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
Vvi18g1380 . . . . . . . . Cmo04g02564 . . . . . . . . Bhi04g01775 . . . Hepe02g2137 . Lcy10g1352 Cla08g00712 Cam08g1139 Cec08g0728 Cco08g0836 Clacu08g0847 . Cre08g0648 . . Cone17ag0785 Cone20ag0379 . . . Cme03g00317 . . . Bda13g01413 . . Bma01g00742 . . . . . . Car04g02357 . Cpe01g02117 . . . . . . . . . . . . . . . Lsi08g00554 . Chy03g00510 .
Vvi18g1381 Blo01g01727 Blo12g00788 . Bda03g00390 Bpe02g00215 Bpe04g00350 Bma04g00367 Bma01g02505 . . . . . . . . . . . . . . . . Cla08g00363 Cam08g0789 Cec08g0349 Cco08g0454 Clacu08g0501 . Cre08g0330 Cone4ag1502 Cone7ag1446 . . . . . . . . Bda11g00876 . . . . . . Cmo01g01051 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1382 . Blo12g00789 . Bda03g00389 . Bpe04g00349 Bma04g00366 . Cmo04g02563 Cmo15g00604 . . . . Sed11g1351 . Cpe13g00682 Bhi04g01778 Tan11g1141 Cmetu03g2202 . Hepe02g2794 . Lcy10g1351 Cla08g00710 Cam08g1138 Cec08g0727 Cco08g0835 Clacu08g0846 . Cre08g0647 Cone4ag1503 . Cone17ag0787 Cone20ag0381 . . . Cme03g00318 . . . . . . . . . . . . . Car04g02356 Car15g00553 Cpe01g02116 . . . . . . . . . . . . . . . . . Chy03g00512 .
Vvi18g1383 Blo01g01725 Blo12g00790 . Bda03g00388 Bpe02g00216 Bpe04g00348 Bma04g00365 Bma01g02504 Cmo04g02562 Cmo15g00605 . . . . Sed11g1350 . . Bhi04g01779 Tan11g1142 Cmetu07g0819 . Hepe02g2793 . Lcy10g1350 Cla08g00709 Cam08g1136 Cec08g0725 Cco08g0833 Clacu08g0844 . Cre08g0645 . . Cone17ag0788 Cone20ag0382 . . . Cme03g00319 . . Bda11g00877 . . . . . . . . . . Car04g02355 . Cpe01g02115 . . . . . . . . . . . . . . . Lsi08g00553 . Chy03g00513 .
Vvi18g1384 . . . . Bpe02g00238 . . . . . . . Car01g00873 . . Cpe06g00902 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi09g01519 . . . . . . Cla09g00935 Cam09g0987 Cec09g0992 Cco09g0997 . . Cre09g0953 . . . .
Vvi18g1385 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1386 Blo01g01724 . . . . . . Bma01g02503 . . . . Car01g00893 . . Cpe06g00880 . . . . . . . . Cla08g00367 Cam08g0791 Cec08g0351 Cco08g0459 Clacu08g0504 . Cre08g0333 . . . Cone20ag0383 . . . . . . Bda11g00878 . . . . . . Cmo01g01050 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1387 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1516 Cone7ag1436 . . . . . . . . . Bda13g01412 . . . . Sed07g2864 Cmo01g01047 . . . . . . . Bhi09g01470 Tan01g3339 Cmetu01g1740 . . Mch11g1397 . Cla09g00900 Cam09g0952 Cec09g0956 Cco09g0958 . . Cre09g0922 . . . .
Vvi18g1388 . . . . . . . . . Cmo15g00606 . . . . . . Cpe13g00681 Bhi04g01780 . . . . . . Cla08g00221 . Cec08g0008 Cco08g0293 . . Cre08g0194 . . . . . . . Cme03g00320 . . . . . . . . . . . . . . Car15g00555 . . . . . . . . . Cla09g00894 Cam09g0945 Cec09g0948 Cco09g0952 . . Cre09g0914 Lsi08g00552 . Chy03g00307 .
Vvi18g1389 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma01g00733 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 3213261 3214622 - Bda033483 Bda03g00388 388
3 3215655 3216941 + Bda016352.1 Bda03g00389 389
3 3228468 3230407 - Bda016353.1 Bda03g00390 390
11 8614273 8616667 - Bda005629.1 Bda11g00876 876
11 8623315 8624738 + Bda005630.2 Bda11g00877 877
11 8625538 8628528 - Bda005631.1 Bda11g00878 878
13 36820973 36830213 - Bda000239.1 Bda13g01412 1412
13 36847609 36849507 + Bda000240.1 Bda13g01413 1413
4 43119108 43122106 - XM_039028364.1 Bhi04g01775 1775
4 43177740 43180027 - XM_039029440.1 Bhi04g01778 1778
4 43181835 43183968 + XM_039030430.1 Bhi04g01779 1779
4 43185274 43189402 + XM_039030426.1 Bhi04g01780 1780
9 37625676 37642331 - XM_039043794.1 Bhi09g01470 1470
9 40221207 40252044 - XM_039041749.1 Bhi09g01519 1519
1 56974446 56977469 + BLOR01724 Blo01g01724 1724
1 56978084 56979347 - BLOR01725 Blo01g01725 1725
1 57005910 57008029 - BLOR01727 Blo01g01727 1727
12 26285447 26287919 - BLOR04807 Blo12g00788 788
12 26294924 26296207 - BLOR04808 Blo12g00789 789
12 26297326 26299860 + BLOR04809 Blo12g00790 790
1 6724220 6724918 + Bma000946.1 Bma01g00733 733
1 6828221 6830092 + Bma000957.1 Bma01g00742 742
1 82735687 82739113 + Bma003382.1 Bma01g02503 2503
1 82739922 82741317 - Bma003383.1 Bma01g02504 2504
1 82747969 82750263 + Bma003384.1 Bma01g02505 2505
4 2934114 2935407 - Bma018823.1 Bma04g00365 365
4 2936433 2937716 + Bma018824.1 Bma04g00366 366
4 2943805 2946230 + Bma018825.1 Bma04g00367 367
2 1497717 1500195 - Bpe025064 Bpe02g00215 215
2 1506324 1507722 + Bpe008063.2 Bpe02g00216 216
2 1624473 1640855 + Bpe008082.1 Bpe02g00238 238
4 2218152 2219574 - Bpe025612 Bpe04g00348 348
4 2220605 2221888 + Bpe015041.1 Bpe04g00349 349
4 2226258 2228704 + Bpe015042.1 Bpe04g00350 350
8 9368873 9371462 + CaPI482276_08g007890.1 Cam08g0789 789
8 9574195 9577852 - CaPI482276_08g007910.1 Cam08g0791 791
8 17701067 17703018 - CaPI482276_08g011360.1 Cam08g1136 1136
8 17706625 17712533 + CaPI482276_08g011380.1 Cam08g1138 1138
8 17730145 17733099 + CaPI482276_08g011390.1 Cam08g1139 1139
9 9719776 9721290 + CaPI482276_09g009450.1 Cam09g0945 945
9 9791368 9800811 - CaPI482276_09g009520.1 Cam09g0952 952
9 10209944 10231936 - CaPI482276_09g009870.1 Cam09g0987 987
1 7936643 7968649 - Carg27550-RA Car01g00873 873
1 8272415 8275718 + Carg27669-RA Car01g00893 893
4 18936354 18937805 - Carg15789-RA Car04g02355 2355
4 18939607 18941978 + Carg15790-RA Car04g02356 2356
4 18947473 18949840 + Carg15791-RA Car04g02357 2357
15 3054616 3055941 - Carg01602-RA Car15g00553 553
15 3060715 3065372 - Carg01600-RA Car15g00555 555
8 5405723 5406994 - CcPI632755_08g002930.1 Cco08g0293 293
8 11275473 11278057 + CcPI632755_08g004540.1 Cco08g0454 454
8 11531589 11535260 - CcPI632755_08g004590.1 Cco08g0459 459
8 20167654 20169566 - CcPI632755_08g008330.1 Cco08g0833 833
8 20173173 20174525 + CcPI632755_08g008350.1 Cco08g0835 835
8 20197648 20200603 + CcPI632755_08g008360.1 Cco08g0836 836
9 8971977 8974787 + CcPI632755_09g009520.1 Cco09g0952 952
9 9046760 9056287 - CcPI632755_09g009580.1 Cco09g0958 958
9 9475683 9498470 - CcPI632755_09g009970.1 Cco09g0997 997
8 178874 180145 + CePI673135_08g000080.1 Cec08g0008 8
8 9266247 9268869 + CePI673135_08g003490.1 Cec08g0349 349
8 9679516 9683193 - CePI673135_08g003510.1 Cec08g0351 351
8 18973328 18975237 - CePI673135_08g007250.1 Cec08g0725 725
8 18978811 18980163 + CePI673135_08g007270.1 Cec08g0727 727
8 19001705 19004561 + CePI673135_08g007280.1 Cec08g0728 728
9 9011058 9012578 + CePI673135_09g009480.1 Cec09g0948 948
9 9087225 9097118 - CePI673135_09g009560.1 Cec09g0956 956
9 9501554 9524128 - CePI673135_09g009920.1 Cec09g0992 992
3 3402447 3403718 - Chy3G052870.1 Chy03g00307 307
3 7006909 7008995 - Chy3G054900.1 Chy03g00510 510
3 7096097 7097446 - Chy3G054920.1 Chy03g00512 512
3 7110707 7112140 + Chy3G054930.1 Chy03g00513 513
8 9245709 9248298 + ClG42_08g0050100.10 Clacu08g0501 501
8 9443728 9447386 - ClG42_08g0050400.10 Clacu08g0504 504
8 18480960 18482893 - ClG42_08g0084400.10 Clacu08g0844 844
8 18486461 18489768 + ClG42_08g0084600.10 Clacu08g0846 846
8 18509495 18512482 + ClG42_08g0084700.10 Clacu08g0847 847
8 4535382 4538182 - ClCG08G002150.2 Cla08g00221 221
8 9412698 9415755 + ClCG08G003510.1 Cla08g00363 363
8 9611535 9615817 - ClCG08G003550.1 Cla08g00367 367
8 19360968 19363779 - ClCG08G006960.2 Cla08g00709 709
8 19367246 19370553 + ClCG08G006970.2 Cla08g00710 710
8 19390302 19393281 + ClCG08G006990.1 Cla08g00712 712
9 9221414 9222928 + ClCG09G009550.1 Cla09g00894 894
9 9320789 9330789 - ClCG09G009620.2 Cla09g00900 900
9 9758609 9784441 - ClCG09G010020.1 Cla09g00935 935
3 4019876 4022452 - MELO3C008342.2.1 Cme03g00317 317
3 4073044 4075114 - MELO3C008343.2.1 Cme03g00318 318
3 4084671 4086915 + MELO3C008344.2.1 Cme03g00319 319
3 4087798 4090059 - MELO3C008345.2.1 Cme03g00320 320
1 18541152 18553815 + PI0007148.1 Cmetu01g1740 1740
3 8808355 8810997 - PI0023321.1 Cmetu03g2202 2202
7 4594454 4598623 + PI0024615.1 Cmetu07g0819 819
1 8265422 8274289 + CmoCh01G010470.1 Cmo01g01047 1047
1 8287073 8290888 + CmoCh01G010500.1 Cmo01g01050 1050
1 8293827 8295664 + CmoCh01G010510.1 Cmo01g01051 1051
4 18766496 18768567 - CmoCh04G025620.1 Cmo04g02562 2562
4 18770153 18771457 + CmoCh04G025630.1 Cmo04g02563 2563
4 18779783 18782387 + CmoCh04G025640.1 Cmo04g02564 2564
15 2938563 2939888 - CmoCh15G006040.1 Cmo15g00604 604
15 2941190 2943585 + CmoCh15G006050.1 Cmo15g00605 605
15 2944868 2947649 - CmoCh15G006060.1 Cmo15g00606 606
4 11686614 11689676 - Conep04aG0155400.1 Cone4ag1502 1502
4 11692774 11694685 - Conep04aG0155500.1 Cone4ag1503 1503
4 11766693 11770379 + Conep04aG0156800.1 Cone4ag1516 1516
7 10183260 10188354 - Conep07aG0147800.1 Cone7ag1436 1436
7 10239024 10242084 + Conep07aG0148800.1 Cone7ag1446 1446
17 6051298 6053378 - Conep17aG0080300.1 Cone17ag0785 785
17 6080905 6082351 - Conep17aG0080500.1 Cone17ag0787 787
17 6091657 6094045 + Conep17aG0080600.1 Cone17ag0788 788
20 1766663 1767774 - Conep20aG0039300.1 Cone20ag0379 379
20 1782599 1785193 - Conep20aG0039500.1 Cone20ag0381 381
20 1786792 1788940 + Conep20aG0039600.1 Cone20ag0382 382
20 1789097 1791599 - Conep20aG0039700.1 Cone20ag0383 383
1 17890615 17892719 - Cp4.1LG01g21160.1 Cpe01g02115 2115
1 17894154 17895461 + Cp4.1LG01g21050.1 Cpe01g02116 2116
1 17901936 17904480 + Cp4.1LG01g21100.1 Cpe01g02117 2117
6 5799879 5806227 - Cp4.1LG06g07730.1 Cpe06g00880 880
6 6148711 6170659 + Cp4.1LG06g07570.1 Cpe06g00902 902
13 6374794 6376050 + Cp4.1LG13g04080.1 Cpe13g00681 681
13 6381999 6383327 + Cp4.1LG13g04050.1 Cpe13g00682 682
8 4397053 4398324 - CrPI670011_08g001940.1 Cre08g0194 194
8 10442483 10445077 + CrPI670011_08g003300.1 Cre08g0330 330
8 10681682 10685345 - CrPI670011_08g003330.1 Cre08g0333 333
8 19393784 19395679 - CrPI670011_08g006450.1 Cre08g0645 645
8 19399284 19402424 + CrPI670011_08g006470.1 Cre08g0647 647
8 19422400 19425376 + CrPI670011_08g006480.1 Cre08g0648 648
9 9217039 9218550 + CrPI670011_09g009140.1 Cre09g0914 914
9 9287188 9296724 - CrPI670011_09g009220.1 Cre09g0922 922
9 9712442 9729684 - CrPI670011_09g009530.1 Cre09g0953 953
2 57306416 57311475 - Hsped.02g21370.1 Hepe02g2137 2137
2 76866884 76869365 - Hsped.02g27930.1 Hepe02g2793 2793
2 76881687 76883024 + Hsped.02g27940.1 Hepe02g2794 2794
10 36651404 36653411 - Maker00008672 Lcy10g1350 1350
10 36657207 36658556 + Maker00008788 Lcy10g1351 1351
10 36671494 36674113 + Maker00008353 Lcy10g1352 1352
8 13684520 13685776 + Lsi08G005520.1 Lsi08g00552 552
8 13686761 13689065 - Lsi08G005530.1 Lsi08g00553 553
8 13722594 13725594 + Lsi08G005540.1 Lsi08g00554 554
11 10126063 10149583 - MC11g1156 Mch11g1397 1397
7 43369675 43377016 + Sed0016522.1 Sed07g2864 2864
11 29532064 29535275 - Sed0019016.3 Sed11g1350 1350
11 29538849 29541563 + Sed0011174.1 Sed11g1351 1351
1 91130494 91153864 - Tan0021949.1 Tan01g3339 3339
11 9028826 9031165 - Tan0012467.1 Tan11g1141 1141
11 9032664 9034736 + Tan0022835.1 Tan11g1142 1142
18 19886385 19888873 - Vvi18g1380 Vvi18g1380 1380
18 19897546 19900584 - Vvi18g1381 Vvi18g1381 1381
18 19919284 19920665 - Vvi18g1382 Vvi18g1382 1382
18 19951231 19959002 + Vvi18g1383 Vvi18g1383 1383
18 19959476 20018606 - Vvi18g1384 Vvi18g1384 1384
18 20019049 20019480 - Vvi18g1385 Vvi18g1385 1385
18 20041687 20046952 - Vvi18g1386 Vvi18g1386 1386
18 20094187 20140310 + Vvi18g1387 Vvi18g1387 1387
18 20141273 20145463 + Vvi18g1388 Vvi18g1388 1388
18 20145937 20146577 - Vvi18g1389 Vvi18g1389 1389
       

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