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
Vvi5g719 . . . . . Bpe14g01260 . . Cmo08g01055 Cmo17g00158 . . . . . . . . . . . . . . Cla06g00670 Cam06g0719 Cec06g0727 Cco06g0735 Clacu06g0710 Cmu06g0696 Cre06g1467 Cone14ag0151 Cone15ag0164 Cone7ag0327 Cone4ag0331 . Csa02g01057 Chy05g00317 . Blo02g00749 Blo07g00267 . . . Bpe13g00555 Bma02g00776 Bma06g01603 Sed12g1127 . . Cma08g01080 Cma17g00160 Car08g00955 Car17g00141 Cpe12g00137 Cpe17g00197 Bhi12g01613 Tan06g2406 Cmetu05g0199 Lac12g2163 Hepe03g0289 . Lcy13g0380 . . . . . . . Lsi09g01230 . . Cme05g00573
Vvi5g720 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g721 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g722 Blo01g00090 . . Bda08g00275 . . . Bma05g01065 Cmo08g01054 Cmo17g00156 . . . . . . . . . . . . . . Cla06g00671 . . . . . . . Cone15ag0165 . . . Csa02g01055 Chy05g00316 . . . . . Bpe05g00857 . . . . . . Cma08g01079 Cma17g00158 Car08g00953 Car17g00140 Cpe12g00136 Cpe17g00198 Bhi12g01611 . . . . . Lcy13g0382 . . . . . . . Lsi09g01229 . . Cme05g00575
Vvi5g723 . . . . . . . . . . . . Car06g01135 . . Cpe08g00337 Cpe03g01519 Bhi01g00722 . . . Hepe05g1661 . . . . . . . . . . . Cone7ag0328 Cone4ag0332 Lsi05g01737 . . Cme06g00484 . . . . . . . . . Cmo06g01327 . . . . . . . . . . . . . . Cla05g00440 Cam05g0478 Cec05g0488 Cco05g0488 . Cmu05g0453 Cre05g0515 . Csa03g01202 Chy06g00466 .
Vvi5g724 . . . . . Bpe14g01261 . . Cmo08g01053 . Cma06g01316 Cma14g01817 Car06g01133 Car14g01629 . Cpe08g00338 Cpe03g01520 Bhi01g00721 . . . . . . Cla06g00672 Cam06g0721 Cec06g0729 Cco06g0737 Clacu06g0712 Cmu06g0698 Cre06g1469 Cone14ag0152 Cone15ag0166 Cone7ag0330 Cone4ag0335 Lsi05g01738 Csa02g01054 Chy05g00315 Cme06g00483 Blo02g00750 Blo07g00269 Bda11g00636 Bda13g00058 . Bpe13g00553 Bma02g00775 Bma06g01604 . Cmo06g01326 Cmo14g01855 Cma08g01078 . Car08g00952 . . Cpe17g00199 Bhi12g01609 Tan06g2404 . . Hepe03g0291 . Lcy13g0383 Cla05g00439 . Cec05g0487 . Clacu05g0474 . . Lsi09g01228 Csa03g01201 Chy06g00465 Cme05g00576
Vvi5g725 . . . . . . . . . . . Cma14g01819 . Car14g01630 . . Cpe03g01521 Bhi01g00719 . . . Hepe05g1664 . . . . . . . . . Cone14ag0155 . . . Lsi05g01740 . . Cme06g00481 . . . . . . . . . . Cmo14g01857 . . . . . . . . . . . . . Cla05g00437 Cam05g0476 Cec05g0485 Cco05g0485 Clacu05g0473 Cmu05g0451 Cre05g0513 . Csa03g01199 Chy06g00463 .
Vvi5g726 . Blo12g00160 . . Bpe04g01006 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g727 Blo01g00089 Blo12g00369 Bda03g00841 Bda08g00276 . . Bma04g00739 . Cmo08g01052 Cmo17g00154 . . . . . . . . . . . . . . Cla06g00675 Cam06g0725 Cec06g0732 Cco06g0741 Clacu06g0716 Cmu06g0701 Cre06g1472 Cone14ag0156 Cone15ag0168 . . . Csa02g01051 Chy05g00312 . . . . . Bpe05g00856 . . . . . . Cma08g01077 Cma17g00155 Car08g00950 Car17g00138 Cpe12g00133 Cpe17g00200 Bhi12g01604 Tan06g2399 . . . . Lcy13g0386 . . . . . . . Lsi09g01225 . . Cme05g00580
Vvi5g728 . . . . . . . . Cmo08g01051 Cmo17g00153 . . . . . . . . . . . . . . Cla06g00676 Cam06g0726 Cec06g0733 Cco06g0742 Clacu06g0717 Cmu06g0702 Cre06g1473 . Cone15ag0169 . . . Csa02g01050 . . . . . . . . . . Sed09g0664 . . Cma08g01076 Cma17g00154 Car08g00949 Car17g00137 Cpe12g00132 Cpe17g00201 Bhi12g01602 Tan06g2397 Cmetu05g0571 . . . Lcy13g0387 . . . . . . . Lsi09g01223 . . Cme05g00581
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 7208002 7218182 - Bda016828.1 Bda03g00841 841
8 2863373 2868401 + Bda024707.3 Bda08g00275 275
8 2876531 2887687 - Bda024708.1 Bda08g00276 276
11 6353291 6364015 + Bda005382.1 Bda11g00636 636
13 830904 845482 - Bda000905.2 Bda13g00058 58
1 13362564 13364299 - XM_039024519.1 Bhi01g00719 719
1 13385739 13392021 - XM_039048128.1 Bhi01g00721 721
1 13395284 13399014 - XM_039022230.1 Bhi01g00722 722
12 51967003 51970494 + XM_039051069.1 Bhi12g01602 1602
12 51971889 51979910 - XM_039051066.1 Bhi12g01604 1604
12 52079598 52084530 - XM_039018581.1 Bhi12g01609 1609
12 52141734 52150038 - XM_039018427.1 Bhi12g01611 1611
12 52171566 52176274 - XM_039018636.1 Bhi12g01613 1613
1 1222607 1243115 + BLOR00089 Blo01g00089 89
1 1250067 1255687 - BLOR00090 Blo01g00090 90
2 24747439 24750342 + BLOR10479 Blo02g00749 749
2 24831855 24835701 + BLOR10480 Blo02g00750 750
7 3197737 3201277 + BLOR18199 Blo07g00267 267
7 3205802 3209500 + BLOR18201 Blo07g00269 269
12 10703777 10705609 + BLOR04179 Blo12g00160 160
12 20077470 20086016 + BLOR04388 Blo12g00369 369
2 41299708 41303543 - Bma015498.1 Bma02g00775 775
2 41355850 41358869 - Bma015499.1 Bma02g00776 776
4 7738115 7740337 - Bma019248.1 Bma04g00739 739
5 49339079 49344054 - Bma022229.2 Bma05g01065 1065
6 52213955 52217258 + Bma024718.1 Bma06g01603 1603
6 52217651 52224647 + Bma024719.1 Bma06g01604 1604
4 7028708 7030540 + Bpe015673.1 Bpe04g01006 1006
5 21748732 21778109 + Bpe018269.1 Bpe05g00856 856
5 21780310 21785438 - Bpe018270.3 Bpe05g00857 857
13 12769165 12772884 - Bpe010256.1 Bpe13g00553 553
13 12776621 12785536 - Bpe010258.3 Bpe13g00555 555
14 9514072 9517077 + Bpe014619.1 Bpe14g01260 1260
14 9519832 9523699 + Bpe014620.1 Bpe14g01261 1261
5 4225266 4226780 - CaPI482276_05g004760.1 Cam05g0476 476
5 4236663 4249117 - CaPI482276_05g004780.1 Cam05g0478 478
6 9737399 9740356 + CaPI482276_06g007190.1 Cam06g0719 719
6 9766439 9775304 + CaPI482276_06g007210.1 Cam06g0721 721
6 9812867 9821363 + CaPI482276_06g007250.1 Cam06g0725 725
6 9822708 9825313 - CaPI482276_06g007260.1 Cam06g0726 726
6 8431480 8437052 - Carg06224-RA Car06g01133 1133
6 8440159 8442836 - Carg06222-RA Car06g01135 1135
8 6345620 6347495 + Carg10974-RA Car08g00949 949
8 6348445 6356410 - Carg10973-RA Car08g00950 950
8 6362500 6366304 - Carg10971-RA Car08g00952 952
8 6369726 6375305 - Carg10970-RA Car08g00953 953
8 6380417 6382953 - Carg10968-RA Car08g00955 955
14 13086752 13092663 + Carg16558-RA Car14g01629 1629
14 13094437 13095883 + Carg16557-RA Car14g01630 1630
17 835270 838502 + Carg10095-RA Car17g00137 137
17 839079 846685 - Carg10094-RA Car17g00138 138
17 866008 872808 - Carg10091-RA Car17g00140 140
17 877597 880534 - Carg10090-RA Car17g00141 141
5 3888635 3890204 - CcPI632755_05g004850.1 Cco05g0485 485
5 3898051 3910596 - CcPI632755_05g004880.1 Cco05g0488 488
6 8374509 8377480 + CcPI632755_06g007350.1 Cco06g0735 735
6 8403535 8412369 + CcPI632755_06g007370.1 Cco06g0737 737
6 8453054 8461351 + CcPI632755_06g007410.1 Cco06g0741 741
6 8462893 8465443 - CcPI632755_06g007420.1 Cco06g0742 742
5 3880603 3882144 - CePI673135_05g004850.1 Cec05g0485 485
5 3888991 3898759 - CePI673135_05g004870.1 Cec05g0487 487
5 3899511 3901454 - CePI673135_05g004880.1 Cec05g0488 488
6 8414614 8417585 + CePI673135_06g007270.1 Cec06g0727 727
6 8446011 8454783 + CePI673135_06g007290.1 Cec06g0729 729
6 8492726 8501118 + CePI673135_06g007320.1 Cec06g0732 732
6 8502644 8505205 - CePI673135_06g007330.1 Cec06g0733 733
5 3095301 3105339 - Chy5G093580.1 Chy05g00312 312
5 3126387 3130362 - Chy5G093610.1 Chy05g00315 315
5 3138712 3144403 - Chy5G093620.1 Chy05g00316 316
5 3155916 3158861 - Chy5G093630.1 Chy05g00317 317
6 3094662 3096394 - Chy6G109910.1 Chy06g00463 463
6 3101390 3106292 - Chy6G109930.1 Chy06g00465 465
6 3114042 3122237 - Chy6G109940.1 Chy06g00466 466
5 3933637 3935165 - ClG42_05g0047300.10 Clacu05g0473 473
5 3938845 3955174 - ClG42_05g0047400.10 Clacu05g0474 474
6 8289163 8292119 + ClG42_06g0071000.10 Clacu06g0710 710
6 8318314 8327214 + ClG42_06g0071200.10 Clacu06g0712 712
6 8369796 8377794 + ClG42_06g0071600.10 Clacu06g0716 716
6 8379695 8382259 - ClG42_06g0071700.10 Clacu06g0717 717
5 3912783 3914311 - ClCG05G004270.1 Cla05g00437 437
5 3922505 3928570 - ClCG05G004280.2 Cla05g00439 439
5 3933745 3936858 - ClCG05G004290.1 Cla05g00440 440
6 8484865 8489432 + ClCG06G007040.2 Cla06g00670 670
6 8500197 8508215 + ClCG06G007050.2 Cla06g00671 671
6 8515602 8525108 + ClCG06G007060.2 Cla06g00672 672
6 8569047 8577911 + ClCG06G007080.2 Cla06g00675 675
6 8579939 8582506 - ClCG06G007090.1 Cla06g00676 676
6 8695431 8700386 - CmaCh06G013160.1 Cma06g01316 1316
8 6703586 6705898 + CmaCh08G010760.1 Cma08g01076 1076
8 6706199 6715340 - CmaCh08G010770.1 Cma08g01077 1077
8 6719781 6725130 - CmaCh08G010780.1 Cma08g01078 1078
8 6729107 6736036 - CmaCh08G010790.1 Cma08g01079 1079
8 6739603 6742413 - CmaCh08G010800.1 Cma08g01080 1080
14 13014810 13020456 + CmaCh14G018170.1 Cma14g01817 1817
14 13022377 13024029 + CmaCh14G018190.1 Cma14g01819 1819
17 777326 780214 + CmaCh17G001540.1 Cma17g00154 154
17 778455 789195 - CmaCh17G001550.1 Cma17g00155 155
17 800797 813310 - CmaCh17G001580.1 Cma17g00158 158
17 817601 821142 - CmaCh17G001600.1 Cma17g00160 160
5 5809776 5817318 + MELO3C023001.2.1 Cme05g00573 573
5 5821826 5829668 + MELO3C023003.2.1 Cme05g00575 575
5 5845667 5851013 + MELO3C023004.2.1 Cme05g00576 576
5 5896440 5905497 + MELO3C023009.2.1 Cme05g00580 580
5 5905674 5908557 - MELO3C023011.2.1 Cme05g00581 581
6 3039015 3040771 - MELO3C006413.2.1 Cme06g00481 481
6 3045400 3051483 - MELO3C006415.2.1 Cme06g00483 483
6 3055298 3057740 - MELO3C006416.2.1 Cme06g00484 484
5 18139030 18141990 - PI0005661.1 Cmetu05g0199 199
5 18072455 18074847 + PI0028337.1 Cmetu05g0571 571
6 9884508 9893072 - CmoCh06G013260.1 Cmo06g01326 1326
6 9893767 9895765 - CmoCh06G013270.1 Cmo06g01327 1327
8 6782247 6784669 + CmoCh08G010510.1 Cmo08g01051 1051
8 6784979 6793305 - CmoCh08G010520.1 Cmo08g01052 1052
8 6797901 6803199 - CmoCh08G010530.1 Cmo08g01053 1053
8 6806948 6813852 - CmoCh08G010540.1 Cmo08g01054 1054
8 6817104 6820036 - CmoCh08G010550.1 Cmo08g01055 1055
14 14001386 14006995 + CmoCh14G018550.1 Cmo14g01855 1855
14 14008792 14010273 + CmoCh14G018570.1 Cmo14g01857 1857
17 876528 879499 + CmoCh17G001530.1 Cmo17g00153 153
17 880411 893936 - CmoCh17G001540.1 Cmo17g00154 154
17 904544 916764 - CmoCh17G001560.1 Cmo17g00156 156
17 921529 925707 - CmoCh17G001580.1 Cmo17g00158 158
5 3769804 3771332 - CmPI595203_05g004510.1 Cmu05g0451 451
5 3780351 3791319 - CmPI595203_05g004530.1 Cmu05g0453 453
6 8101298 8104254 + CmPI595203_06g006960.1 Cmu06g0696 696
6 8130668 8139563 + CmPI595203_06g006980.1 Cmu06g0698 698
6 8182100 8190428 + CmPI595203_06g007010.1 Cmu06g0701 701
6 8191998 8194567 - CmPI595203_06g007020.1 Cmu06g0702 702
4 1530887 1534957 + Conep04aG0034300.1 Cone4ag0331 331
4 1535760 1537547 + Conep04aG0034400.1 Cone4ag0332 332
4 1545198 1549245 + Conep04aG0034700.1 Cone4ag0335 335
7 1432532 1436598 + Conep07aG0033500.1 Cone7ag0327 327
7 1437446 1439161 + Conep07aG0033600.1 Cone7ag0328 328
7 1441874 1445816 + Conep07aG0033800.1 Cone7ag0330 330
14 738248 742111 + Conep14aG0015500.1 Cone14ag0151 151
14 750312 753296 + Conep14aG0015600.1 Cone14ag0152 152
14 757657 758997 + Conep14aG0015900.1 Cone14ag0155 155
14 759837 765997 + Conep14aG0016000.1 Cone14ag0156 156
15 788981 792806 + Conep15aG0016800.1 Cone15ag0164 164
15 793624 798580 + Conep15aG0016900.1 Cone15ag0165 165
15 799760 803676 + Conep15aG0017000.1 Cone15ag0166 166
15 809697 816397 + Conep15aG0017200.1 Cone15ag0168 168
15 816568 817680 - Conep15aG0017300.1 Cone15ag0169 169
3 11895029 11897468 + Cp4.1LG03g10170.1 Cpe03g01519 1519
3 11900130 11907118 + Cp4.1LG03g09870.1 Cpe03g01520 1520
3 11907955 11909427 + Cp4.1LG03g09860.1 Cpe03g01521 1521
8 2102329 2104178 + Cp4.1LG08g03420.1 Cpe08g00337 337
8 2107895 2113341 + Cp4.1LG08g03410.1 Cpe08g00338 338
12 833609 837711 + Cp4.1LG12g01250.1 Cpe12g00132 132
12 836048 845333 - Cp4.1LG12g01320.1 Cpe12g00133 133
12 864627 872807 - Cp4.1LG12g01340.1 Cpe12g00136 136
12 875300 880088 - Cp4.1LG12g01380.1 Cpe12g00137 137
17 1270293 1274180 + Cp4.1LG17g01930.1 Cpe17g00197 197
17 1277546 1284447 + Cp4.1LG17g01940.1 Cpe17g00198 198
17 1287782 1292366 + Cp4.1LG17g01950.1 Cpe17g00199 199
17 1297414 1305835 + Cp4.1LG17g01920.1 Cpe17g00200 200
17 1306699 1308462 - Cp4.1LG17g02300.1 Cpe17g00201 201
5 4565655 4567192 - CrPI670011_05g005130.1 Cre05g0513 513
5 4574974 4588917 - CrPI670011_05g005150.1 Cre05g0515 515
6 9209968 9212925 + CrPI670011_06g014670.1 Cre06g1467 1467
6 9240329 9249150 + CrPI670011_06g014690.1 Cre06g1469 1469
6 9287448 9295821 + CrPI670011_06g014720.1 Cre06g1472 1472
6 9297388 9299963 - CrPI670011_06g014730.1 Cre06g1473 1473
2 10191814 10194224 + CsaV3_2G012660.1 Csa02g01050 1050
2 10192850 10204168 - CsaV3_2G012670.1 Csa02g01051 1051
2 10223262 10229046 - CsaV3_2G012700.1 Csa02g01054 1054
2 10236107 10243761 - CsaV3_2G012710.1 Csa02g01055 1055
2 10253196 10256475 - CsaV3_2G012730.1 Csa02g01057 1057
3 9275443 9276892 - CsaV3_3G011990.1 Csa03g01199 1199
3 9281415 9287205 - CsaV3_3G012010.1 Csa03g01201 1201
3 9289874 9297483 - CsaV3_3G012020.1 Csa03g01202 1202
3 3851640 3856158 + Hsped.03g02890.1 Hepe03g0289 289
3 3893183 3898146 + Hsped.03g02910.1 Hepe03g0291 291
5 66499909 66513860 + Hsped.05g16610.1 Hepe05g1661 1661
5 66524638 66526107 + Hsped.05g16640.1 Hepe05g1664 1664
12 38724646 38727568 - Lag0016535.1 Lac12g2163 2163
13 4342625 4346868 + Maker00023515 Lcy13g0380 380
13 4356987 4362180 + Maker00023935 Lcy13g0382 382
13 4374907 4380307 + Maker00023990 Lcy13g0383 383
13 4404331 4413933 + Maker00023302 Lcy13g0386 386
13 4414263 4417484 - Maker00023332 Lcy13g0387 387
5 24800982 24804742 + Lsi05G017370.1 Lsi05g01737 1737
5 24810238 24816658 + Lsi05G017380.1 Lsi05g01738 1738
5 24819707 24824296 + Lsi05G017400.1 Lsi05g01740 1740
9 19652763 19655777 + Lsi09G012230.1 Lsi09g01223 1223
9 19664184 19665968 - Lsi09G012250.1 Lsi09g01225 1225
9 19692052 19698774 - Lsi09G012280.1 Lsi09g01228 1228
9 19708524 19718309 - Lsi09G012290.1 Lsi09g01229 1229
9 19734918 19740379 - Lsi09G012300.1 Lsi09g01230 1230
9 8702663 8705695 + Sed0017735.2 Sed09g0664 664
12 7447746 7457249 + Sed0017894.1 Sed12g1127 1127
6 76260356 76263221 + Tan0004473.1 Tan06g2397 2397
6 76264626 76274381 - Tan0007808.2 Tan06g2399 2399
6 76299107 76306515 - Tan0004631.2 Tan06g2404 2404
6 76361354 76366162 - Tan0004569.1 Tan06g2406 2406
5 8274024 8280970 + Vvi5g719 Vvi5g719 719
5 8298353 8300328 - Vvi5g720 Vvi5g720 720
5 8304071 8304834 - Vvi5g721 Vvi5g721 721
5 8339149 8359048 + Vvi5g722 Vvi5g722 722
5 8359942 8367514 + Vvi5g723 Vvi5g723 723
5 8390855 8397659 + Vvi5g724 Vvi5g724 724
5 8485997 8487467 + Vvi5g725 Vvi5g725 725
5 8499366 8501424 + Vvi5g726 Vvi5g726 726
5 8510748 8520878 + Vvi5g727 Vvi5g727 727
5 8521273 8525357 - Vvi5g728 Vvi5g728 728
       

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