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
Vvi17g366 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g367 . . . . . . . . Cmo13g01082 . . . . . . Cpe20g00107 . . . . . . . . . . . . . . . Cone2ag0646 . . . Lsi02g00164 Csa01g00648 Chy12g01454 Cme12g01894 . . . Bda14g00912 . Bpe15g00546 Bma03g00887 . . . . Cma13g01041 . Car13g00873 . . . Bhi08g01209 . . Lac10g0216 . . . Cla04g01110 Cam04g1162 Cec01g1673 Cco01g1719 Clacu04g1190 Cmu04g1170 Cre01g1467 . . . .
Vvi17g368 . . . Bda15g00652 Bpe12g00502 . . . . . Cma10g00255 Cma11g00246 Car10g00240 Car11g00226 . . . Bhi02g00005 . . . . . . Cla06g01491 Cam06g1645 Cec06g1705 Cco06g1703 Clacu06g1611 Cmu06g1560 Cre06g2372 . . . . . . . . . Blo15g00363 . . Bpe07g00734 . . . . Cmo10g00272 Cmo11g00253 . . . . . Cpe18g00740 . . . . . . . . . . . . . . Lsi06g01355 Csa01g00357 . Cme02g01771
Vvi17g369 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g370 . . Bda06g00494 Bda15g00651 . . . . . . Cma10g00256 Cma11g00245 Car10g00241 Car11g00225 . . . Bhi02g00007 . . . . . . Cla06g01492 Cam06g1646 Cec06g1706 Cco06g1704 Clacu06g1612 Cmu06g1561 Cre06g2373 . . . . . . . . . Blo15g00362 . . Bpe07g00735 . . . . Cmo10g00273 Cmo11g00252 . . . . . Cpe18g00739 . . . . . . . . . . . . . . Lsi06g01357 Csa01g00356 Chy02g02387 Cme02g01772
Vvi17g371 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g372 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0001 Cone19ag0002 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g373 . . Bda06g00495 . . . . Bma12g00944 Cmo13g01084 . . . . . . Cpe20g00105 . . . . . . . . . . . . . . . . . . . Lsi02g00371 Csa01g00850 Chy12g01456 Cme12g01896 . Blo15g00358 . . Bpe07g00736 . . . . . . Cma13g01043 . Car13g00875 . . . Bhi08g01202 . . . . . . Cla04g01112 Cam04g1164 Cec01g1675 Cco01g1723 Clacu04g1192 Cmu04g1172 Cre01g1470 . . . .
Vvi17g374 . . . . . . . . . Cmo18g00024 . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0002 Cone19ag0003 Lsi02g00159 Csa01g00644 Chy12g01458 Cme12g01898 . . . Bda14g00908 . Bpe15g00550 Bma03g00883 . Sed08g2161 . . . . Car13g00876 Car18g00160 . . Bhi08g01195 Tan05g2296 Cmetu12g0160 Lac10g0211 Hepe07g2418 . . Cla04g01114 Cam04g1167 Cec01g1678 Cco01g1726 Clacu04g1195 Cmu04g1174 Cre01g1473 . . . .
Vvi17g375 . . . . . Bpe13g00337 Bma06g00005 . Cmo13g01086 . . . . . . Cpe20g00103 . . . . . . . . . . . . . . . . Cone16ag0270 . . Lsi02g00158 Csa01g00643 Chy12g01459 Cme12g01899 . . . . . . . . Sed08g2160 . . Cma13g01045 . Car13g00878 . . . Bhi08g01035 Tan05g2298 Cmetu12g0465 Lac10g0210 Hepe07g2419 . . Cla04g01115 Cam04g1168 Cec01g1679 Cco01g1727 Clacu04g1196 Cmu04g1175 Cre01g1474 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 7025917 7031479 + Bda023741.1 Bda06g00494 494
6 7053245 7054771 - Bda023743.2 Bda06g00495 495
14 7048235 7049388 - Bda027688.1 Bda14g00908 908
14 7085406 7113643 + Bda027692.1 Bda14g00912 912
15 9958601 9963009 - Bda012498.2 Bda15g00651 651
15 9969824 9970318 + Bda012499.1 Bda15g00652 652
2 220509 222352 + XM_039023841.1 Bhi02g00005 5
2 232246 237392 - XM_039023412.1 Bhi02g00007 7
8 33816661 33824267 - XM_039039103.1 Bhi08g01035 1035
8 37356407 37358502 - XM_039039669.1 Bhi08g01195 1195
8 37475623 37479523 - XM_039037966.1 Bhi08g01202 1202
8 37586988 37622295 + XM_039038723.1 Bhi08g01209 1209
15 4578285 4579843 + BLOR06752 Blo15g00358 358
15 4658275 4663533 - BLOR06756 Blo15g00362 362
15 4679032 4679505 + BLOR06757 Blo15g00363 363
3 8630634 8631309 - Bma017202.1 Bma03g00883 883
3 8657535 8667519 + Bma017206.1 Bma03g00887 887
6 200068 205269 - Bma022606.1 Bma06g00005 5
12 41274480 41276138 - Bma008285.1 Bma12g00944 944
7 13888787 13889242 - Bpe021578.1 Bpe07g00734 734
7 13891383 13895892 + Bpe026078 Bpe07g00735 735
7 13908697 13910696 - Bpe021580.1 Bpe07g00736 736
12 10845361 10845855 - Bpe005764.1 Bpe12g00502 502
13 11228769 11231392 + Bpe006464.1 Bpe13g00337 337
15 16551448 16573408 - Bpe001481.1 Bpe15g00546 546
15 16584799 16585935 + Bpe001485.1 Bpe15g00550 550
4 25694957 25717612 - CaPI482276_04g011620.1 Cam04g1162 1162
4 25731486 25734611 - CaPI482276_04g011640.1 Cam04g1164 1164
4 25744323 25745947 + CaPI482276_04g011670.1 Cam04g1167 1167
4 25746812 25752695 - CaPI482276_04g011680.1 Cam04g1168 1168
6 27899497 27899949 + CaPI482276_06g016450.1 Cam06g1645 1645
6 27902161 27906605 - CaPI482276_06g016460.1 Cam06g1646 1646
10 1147204 1147668 + Carg17903-RA Car10g00240 240
10 1148295 1153605 - Carg17902-RA Car10g00241 241
11 1271692 1277151 + Carg09164-RA Car11g00225 225
11 1277703 1278152 - Carg09163-RA Car11g00226 226
13 9238125 9250147 - Carg04799-RA Car13g00873 873
13 9255094 9257136 - Carg04797-RA Car13g00875 875
13 9258575 9261556 + Carg04796-RA Car13g00876 876
13 9261942 9267400 - Carg04794-RA Car13g00878 878
18 869626 872913 - Carg06726-RA Car18g00160 160
1 29949738 29971519 - CcPI632755_01g017190.1 Cco01g1719 1719
1 29986941 29990068 - CcPI632755_01g017230.1 Cco01g1723 1723
1 29999692 30001328 + CcPI632755_01g017260.1 Cco01g1726 1726
1 30002225 30008103 - CcPI632755_01g017270.1 Cco01g1727 1727
6 27595900 27596352 + CcPI632755_06g017030.1 Cco06g1703 1703
6 27598309 27602778 - CcPI632755_06g017040.1 Cco06g1704 1704
1 31375328 31396783 - CePI673135_01g016730.1 Cec01g1673 1673
1 31411584 31414723 - CePI673135_01g016750.1 Cec01g1675 1675
1 31424405 31426026 + CePI673135_01g016780.1 Cec01g1678 1678
1 31426887 31432787 - CePI673135_01g016790.1 Cec01g1679 1679
6 30645269 30645721 + CePI673135_06g017050.1 Cec06g1705 1705
6 30647590 30652010 - CePI673135_06g017060.1 Cec06g1706 1706
2 27674924 27679146 - Chy2G046540.1 Chy02g02387 2387
12 18521385 18537670 - Chy12G220540.1 Chy12g01454 1454
12 18545663 18548103 - Chy12G220560.1 Chy12g01456 1456
12 18554279 18555219 + Chy12G220580.1 Chy12g01458 1458
12 18556013 18560603 - Chy12G220590.1 Chy12g01459 1459
4 26083079 26105465 - ClG42_04g0119000.10 Clacu04g1190 1190
4 26119336 26122481 - ClG42_04g0119200.10 Clacu04g1192 1192
4 26132150 26133774 + ClG42_04g0119500.10 Clacu04g1195 1195
4 26134626 26140506 - ClG42_04g0119600.10 Clacu04g1196 1196
6 26951205 26951657 + ClG42_06g0161100.10 Clacu06g1611 1611
6 26953755 26958195 - ClG42_06g0161200.10 Clacu06g1612 1612
4 26303456 26326114 - ClCG04G011280.2 Cla04g01110 1110
4 26343060 26346204 - ClCG04G011310.2 Cla04g01112 1112
4 26358610 26360234 + ClCG04G011330.1 Cla04g01114 1114
4 26360495 26366966 - ClCG04G011340.2 Cla04g01115 1115
6 28478239 28478691 + ClCG06G015070.1 Cla06g01491 1491
6 28480294 28485526 - ClCG06G015080.1 Cla06g01492 1492
10 1137997 1138461 + CmaCh10G002550.1 Cma10g00255 255
10 1139004 1144326 - CmaCh10G002560.1 Cma10g00256 256
11 1244761 1250245 + CmaCh11G002450.1 Cma11g00245 245
11 1250808 1251453 - CmaCh11G002460.1 Cma11g00246 246
13 7939023 7956807 - CmaCh13G010410.1 Cma13g01041 1041
13 7961352 7964010 - CmaCh13G010430.1 Cma13g01043 1043
13 7967963 7973595 - CmaCh13G010450.1 Cma13g01045 1045
2 24608225 24608983 + MELO3C017282.2.1 Cme02g01771 1771
2 24610194 24615291 - MELO3C017281.2.1 Cme02g01772 1772
12 25090713 25113442 - MELO3C002074.2.1 Cme12g01894 1894
12 25121796 25124655 - MELO3C002072.2.1 Cme12g01896 1896
12 25129137 25130939 + MELO3C002070.2.1 Cme12g01898 1898
12 25131123 25136654 - MELO3C002069.2.1 Cme12g01899 1899
12 1078162 1079826 - PI0008727.1 Cmetu12g0160 160
12 1072322 1078045 + PI0025875.1 Cmetu12g0465 465
10 1220060 1220524 + CmoCh10G002720.1 Cmo10g00272 272
10 1221877 1226387 - CmoCh10G002730.1 Cmo10g00273 273
11 1242944 1246047 + CmoCh11G002520.1 Cmo11g00252 252
11 1246052 1246501 - CmoCh11G002530.1 Cmo11g00253 253
13 8947356 8965408 - CmoCh13G010820.1 Cmo13g01082 1082
13 8971326 8973711 - CmoCh13G010840.1 Cmo13g01084 1084
13 8978787 8984452 - CmoCh13G010860.1 Cmo13g01086 1086
18 103021 104548 + CmoCh18G000240.1 Cmo18g00024 24
4 26264856 26287239 - CmPI595203_04g011700.1 Cmu04g1170 1170
4 26301113 26304256 - CmPI595203_04g011720.1 Cmu04g1172 1172
4 26313927 26315551 + CmPI595203_04g011740.1 Cmu04g1174 1174
4 26316403 26322283 - CmPI595203_04g011750.1 Cmu04g1175 1175
6 26853882 26854334 + CmPI595203_06g015600.1 Cmu06g1560 1560
6 26856439 26860879 - CmPI595203_06g015610.1 Cmu06g1561 1561
2 31145654 31191240 - Conep02aG0165700.1 Cone2ag0646 646
13 6455 15096 + Conep13aG0000100.1 Cone13ag0001 1
13 15809 16346 + Conep13aG0000200.1 Cone13ag0002 2
16 3023166 3031032 - Conep16aG0261900.1 Cone16ag0270 270
19 35433 40101 + Conep19aG0000200.1 Cone19ag0002 2
19 40469 43993 + Conep19aG0000300.1 Cone19ag0003 3
18 7184511 7189808 + Cp4.1LG18g07260.1 Cpe18g00739 739
18 7190771 7191235 - Cp4.1LG18g07310.1 Cpe18g00740 740
20 544733 550457 + Cp4.1LG20g00940.1 Cpe20g00103 103
20 554937 557788 + Cp4.1LG20g00950.1 Cpe20g00105 105
20 562593 580583 + Cp4.1LG20g00990.1 Cpe20g00107 107
1 27912781 27935452 - CrPI670011_01g014670.1 Cre01g1467 1467
1 27949560 27952697 - CrPI670011_01g014700.1 Cre01g1470 1470
1 27962497 27964107 + CrPI670011_01g014730.1 Cre01g1473 1473
1 27964971 27970863 - CrPI670011_01g014740.1 Cre01g1474 1474
6 31663327 31663779 + CrPI670011_06g023720.1 Cre06g2372 2372
6 31665928 31670395 - CrPI670011_06g023730.1 Cre06g2373 2373
1 2213060 2218204 + CsaV3_1G003560.1 Csa01g00356 356
1 2219167 2220143 - CsaV3_1G003570.1 Csa01g00357 357
1 4095884 4101614 + CsaV3_1G006430.1 Csa01g00643 643
1 4098779 4103129 - CsaV3_1G006440.1 Csa01g00644 644
1 4118084 4135335 + CsaV3_1G006480.1 Csa01g00648 648
1 5321745 5326440 - CsaV3_1G008500.1 Csa01g00850 850
7 68562915 68564300 + Hsped.07g24180.1 Hepe07g2418 2418
7 68564875 68570536 - Hsped.07g24190.1 Hepe07g2419 2419
10 1630624 1635567 + Lag0024255.1 Lac10g0210 210
10 1636347 1637696 - Lag0024256.1 Lac10g0211 211
10 1668469 1686675 + Lag0024261.1 Lac10g0216 216
2 1313438 1319208 + Lsi02G001580.1 Lsi02g00158 158
2 1319334 1321299 - Lsi02G001590.1 Lsi02g00159 159
2 1357907 1370584 + Lsi02G001640.1 Lsi02g00164 164
2 3196590 3217853 - Lsi02G003710.1 Lsi02g00371 371
6 24134463 24134915 + Lsi06G013550.1 Lsi06g01355 1355
6 24147933 24153942 + Lsi06G013570.1 Lsi06g01357 1357
8 35531308 35536564 + Sed0001077.1 Sed08g2160 2160
8 35537969 35539405 - Sed0007811.1 Sed08g2161 2161
5 74462702 74464017 + Tan0018032.1 Tan05g2296 2296
5 74464694 74470431 - Tan0019023.2 Tan05g2298 2298
17 4378225 4378408 - Vvi17g366 Vvi17g366 366
17 4393225 4459556 - Vvi17g367 Vvi17g367 367
17 4474479 4477370 - Vvi17g368 Vvi17g368 368
17 4477985 4479788 - Vvi17g369 Vvi17g369 369
17 4483061 4492879 + Vvi17g370 Vvi17g370 370
17 4493027 4493183 - Vvi17g371 Vvi17g371 371
17 4493689 4501284 - Vvi17g372 Vvi17g372 372
17 4502587 4505873 - Vvi17g373 Vvi17g373 373
17 4509161 4510718 + Vvi17g374 Vvi17g374 374
17 4510754 4521210 - Vvi17g375 Vvi17g375 375
       

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