01423 1423
13 36940146 36944517 - Bda000251.1 Bda13g01424 1424
13 36947009 36962055 - Bda032810 Bda13g01425 1425
4 42889976 42893834 - XM_039028120.1 Bhi04g01760 1760
4 59590850 59596913 + XM_039030243.1 Bhi04g02172 2172
4 59726222 59728434 + XM_039029789.1 Bhi04g02173 2173
4 59836140 59846145 - XM_039030114.1 Bhi04g02176 2176
1 57039789 57060880 + BLOR01734 Blo01g01734 1734
1 57071448 57072858 + BLOR01736 Blo01g01736 1736
12 26183852 26187047 - BLOR04798 Blo12g00779 779
12 26196583 26199085 - BLOR04799 Blo12g00780 780
17 1287910 1289210 + BLOR15959 Blo17g00138 138
17 1294428 1296066 - BLOR15960 Blo17g00139 139
17 1304438 1307301 - BLOR15961 Blo17g00140 140
17 1309809 1315616 - BLOR15962 Blo17g00141 141
18 1371747 1372826 + BLOR08637 Blo18g00149 149
18 1375298 1376989 - BLOR08638 Blo18g00150 150
18 1380176 1386137 - BLOR08639 Blo18g00151 151
18 1398717 1399570 + BLOR08641 Blo18g00153 153
1 24388692 24392044 + Bma001807.1 Bma01g01434 1434
1 24452987 24456768 - Bma001810.1 Bma01g01436 1436
1 82789972 82798985 + Bma003391.2 Bma01g02511 2511
1 82808105 82809504 + Bma003393.1 Bma01g02513 2513
2 1392021 1393839 + Bma014612.1 Bma02g00157 157
2 1404509 1405225 - Bma014613.1 Bma02g00158 158
2 1412195 1415694 - Bma014614.1 Bma02g00159 159
2 1417473 1424811 - Bma014615.1 Bma02g00160 160
4 3031270 3040535 + Bma018838.1 Bma04g00380 380
4 3049718 3050920 + Bma018839.1 Bma04g00381 381
2 1440430 1441119 - Bpe008057.1 Bpe02g00207 207
2 1451293 1453749 - Bpe008058.2 Bpe02g00209 209
2 14618916 14620637 + Bpe008958.1 Bpe02g01100 1100
2 14624963 14625697 + Bpe008959.1 Bpe02g01101 1101
2 14632657 14636147 - Bpe008960.1 Bpe02g01102 1102
4 2280240 2282708 + Bpe015053.1 Bpe04g00362 362
4 2287335 2288528 + Bpe015054.1 Bpe04g00363 363
14 3992106 3994413 + Bpe007084.1 Bpe14g00433 433
14 4000360 4001909 + Bpe007085.1 Bpe14g00434 434
14 4008375 4012002 - Bpe007086.1 Bpe14g00435 435
8 1380931 1414406 + CaPI482276_08g000770.1 Cam08g0077 77
8 5922821 5924828 + CaPI482276_08g007080.1 Cam08g0708 708
8 6075724 6082586 - CaPI482276_08g007170.1 Cam08g0717 717
8 17824900 17828879 + CaPI482276_08g011490.1 Cam08g1149 1149
11 10494293 10495527 - CaPI482276_11g008240.1 Cam11g0824 824
4 18985741 18986993 + Carg15798-RA Car04g02363 2363
9 9365576 9367845 + Carg27430-RA Car09g01057 1057
9 9559265 9560047 + Carg26415-RA Car09g01066 1066
15 2981908 2988822 + Carg01612-RA Car15g00544 544
15 3000632 3003851 - Carg01610-RA Car15g00546 546
8 2095190 2129126 + CcPI632755_08g001340.1 Cco08g0134 134
8 7135026 7137040 + CcPI632755_08g003550.1 Cco08g0355 355
8 7287126 7293981 - CcPI632755_08g003640.1 Cco08g0364 364
8 20293157 20297160 + CcPI632755_08g008450.1 Cco08g0845 845
11 9311955 9312785 - CcPI632755_11g008120.1 Cco11g0812 812
8 3372269 3405909 - CePI673135_08g001740.1 Cec08g0174 174
8 5345740 5347745 + CePI673135_08g002690.1 Cec08g0269 269
8 5472759 5479612 - CePI673135_08g002710.1 Cec08g0271 271
8 19112040 19116075 + CePI673135_08g007390.1 Cec08g0739 739
11 9566741 9567571 - CePI673135_11g008060.1 Cec11g0806 806
3 2348198 2350389 - Chy3G052270.1 Chy03g00247 247
3 2747845 2756390 + Chy3G052480.1 Chy03g00268 268
3 2801795 2807835 - Chy3G052510.1 Chy03g00271 271
3 6863400 6865205 - Chy3G054760.1 Chy03g00496 496
3 6883255 6885027 - Chy3G054770.1 Chy03g00497 497
8 1784625 1806488 + ClG42_08g0009000.10 Clacu08g0090 90
8 5748719 5750724 + ClG42_08g0041800.10 Clacu08g0418 418
8 5901625 5908489 - ClG42_08g0042700.10 Clacu08g0427 427
8 18603874 18607879 + ClG42_08g0085700.10 Clacu08g0857 857
11 12797269 12798503 + ClG42_11g0103300.10 Clacu11g1033 1033
8 1644569 1678348 + ClCG08G000780.1 Cla08g00080 80
8 5730290 5732603 + ClCG08G002610.1 Cla08g00268 268
8 5898679 5906220 - ClCG08G002670.2 Cla08g00276 276
8 19488486 19492722 + ClCG08G007080.1 Cla08g00721 721
11 11397983 11398813 - ClCG11G008270.1 Cla11g00791 791
1 5750437 5761210 - CmaCh01G009280.1 Cma01g00928 928
9 7508221 7511015 + CmaCh09G011820.1 Cma09g01182 1182
3 3843273 3845450 - MELO3C008331.2.1 Cme03g00299 299
3 3880416 3884503 - MELO3C008332.2.1 Cme03g00300 300
3 17472969 17479540 + MELO3C024986.2.1 Cme03g00914 914
3 17583193 17593013 + MELO3C024993.2.1 Cme03g00918 918
3 18339620 18342071 + MELO3C025030.2.1 Cme03g00962 962
3 8674678 8678297 - PI0028100.1 Cmetu03g1405 1405
1 5601000 5603863 - CmoCh01G009420.1 Cmo01g00942 942
4 18820203 18821836 + CmoCh04G025710.1 Cmo04g02571 2571
9 8692367 8695266 + CmoCh09G011860.1 Cmo09g01186 1186
9 10711480 10713377 + CmoCh09G012450.1 Cmo09g01245 1245
15 2863952 2870723 + CmoCh15G005920.1 Cmo15g00592 592
15 2876855 2878432 - CmoCh15G005930.1 Cmo15g00593 593
15 2884316 2887558 - CmoCh15G005940.1 Cmo15g00594 594
8 1710056 1736507 + CmPI595203_08g000890.1 Cmu08g0089 89
11 12126327 12127561 + CmPI595203_11g008940.1 Cmu11g0894 894
4 11608182 11611756 + Conep04aG0153400.1 Cone4ag1482 1482
4 11619194 11620722 - Conep04aG0153500.1 Cone4ag1483 1483
4 11629965 11632285 - Conep04aG0153700.1 Cone4ag1485 1485
7 10300343 10302837 + Conep07aG0150100.1 Cone7ag1459 1459
7 10308973 10310198 + Conep07aG0150300.1 Cone7ag1461 1461
7 10314403 10317982 - Conep07aG0150400.1 Cone7ag1462 1462
17 5888279 5889936 - Conep17aG0079400.1 Cone17ag0776 776
17 5949051 5951460 - Conep17aG0079500.1 Cone17ag0777 777
20 1675514 1677510 - Conep20aG0038200.1 Cone20ag0368 368
2 7964825 7967817 + Cp4.1LG02g09450.1 Cpe02g00947 947
6 9131201 9139335 + Cp4.1LG06g09550.1 Cpe06g00967 967
13 6434391 6437628 + Cp4.1LG13g04030.1 Cpe13g00688 688
13 6449150 6456041 - Cp4.1LG13g03960.1 Cpe13g00691 691
8 1639000 1672808 + CrPI670011_08g000780.1 Cre08g0078 78
8 6344682 6346711 + CrPI670011_08g002460.1 Cre08g0246 246
8 6461464 6468290 - CrPI670011_08g002520.1 Cre08g0252 252
8 19518911 19522912 + CrPI670011_08g006570.1 Cre08g0657 657
11 11201102 11201932 - CrPI670011_11g012680.1 Cre11g1268 1268
2 77053422 77057194 + Hsped.02g28020.1 Hepe02g2802 2802
10 36766400 36769992 + Maker00008709 Lcy10g1360 1360
8 5362998 5372328 + Lsi08G002430.1 Lsi08g00243 243
8 5548347 5554544 - Lsi08G002480.1 Lsi08g00248 248
8 13824850 13828778 + Lsi08G005630.1 Lsi08g00563 563
8 13859192 13861666 + Lsi08G005640.1 Lsi08g00564 564
11 29663961 29669651 + Sed0023841.1 Sed11g1366 1366
11 8901284 8905359 - Tan0001458.1 Tan11g1122 1122
18 19328723 19350461 + Vvi18g1350 Vvi18g1350 1350
18 19427036 19431008 - Vvi18g1351 Vvi18g1351 1351
18 19462138 19464089 - Vvi18g1352 Vvi18g1352 1352
18 19466089 19471788 + Vvi18g1353 Vvi18g1353 1353
18 19476892 19480968 - Vvi18g1354 Vvi18g1354 1354
18 19481411 19491537 - Vvi18g1355 Vvi18g1355 1355
18 19496009 19497154 - Vvi18g1356 Vvi18g1356 1356
18 19508350 19517807 + Vvi18g1357 Vvi18g1357 1357
18 19526361 19539811 - Vvi18g1358 Vvi18g1358 1358
18 19559679 19564675 + Vvi18g1359 Vvi18g1359 1359
       

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