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
Vvi4g362 Blo01g01712 . . . . Bpe02g00231 . Bma01g02491 . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag1410 Cone17ag1105 . . . . . . . . . . Bpe04g00008 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g363 Blo01g01713 . . Bda03g00378 . Bpe02g00230 Bma04g00355 Bma01g02492 Cmo05g00633 . . Cma05g00607 . . . . . Bhi04g00815 . . . Hepe10g0341 . Lcy13g1386 . . . . . . . Cone4ag1542 . Cone17ag1104 Cone20ag0615 . . . Cme03g01724 . . . . . . . . . . . . . . Car05g00550 Cpe11g00530 . . . . . . . . Cla08g01239 Cam08g1697 Cec08g1276 Cco08g1398 . . Cre08g1179 . . Chy03g01229 .
Vvi4g364 . . . . Bpe02g01198 . . . Cmo05g00634 . . Cma05g00608 . . Sed01g1289 . . Bhi04g00814 Tan02g2583 Cmetu03g0841 . Hepe10g0340 . Lcy13g1385 . . . . . . . . . . Cone20ag0616 . . . Cme03g01723 . Blo18g00067 Bda01g00951 . . . Bma01g01330 . . . . . . . Car05g00551 Cpe11g00531 . . . . . . . . Cla08g01240 Cam08g1698 Cec08g1277 Cco08g1399 Clacu08g1394 . Cre08g1180 Lsi08g01102 . Chy03g01228 .
Vvi4g365 . . . . . . . Bma01g02161 . . . Cma05g00437 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g366 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy03g01168 .
Vvi4g367 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g368 . Blo12g01089 Bda01g00725 . . Bpe02g00582 . Bma01g02152 . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag1730 . . . . Chy04g00342 . . . . . . Bpe04g00043 . . Sed05g1679 . . . . . . . Cpe02g00434 Bhi09g02286 Tan01g3680 Cmetu04g0507 . Hepe01g2047 Mch11g0583 . . . . . . . . . . . Cme04g00381
Vvi4g369 . . . . . . . . Cmo05g00676 . . Cma05g00646 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe11g00570 . . . . . . . . . . . . . . . . . . .
Vvi4g370 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g371 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag1732 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 34532308 34536358 - Bda002762.1 Bda01g00725 725
1 43048468 43050730 + Bda003107.1 Bda01g00951 951
3 3152757 3153841 - Bda016341.1 Bda03g00378 378
4 20580660 20584834 - XM_039030186.1 Bhi04g00814 814
4 20600176 20604065 + XM_039029902.1 Bhi04g00815 815
9 63690249 63697048 + XM_039043199.1 Bhi09g02286 2286
1 56873847 56876962 + BLOR01712 Blo01g01712 1712
1 56878649 56879061 - BLOR01713 Blo01g01713 1713
12 28551756 28556751 + BLOR05108 Blo12g01089 1089
18 487882 493717 - BLOR08555 Blo18g00067 67
1 18195748 18198581 - Bma001649.1 Bma01g01330 1330
1 78043311 78047325 - Bma002995.1 Bma01g02152 2152
1 78451632 78455186 + Bma003006.1 Bma01g02161 2161
1 82647630 82651303 + Bma003369.1 Bma01g02491 2491
1 82652045 82653219 - Bma030306 Bma01g02492 2492
4 2866433 2867520 - Bma018814.1 Bma04g00355 355
2 1579901 1580292 + Bpe008074.1 Bpe02g00230 230
2 1581852 1585105 - Bpe008075.1 Bpe02g00231 231
2 3771515 3787626 + Bpe008424.1 Bpe02g00582 582
2 15707096 15710195 + Bpe025122 Bpe02g01198 1198
4 87950 91682 - Bpe025560 Bpe04g00008 8
4 416855 421943 - Bpe014767.1 Bpe04g00043 43
8 23288984 23292065 - CaPI482276_08g016970.1 Cam08g1697 1697
8 23295229 23299034 + CaPI482276_08g016980.1 Cam08g1698 1698
5 3232993 3235776 - Carg08293-RA Car05g00550 550
5 3237903 3241905 + Carg08294-RA Car05g00551 551
8 25921859 25925171 - CcPI632755_08g013980.1 Cco08g1398 1398
8 25928228 25932023 + CcPI632755_08g013990.1 Cco08g1399 1399
8 24770668 24773938 - CePI673135_08g012760.1 Cec08g1276 1276
8 24777015 24780811 + CePI673135_08g012770.1 Cec08g1277 1277
3 14880860 14883927 + Chy3G061480.1 Chy03g01168 1168
3 15358879 15362665 - Chy3G062080.1 Chy03g01228 1228
3 15364308 15367003 + Chy3G062090.1 Chy03g01229 1229
4 3059342 3064555 - Chy4G070600.1 Chy04g00342 342
8 24047418 24051219 + ClG42_08g0139400.10 Clacu08g1394 1394
8 25336906 25340241 - ClCG08G012410.2 Cla08g01239 1239
8 25343066 25347460 + ClCG08G012420.1 Cla08g01240 1240
5 1983570 1994133 - CmaCh05G004370.1 Cma05g00437 437
5 3054989 3057600 - CmaCh05G006070.1 Cma05g00607 607
5 3059476 3063735 + CmaCh05G006080.1 Cma05g00608 608
5 3272232 3274696 + CmaCh05G006460.1 Cma05g00646 646
3 25802383 25806538 - MELO3C011161.2.1 Cme03g01723 1723
3 25807532 25810889 + MELO3C011160.2.1 Cme03g01724 1724
4 3058212 3064965 - MELO3C003672.2.1 Cme04g00381 381
3 3631656 3635736 + PI0023594.1 Cmetu03g0841 841
4 30294381 30299666 + PI0017108.1 Cmetu04g0507 507
5 3204450 3206500 - CmoCh05G006330.1 Cmo05g00633 633
5 3206631 3212798 + CmoCh05G006340.1 Cmo05g00634 634
5 3427695 3430521 + CmoCh05G006760.1 Cmo05g00676 676
4 11903152 11904754 - Conep04aG0159400.1 Cone4ag1542 1542
7 10076042 10078913 - Conep07aG0145200.1 Cone7ag1410 1410
7 11463130 11466044 + Conep07aG0178300.1 Cone7ag1730 1730
7 11469243 11472077 + Conep07aG0178500.1 Cone7ag1732 1732
17 8187215 8188256 + Conep17aG0113200.1 Cone17ag1104 1104
17 8189584 8192315 - Conep17aG0113300.1 Cone17ag1105 1105
20 3645897 3646511 - Conep20aG0063200.1 Cone20ag0615 615
20 3647001 3650116 + Conep20aG0063300.1 Cone20ag0616 616
2 2437300 2443961 - Cp4.1LG02g04290.1 Cpe02g00434 434
11 3159225 3161254 - Cp4.1LG11g05340.1 Cpe11g00530 530
11 3163181 3169681 + Cp4.1LG11g05230.1 Cpe11g00531 531
11 3379573 3382868 + Cp4.1LG11g05550.1 Cpe11g00570 570
8 25081460 25084780 - CrPI670011_08g011790.1 Cre08g1179 1179
8 25087677 25091467 + CrPI670011_08g011800.1 Cre08g1180 1180
1 85134402 85141815 + Hsped.01g20470.1 Hepe01g2047 2047
10 3647195 3650915 - Hsped.10g03400.1 Hepe10g0340 340
10 3653009 3663103 + Hsped.10g03410.1 Hepe10g0341 341
13 32003062 32007492 - Maker00025520 Lcy13g1385 1385
13 32012154 32015117 + Maker00025694 Lcy13g1386 1386
8 19685346 19689721 + Lsi08G011020.1 Lsi08g01102 1102
11 3718821 3725181 + MC11g0482 Mch11g0583 583
1 9630734 9634964 + Sed0015716.2 Sed01g1289 1289
5 30582433 30589514 - Sed0017078.1 Sed05g1679 1679
1 101634757 101642547 + Tan0017188.1 Tan01g3680 3680
2 94505496 94509909 + Tan0004877.1 Tan02g2583 2583
4 3540646 3545598 + Vvi4g362 Vvi4g362 362
4 3574951 3579692 - Vvi4g363 Vvi4g363 363
4 3580615 3585025 + Vvi4g364 Vvi4g364 364
4 3596650 3605452 - Vvi4g365 Vvi4g365 365
4 3609186 3613291 + Vvi4g366 Vvi4g366 366
4 3613653 3623291 - Vvi4g367 Vvi4g367 367
4 3630777 3637892 + Vvi4g368 Vvi4g368 368
4 3642860 3645919 - Vvi4g369 Vvi4g369 369
4 3645977 3647113 - Vvi4g370 Vvi4g370 370
4 3662643 3669042 + Vvi4g371 Vvi4g371 371
       

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