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
Vvi3g146 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g147 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g148 . . . Bda08g00997 . . Bma05g00361 . . . Cma02g00252 . . . . . . . . . . . . . . . . . . . . . . . . Lsi10g00490 . Chy11g00261 . . . . . . Bpe05g00284 . . Sed02g0073 Cmo02g00251 . . . . . . Cpe05g01377 Bhi10g01858 Tan05g1147 Cmetu11g2225 . Hepe08g0287 . . Cla02g01162 Cam02g1238 Cec02g1247 Cco02g1287 Clacu02g1220 Cmu02g1188 Cre02g1499 . Csa02g01384 . Cme11g00386
Vvi3g149 . . . . . Bpe12g00118 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag1279 . . . . . . Blo04g00563 Blo13g00510 Bda15g01037 Bda14g00612 . . Bma03g00603 Bma08g00758 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g150 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g151 . Blo15g00376 . Bda08g00995 . Bpe12g00119 Bma05g00363 . Cmo19g00741 . Cma02g00253 Cma20g00756 . Car20g00657 . . . Bhi05g01727 . . . . . . Cla02g00434 . . . . . . . . . . . . . . . Blo13g00508 Bda15g01036 . . Bpe05g00285 Bma03g00604 Bma08g00755 . Cmo02g00252 Cmo20g00752 . Cma19g00733 . Car19g00562 Cpe16g00313 . Bhi10g01253 . . . Hepe08g0339 . . Cla02g01163 . . . . . . . . . Cme11g00385
Vvi3g152 . . . . . . . . Cmo19g00742 . . . . . Sed05g2222 . Cpe15g00587 Bhi05g01726 Tan02g0695 Cmetu01g1029 . Hepe02g0430 . . . . . . . . . Cone12ag1229 Cone8ag1280 . . . Csa07g00093 . Cme01g01269 Blo04g00564 . . Bda14g00613 Bpe15g00817 . Bma03g00605 . . . . . . . Car19g00563 . . . . . . . . . . . . . . . . Lsi11g01196 . Chy01g00685 .
Vvi3g153 . . . . . . . . Cmo19g00743 . . Cma20g00755 . Car20g00656 Sed05g2221 . Cpe15g00588 Bhi05g01723 Tan02g0693 Cmetu01g1869 . Hepe02g0429 . . Cla02g00433 Cam02g0442 Cec02g0440 Cco02g0458 Clacu02g0443 Cmu02g0438 Cre02g0772 Cone12ag1230 Cone8ag1282 . . Lsi10g00492 Csa07g00094 Chy11g00259 Cme01g01268 Blo04g00565 . . Bda14g00614 Bpe15g00816 . Bma03g00606 . Sed01g0198 . Cmo20g00751 . Cma19g00735 . Car19g00564 Cpe16g00314 . Bhi10g01856 Tan05g1144 Cmetu11g0298 . Hepe08g0289 . . Cla02g01164 Cam02g1241 Cec02g1250 Cco02g1291 Clacu02g1223 Cmu02g1191 Cre02g1502 . Csa02g01388 . Cme11g00384
Vvi3g154 . . . . . Bpe12g00120 . . . . Cma02g00257 Cma20g00754 . Car20g00655 . . . . . . . . . . . . . . . . . . . . Cone10ag1234 . . Chy11g00258 . Blo04g00566 Blo13g00505 Bda15g01035 . Bpe15g00815 . Bma03g00607 Bma08g00752 Sed01g0197 Cmo02g00253 Cmo20g00750 . . . . Cpe16g00315 Cpe05g01375 Bhi10g01854 Tan05g1142 Cmetu11g0032 . Hepe08g0290 . . Cla02g01165 Cam02g1242 Cec02g1251 Cco02g1292 Clacu02g1224 Cmu02g1192 Cre02g1504 . Csa02g01389 . Cme11g00383
Vvi3g155 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 20319679 20320535 + Bda029669.1 Bda08g00995 995
8 20563441 20565207 + Bda029674.1 Bda08g00997 997
14 4597232 4604062 - Bda027366.1 Bda14g00612 612
14 4606072 4611347 - Bda027367.1 Bda14g00613 613
14 4613425 4623054 - Bda027368.1 Bda14g00614 614
15 19333013 19343273 - Bda013020.1 Bda15g01035 1035
15 19388633 19389533 + Bda013023.1 Bda15g01036 1036
15 19399714 19402760 + Bda013024.1 Bda15g01037 1037
5 55663132 55670575 + XM_039031639.1 Bhi05g01723 1723
5 55706288 55710744 + XM_039032199.1 Bhi05g01726 1726
5 55718388 55719924 + XM_039031491.1 Bhi05g01727 1727
10 29142527 29146522 - XM_039044485.1 Bhi10g01253 1253
10 46073809 46087884 - XM_039045391.1 Bhi10g01854 1854
10 46154278 46160048 + XM_039045951.1 Bhi10g01856 1856
10 46224324 46228667 - XM_039045766.1 Bhi10g01858 1858
4 4844105 4851515 - BLOR13475 Blo04g00563 563
4 4853899 4857349 - BLOR13476 Blo04g00564 564
4 4858594 4862751 - BLOR13477 Blo04g00565 565
4 4867342 4882643 + BLOR13478 Blo04g00566 566
13 26382024 26394906 - BLOR05786 Blo13g00505 505
13 26491298 26492141 + BLOR05789 Blo13g00508 508
13 26592184 26594997 + BLOR05791 Blo13g00510 510
15 5248512 5249341 - BLOR06770 Blo15g00376 376
3 4979065 4981193 - Bma016895.1 Bma03g00603 603
3 4985123 4985988 - Bma016896.1 Bma03g00604 604
3 4987954 4991408 - Bma016897.1 Bma03g00605 605
3 4992019 4995824 - Bma030979 Bma03g00606 606
3 4996965 5007123 + Bma016898.1 Bma03g00607 607
5 11094777 11096532 - Bma021171.1 Bma05g00361 361
5 11218842 11219695 - Bma021175.1 Bma05g00363 363
8 43967032 43983882 - Bma028127.1 Bma08g00752 752
8 44301607 44302507 + Bma028130.1 Bma08g00755 755
8 44528902 44533892 + Bma028134.1 Bma08g00758 758
5 15997271 15998983 + Bpe017698.1 Bpe05g00284 284
5 16009870 16010724 - Bpe017699.1 Bpe05g00285 285
12 837392 840418 - Bpe005358.1 Bpe12g00118 118
12 847924 848816 - Bpe005359.1 Bpe12g00119 119
12 857089 867434 + Bpe005360.1 Bpe12g00120 120
15 18282935 18295448 - Bpe001741.1 Bpe15g00815 815
15 18296562 18300839 + Bpe001742.1 Bpe15g00816 816
15 18301489 18304933 + Bpe001743.1 Bpe15g00817 817
2 5122350 5126916 + CaPI482276_02g004420.1 Cam02g0442 442
2 24526279 24529162 + CaPI482276_02g012380.1 Cam02g1238 1238
2 24566391 24571898 - CaPI482276_02g012410.1 Cam02g1241 1241
2 24610580 24629868 + CaPI482276_02g012420.1 Cam02g1242 1242
19 7127911 7128829 - Carg19357-RA Car19g00562 562
19 7133168 7137095 - Carg19356-RA Car19g00563 563
19 7138109 7145536 - Carg19355-RA Car19g00564 564
20 3686300 3699442 - Carg16175-RA Car20g00655 655
20 3701608 3705969 + Carg16176-RA Car20g00656 656
20 3710472 3711821 + Carg16177-RA Car20g00657 657
2 4129367 4133846 + CcPI632755_02g004580.1 Cco02g0458 458
2 24517860 24520842 + CcPI632755_02g012870.1 Cco02g1287 1287
2 24564368 24569836 - CcPI632755_02g012910.1 Cco02g1291 1291
2 24602835 24623376 + CcPI632755_02g012920.1 Cco02g1292 1292
2 4142656 4146862 + CePI673135_02g004400.1 Cec02g0440 440
2 28993247 28996232 + CePI673135_02g012470.1 Cec02g1247 1247
2 29033640 29039126 - CePI673135_02g012500.1 Cec02g1250 1250
2 29090024 29110053 + CePI673135_02g012510.1 Cec02g1251 1251
1 4981703 4986283 + Chy1G006850.1 Chy01g00685 685
11 2411806 2421592 - Chy11G188380.1 Chy11g00258 258
11 2430767 2436360 + Chy11G188390.1 Chy11g00259 259
11 2458970 2462011 - Chy11G188410.1 Chy11g00261 261
2 3995253 3999742 + ClG42_02g0044300.10 Clacu02g0443 443
2 24699663 24702564 + ClG42_02g0122000.10 Clacu02g1220 1220
2 24739615 24744969 - ClG42_02g0122300.10 Clacu02g1223 1223
2 24771473 24792127 + ClG42_02g0122400.10 Clacu02g1224 1224
2 4231990 4247046 + ClCG02G004170.2 Cla02g00433 433
2 4252466 4253829 + ClCG02G004190.2 Cla02g00434 434
2 24990143 24993269 + ClCG02G011850.1 Cla02g01162 1162
2 25023086 25024465 - ClCG02G011860.1 Cla02g01163 1163
2 25035574 25040928 - ClCG02G011870.2 Cla02g01164 1164
2 25067112 25090989 + ClCG02G011880.2 Cla02g01165 1165
2 1127278 1130280 + CmaCh02G002520.1 Cma02g00252 252
2 1134786 1136212 - CmaCh02G002530.1 Cma02g00253 253
2 1147855 1169131 + CmaCh02G002570.1 Cma02g00257 257
19 7360540 7361596 - CmaCh19G007330.1 Cma19g00733 733
19 7366044 7377983 - CmaCh19G007350.1 Cma19g00735 735
20 3535112 3550794 - CmaCh20G007540.1 Cma20g00754 754
20 3550894 3557453 + CmaCh20G007550.1 Cma20g00755 755
20 3560838 3562536 + CmaCh20G007560.1 Cma20g00756 756
1 16029869 16034410 + MELO3C013361.2.1 Cme01g01268 1268
1 16035569 16040779 + MELO3C013362.2.1 Cme01g01269 1269
11 3855221 3865996 - MELO3C020814.2.1 Cme11g00383 383
11 3874081 3879361 + MELO3C020813.2.1 Cme11g00384 384
11 3887565 3889194 + MELO3C020812.2.1 Cme11g00385 385
11 3903103 3906444 - MELO3C020811.2.1 Cme11g00386 386
1 5284140 5289684 + PI0006752.2 Cmetu01g1029 1029
1 5276221 5282814 + PI0024841.1 Cmetu01g1869 1869
11 28581892 28591686 + PI0010703.1 Cmetu11g0032 32
11 28566781 28571890 - PI0013518.1 Cmetu11g0298 298
11 28537348 28540909 + PI0018353.1 Cmetu11g2225 2225
2 1181524 1184938 + CmoCh02G002510.1 Cmo02g00251 251
2 1190454 1200490 - CmoCh02G002520.1 Cmo02g00252 252
2 1202717 1213685 + CmoCh02G002530.1 Cmo02g00253 253
19 7616636 7617597 - CmoCh19G007410.1 Cmo19g00741 741
19 7621692 7625868 - CmoCh19G007420.1 Cmo19g00742 742
19 7626721 7634112 - CmoCh19G007430.1 Cmo19g00743 743
20 3750324 3763483 - CmoCh20G007500.1 Cmo20g00750 750
20 3765811 3769759 + CmoCh20G007510.1 Cmo20g00751 751
20 3778404 3779972 + CmoCh20G007520.1 Cmo20g00752 752
2 3991207 3995697 + CmPI595203_02g004380.1 Cmu02g0438 438
2 24567304 24570203 + CmPI595203_02g011880.1 Cmu02g1188 1188
2 24607157 24612569 - CmPI595203_02g011910.1 Cmu02g1191 1191
2 24639090 24662170 + CmPI595203_02g011920.1 Cmu02g1192 1192
8 10545720 10547968 - Conep08aG0131700.1 Cone8ag1279 1279
8 10553592 10554644 - Conep08aG0131800.1 Cone8ag1280 1280
8 10561172 10564938 - Conep08aG0132000.1 Cone8ag1282 1282
10 9320498 9333188 + Conep10aG0126900.1 Cone10ag1234 1234
12 9537443 9541007 - Conep12aG0126900.1 Cone12ag1229 1229
12 9541489 9545110 - Conep12aG0127000.1 Cone12ag1230 1230
5 9662322 9683492 - Cp4.1LG05g13790.1 Cpe05g01375 1375
5 9700941 9704087 - Cp4.1LG05g13780.1 Cpe05g01377 1377
15 6658067 6667567 - Cp4.1LG15g06000.1 Cpe15g00587 587
15 6668193 6674424 - Cp4.1LG15g06010.1 Cpe15g00588 588
16 5007756 5008560 - Cp4.1LG16g03130.1 Cpe16g00313 313
16 5012494 5016253 - Cp4.1LG16g03100.1 Cpe16g00314 314
16 5018252 5031218 + Cp4.1LG16g03190.1 Cpe16g00315 315
2 4561722 4566211 + CrPI670011_02g007720.1 Cre02g0772 772
2 27121824 27124818 + CrPI670011_02g014990.1 Cre02g1499 1499
2 27162394 27167900 - CrPI670011_02g015020.1 Cre02g1502 1502
2 27226386 27231155 + CrPI670011_02g015040.1 Cre02g1504 1504
2 13267102 13273555 + CsaV3_2G016000.1 Csa02g01384 1384
2 13293670 13299825 - CsaV3_2G016040.1 Csa02g01388 1388
2 13307366 13318237 + CsaV3_2G016050.1 Csa02g01389 1389
7 874920 880137 - CsaV3_7G000930.1 Csa07g00093 93
7 881728 888108 - CsaV3_7G000940.1 Csa07g00094 94
2 4132222 4138025 + Hsped.02g04290.1 Hepe02g0429 429
2 4140414 4145258 + Hsped.02g04300.1 Hepe02g0430 430
8 2596180 2598675 + Hsped.08g02870.1 Hepe08g0287 287
8 2616849 2620675 - Hsped.08g02890.1 Hepe08g0289 289
8 2627081 2642972 + Hsped.08g02900.1 Hepe08g0290 290
8 3052242 3055900 - Hsped.08g03390.1 Hepe08g0339 339
10 7028264 7032458 + Lsi10G004900.1 Lsi10g00490 490
10 7058208 7064283 - Lsi10G004920.1 Lsi10g00492 492
11 20441725 20467774 - Lsi11G011960.1 Lsi11g01196 1196
1 1519695 1532563 - Sed0004775.1 Sed01g0197 197
1 1546228 1550796 + Sed0015675.1 Sed01g0198 198
2 9023549 9028764 + Sed0013235.1 Sed02g0073 73
5 34971764 34979607 + Sed0000274.1 Sed05g2221 2221
5 34980340 34984724 + Sed0004709.1 Sed05g2222 2222
2 6467022 6473050 + Tan0000413.1 Tan02g0693 693
2 6476125 6480801 + Tan0012497.2 Tan02g0695 695
5 10187885 10205395 - Tan0010641.1 Tan05g1142 1142
5 10253697 10257225 + Tan0005487.2 Tan05g1144 1144
5 10316444 10319283 - Tan0010980.2 Tan05g1147 1147
3 1540152 1548972 - Vvi3g146 Vvi3g146 146
3 1549918 1551865 - Vvi3g147 Vvi3g147 147
3 1559955 1564835 + Vvi3g148 Vvi3g148 148
3 1565071 1567815 - Vvi3g149 Vvi3g149 149
3 1570598 1575263 + Vvi3g150 Vvi3g150 150
3 1583961 1585390 - Vvi3g151 Vvi3g151 151
3 1587483 1594374 - Vvi3g152 Vvi3g152 152
3 1595360 1600111 - Vvi3g153 Vvi3g153 153
3 1612328 1639335 + Vvi3g154 Vvi3g154 154
3 1639343 1639821 + Vvi3g155 Vvi3g155 155
       

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