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
Vvi18g290 . . . . Bpe02g00075 . . Bma01g02643 . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1391 Cone7ag1545 . . Lsi04g02381 Csa04g01811 . . . . Bda11g00743 . . . . . . . . . . . . . . Bhi09g02662 . . . Hepe01g2274 Mch11g0821 . . . . . . . . . . Chy07g00658 Cme07g00865
Vvi18g291 . Blo12g00673 . Bda03g00531 . Bpe04g00485 . . . . . Cma09g00804 . . . Cpe06g00639 . . . . . . . . . . . . . . . Cone4ag1390 . . . Lsi04g02380 Csa04g01892 . . . . . . . . . . . . Cmo09g00797 . . . Car09g00720 . . Bhi09g02658 . . . Hepe01g2273 Mch11g0820 . Cla11g01527 . . . . . . . . Chy07g00659 Cme07g00866
Vvi18g292 . Blo12g00674 . Bda03g00530 Bpe02g00076 Bpe04g00484 . . Cmo04g02460 Cmo15g00707 . Cma09g00805 . . . Cpe06g00640 . . . . . . . . Cla08g00565 Cam08g0982 Cec08g0571 Cco08g0681 Clacu08g0690 . Cre08g0504 Cone4ag1389 Cone7ag1546 Cone17ag1274 Cone20ag0452 Lsi04g02379 Csa04g01814 . . . . Bda11g00744 . . . . . . . Cmo09g00798 . . Car04g02278 Car09g00721 Cpe01g02040 . Bhi09g02656 . . . Hepe01g2270 Mch11g0819 . Cla11g01525 Cam11g1585 Cec11g1614 Cco11g1615 Clacu11g1742 Cmu11g1560 Cre11g1976 Lsi08g00414 . Chy07g00660 Cme07g00868
Vvi18g293 . . . Bda03g00529 . . . Bma01g02642 . . . Cma09g00806 . . . Cpe06g00641 . . . . . . . . . . . . . . . Cone4ag1388 Cone7ag1547 . . Lsi04g02378 Csa04g01815 . . . . . . . . . . . . Cmo09g00799 . . . Car09g00722 . . Bhi09g02655 . . . . . . Cla11g01524 Cam11g1584 Cec11g1613 Cco11g1614 Clacu11g1741 Cmu11g1559 Cre11g1975 . . Chy07g00661 Cme07g00869
Vvi18g294 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1387 . . . . . . . . Blo18g00188 . Bda01g01419 Bpe02g01634 . Bma01g00827 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g295 . Blo12g00675 . Bda03g00528 . Bpe04g00483 . . Cmo04g02459 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car04g02277 . Cpe01g02039 . . . . . . . . . . . . . . . . . Chy03g00357 .
Vvi18g296 . Blo12g00677 . . . . . . . . . Cma09g00809 . . . Cpe06g00643 . . . . . . . . . . . . . . . . . . . Lsi04g02376 Csa04g01817 . . . . . . . . . . . . Cmo09g00802 . . . Car09g00724 . . Bhi09g02649 . . . . . . Cla11g00771 Cam11g0806 Cec11g0787 Cco11g0793 Clacu11g1052 Cmu11g0913 Cre11g1251 . . Chy07g00665 Cme07g00873
Vvi18g297 . . . . . . . . Cmo04g02458 Cmo15g00709 . . . . Sed11g2304 . . Bhi04g02509 Tan11g0076 Cmetu03g1361 . . . Lcy10g2336 Cla08g00563 Cam08g0980 . Cco08g0679 Clacu08g0688 . Cre08g0502 . . Cone17ag1271 . . . . . Blo17g00182 . . Bda01g01418 Bpe02g01633 Bpe14g00376 Bma01g00828 Bma02g00223 . . . . . Car04g02276 Car15g00639 Cpe01g02038 . . . . . . . . . . . . . . . Lsi08g00412 . Chy03g00355 .
Vvi18g298 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g299 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 50084215 50088365 + Bda003661.1 Bda01g01418 1418
1 50101050 50102549 + Bda003662.1 Bda01g01419 1419
3 4410623 4415978 + Bda016498.1 Bda03g00528 528
3 4416873 4419322 + Bda016499.1 Bda03g00529 529
3 4420530 4422507 + Bda016500.1 Bda03g00530 530
3 4425960 4426952 + Bda016501.1 Bda03g00531 531
11 7465210 7468997 + Bda033058 Bda11g00743 743
11 7471724 7473427 - Bda005491.1 Bda11g00744 744
4 67789694 67795011 + XM_039030012.1 Bhi04g02509 2509
9 71380217 71383386 + XM_039043194.1 Bhi09g02649 2649
9 71422458 71425643 + XM_039042631.1 Bhi09g02655 2655
9 71429909 71432463 + XM_039043978.1 Bhi09g02656 2656
9 71447738 71450268 + XM_039042079.1 Bhi09g02658 2658
9 71450431 71456498 - XM_039042084.1 Bhi09g02662 2662
12 25031418 25032476 - BLOR04692 Blo12g00673 673
12 25036310 25038367 - BLOR04693 Blo12g00674 674
12 25039341 25044502 - BLOR04694 Blo12g00675 675
12 25047748 25050940 - BLOR04696 Blo12g00677 677
17 1858004 1863916 - BLOR16003 Blo17g00182 182
18 1809599 1811128 - BLOR08676 Blo18g00188 188
1 7783135 7784631 - Bma001047.1 Bma01g00827 827
1 7791878 7797197 - Bma001048.1 Bma01g00828 828
1 83925549 83928160 + Bma003528.1 Bma01g02642 2642
1 83940825 83944615 - Bma003529.1 Bma01g02643 2643
2 2362637 2367921 - Bma014679.1 Bma02g00223 223
2 573019 576816 + Bpe025056 Bpe02g00075 75
2 579588 581270 - Bpe007927.2 Bpe02g00076 76
2 19146849 19147475 + Bpe009479.1 Bpe02g01633 1633
2 19156653 19158152 + Bpe009480.1 Bpe02g01634 1634
4 3045492 3046619 + Bpe015168.1 Bpe04g00483 483
4 3051545 3053562 + Bpe025628 Bpe04g00484 484
4 3056688 3057689 + Bpe015169.1 Bpe04g00485 485
14 3562062 3567355 + Bpe007030.1 Bpe14g00376 376
8 15755099 15760664 + CaPI482276_08g009800.1 Cam08g0980 980
8 15776089 15778140 - CaPI482276_08g009820.1 Cam08g0982 982
11 10216186 10220769 + CaPI482276_11g008060.1 Cam11g0806 806
11 28585911 28589258 + CaPI482276_11g015840.1 Cam11g1584 1584
11 28591974 28594024 + CaPI482276_11g015850.1 Cam11g1585 1585
4 18323119 18328779 + Carg24453-RA Car04g02276 2276
4 18329923 18331259 + Carg24452-RA Car04g02277 2277
4 18335485 18337758 - Carg24451-RA Car04g02278 2278
9 4267063 4268661 - Carg17040-RA Car09g00720 720
9 4273677 4276483 - Carg17041-RA Car09g00721 721
9 4277579 4281506 - Carg17042-RA Car09g00722 722
9 4286241 4290285 - Carg17044-RA Car09g00724 724
15 3534543 3541065 - Carg01516-RA Car15g00639 639
8 18112488 18118040 + CcPI632755_08g006790.1 Cco08g0679 679
8 18133694 18135378 - CcPI632755_08g006810.1 Cco08g0681 681
11 9044002 9048594 + CcPI632755_11g007930.1 Cco11g0793 793
11 28963772 28964881 + CcPI632755_11g016140.1 Cco11g1614 1614
11 28967537 28969578 + CcPI632755_11g016150.1 Cco11g1615 1615
8 16953281 16955367 - CePI673135_08g005710.1 Cec08g0571 571
11 9264902 9269485 + CePI673135_11g007870.1 Cec11g0787 787
11 30413930 30417275 + CePI673135_11g016130.1 Cec11g1613 1613
11 30420211 30422242 + CePI673135_11g016140.1 Cec11g1614 1614
3 4833427 4839098 + Chy3G053350.1 Chy03g00355 355
3 4856322 4857122 + Chy3G053370.1 Chy03g00357 357
7 6321680 6325278 + Chy7G134880.1 Chy07g00658 658
7 6326786 6327754 - Chy7G134890.1 Chy07g00659 659
7 6345598 6348445 - Chy7G134900.1 Chy07g00660 660
7 6351234 6354031 - Chy7G134910.1 Chy07g00661 661
7 6380697 6384070 - Chy7G134950.1 Chy07g00665 665
8 16451436 16457144 + ClG42_08g0068800.10 Clacu08g0688 688
8 16471990 16474024 - ClG42_08g0069000.10 Clacu08g0690 690
11 13080739 13085312 - ClG42_11g0105200.10 Clacu11g1052 1052
11 28610655 28613984 + ClG42_11g0174100.10 Clacu11g1741 1741
11 28616674 28618724 + ClG42_11g0174200.10 Clacu11g1742 1742
8 17172193 17178491 + ClCG08G005400.1 Cla08g00563 563
8 17194425 17196315 - ClCG08G005420.1 Cla08g00565 565
11 11089585 11094614 + ClCG11G008070.1 Cla11g00771 771
11 28885509 28889343 + ClCG11G015610.1 Cla11g01524 1524
11 28891953 28894522 + ClCG11G015620.1 Cla11g01525 1525
11 28904384 28906648 + ClCG11G015630.2 Cla11g01527 1527
9 3925249 3926367 - CmaCh09G008040.1 Cma09g00804 804
9 3930776 3933404 - CmaCh09G008050.1 Cma09g00805 805
9 3934457 3938409 - CmaCh09G008060.1 Cma09g00806 806
9 3943534 3947243 - CmaCh09G008090.1 Cma09g00809 809
7 8643562 8648563 + MELO3C032634.2.1 Cme07g00865 865
7 8648029 8649691 - MELO3C010463.2.1 Cme07g00866 866
7 8696884 8699513 - MELO3C010462.2.1 Cme07g00868 868
7 8702181 8705415 - MELO3C010461.2.1 Cme07g00869 869
7 8732580 8736561 - MELO3C010459.2.1 Cme07g00873 873
3 25906772 25910626 + PI0014998.2 Cmetu03g1361 1361
4 18180260 18186497 + CmoCh04G024580.1 Cmo04g02458 2458
4 18187348 18188422 + CmoCh04G024590.1 Cmo04g02459 2459
4 18192710 18195472 - CmoCh04G024600.1 Cmo04g02460 2460
9 4079832 4080809 - CmoCh09G007970.1 Cmo09g00797 797
9 4085920 4088461 - CmoCh09G007980.1 Cmo09g00798 798
9 4089673 4093811 - CmoCh09G007990.1 Cmo09g00799 799
9 4098856 4102476 - CmoCh09G008020.1 Cmo09g00802 802
15 3437314 3439163 + CmoCh15G007070.1 Cmo15g00707 707
15 3443664 3449235 - CmoCh15G007090.1 Cmo15g00709 709
11 12409835 12414408 - CmPI595203_11g009130.1 Cmu11g0913 913
11 27862783 27866112 + CmPI595203_11g015590.1 Cmu11g1559 1559
11 27868802 27870852 + CmPI595203_11g015600.1 Cmu11g1560 1560
4 11215157 11216740 + Conep04aG0143600.1 Cone4ag1387 1387
4 11217878 11220094 + Conep04aG0143700.1 Cone4ag1388 1388
4 11220689 11222509 + Conep04aG0143800.1 Cone4ag1389 1389
4 11224883 11225917 + Conep04aG0143900.1 Cone4ag1390 1390
4 11227212 11229903 - Conep04aG0144000.1 Cone4ag1391 1391
7 10654158 10656868 + Conep07aG0159100.1 Cone7ag1545 1545
7 10661023 10662740 - Conep07aG0159200.1 Cone7ag1546 1546
7 10663220 10665271 - Conep07aG0159300.1 Cone7ag1547 1547
17 9158190 9163005 - Conep17aG0130200.1 Cone17ag1271 1271
17 9171129 9173207 + Conep17aG0130500.1 Cone17ag1274 1274
20 2319023 2321496 - Conep20aG0046700.1 Cone20ag0452 452
1 17318154 17324404 + Cp4.1LG01g20370.1 Cpe01g02038 2038
1 17325332 17326828 + Cp4.1LG01g20340.1 Cpe01g02039 2039
1 17330454 17333399 - Cp4.1LG01g20470.1 Cpe01g02040 2040
6 3956388 3957506 - Cp4.1LG06g06380.1 Cpe06g00639 639
6 3962268 3964893 - Cp4.1LG06g06370.1 Cpe06g00640 640
6 3966027 3969967 - Cp4.1LG06g06360.1 Cpe06g00641 641
6 3974571 3978720 - Cp4.1LG06g06390.1 Cpe06g00643 643
8 17437508 17443457 + CrPI670011_08g005020.1 Cre08g0502 502
8 17458537 17460556 - CrPI670011_08g005040.1 Cre08g0504 504
11 10880793 10885391 + CrPI670011_11g012510.1 Cre11g1251 1251
11 31509918 31513279 + CrPI670011_11g019750.1 Cre11g1975 1975
11 31515971 31518012 + CrPI670011_11g019760.1 Cre11g1976 1976
4 17770406 17774508 + CsaV3_4G028370.1 Csa04g01811 1811
4 17794392 17797083 - CsaV3_4G028400.1 Csa04g01814 1814
4 17798922 17802334 - CsaV3_4G028410.1 Csa04g01815 1815
4 17814256 17818437 - CsaV3_4G028430.1 Csa04g01817 1817
4 18679570 18682864 - CsaV3_4G029180.1 Csa04g01892 1892
1 87315093 87317676 + Hsped.01g22700.1 Hepe01g2270 2270
1 87327404 87329394 + Hsped.01g22730.1 Hepe01g2273 2273
1 87329211 87334826 - Hsped.01g22740.1 Hepe01g2274 2274
10 46956212 46960845 + Maker00039345 Lcy10g2336 2336
4 30900819 30904427 + Lsi04G023760.1 Lsi04g02376 2376
4 30909850 30913596 + Lsi04G023780.1 Lsi04g02378 2378
4 30916089 30918718 + Lsi04G023790.1 Lsi04g02379 2379
4 30927669 30928637 + Lsi04G023800.1 Lsi04g02380 2380
4 30929644 30935375 - Lsi04G023810.1 Lsi04g02381 2381
8 11544273 11550469 + Lsi08G004120.1 Lsi08g00412 412
8 11584026 11586083 - Lsi08G004140.1 Lsi08g00414 414
11 5517684 5520207 + MC11g0689 Mch11g0819 819
11 5526289 5528211 + MC11g0690 Mch11g0820 820
11 5528671 5533089 - MC11g_new0131 Mch11g0821 821
11 36090263 36096549 + Sed0016927.6 Sed11g2304 2304
11 915203 919373 - Tan0013162.4 Tan11g0076 76
18 3222097 3232606 + Vvi18g290 Vvi18g290 290
18 3233802 3234804 - Vvi18g291 Vvi18g291 291
18 3244466 3247061 - Vvi18g292 Vvi18g292 292
18 3249404 3253155 - Vvi18g293 Vvi18g293 293
18 3253823 3256064 - Vvi18g294 Vvi18g294 294
18 3261408 3268404 - Vvi18g295 Vvi18g295 295
18 3269850 3281510 - Vvi18g296 Vvi18g296 296
18 3282680 3291682 - Vvi18g297 Vvi18g297 297
18 3298908 3306668 + Vvi18g298 Vvi18g298 298
18 3307439 3307550 - Vvi18g299 Vvi18g299 299
       

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