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
Vvi1g1011 . Blo16g01071 . Bda11g01160 Bpe13g01358 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone9ag0511 . . . . . . . Bda11g01160 . . . Bma06g00749 . . Cmo15g00878 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1012 . . . . . . . . Cmo04g01640 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1013 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1014 . . . . . . . . . . . . . . . . . . . . . . . . Cla05g02366 . Cec05g2565 Cco05g2604 Clacu05g2532 . . . . . . Lsi04g00327 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1015 . . . . . . . . Cmo04g01639 . . . . . . . . Bhi07g01426 . . . . . . . . . . . . . . . . . . Csa05g02543 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1016 . . . . . . . . Cmo04g01638 . . . Car04g01619 . . . Cpe01g01391 Bhi07g01424 . . . . . . Cla05g02365 Cam05g2535 Cec05g2564 Cco05g2603 Clacu05g2531 Cmu05g2391 Cre05g2507 . . . . Lsi04g00326 . Chy10g01084 Cme10g00326 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1017 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1018 . . . . . . . . Cmo04g01637 . . . . . Sed06g1824 . . Bhi07g01422 Tan04g0939 Cmetu10g0984 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1019 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1020 . . . . . Bpe10g00922 . Bma15g00101 . Cmo18g01097 . Cma18g01075 . Car18g00998 Sed06g1826 Cpe09g00248 . Bhi07g01420 Tan04g0938 Cmetu10g1844 Lac13g0422 Hepe10g1836 . . Cla05g02364 Cam05g2534 Cec05g2563 Cco05g2602 Clacu05g2529 Cmu05g2389 Cre05g2505 . . . . Lsi04g00325 Csa05g02544 . Cme10g00325 Blo06g00949 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 11862908 11864858 - Bda007651.1 Bda11g01160 1160
7 42295419 42301315 + XM_039036078.1 Bhi07g01420 1420
7 42308213 42326523 + XM_039037448.1 Bhi07g01422 1422
7 42308214 42326523 + XM_039037449.1 Bhi07g01424 1424
7 42309052 42326523 + XM_039037453.1 Bhi07g01426 1426
6 32710062 32715385 - BLOR17532 Blo06g00949 949
16 39256597 39266267 - BLOR21858 Blo16g01071 1071
6 38851699 38854974 + Bma023738.2 Bma06g00749 749
15 1093727 1098196 + Bma030766 Bma15g00101 101
10 14826742 14831587 - Bpe003225.1 Bpe10g00922 922
13 18827405 18829452 - Bpe011020.1 Bpe13g01358 1358
5 33161716 33168037 + CaPI482276_05g025340.1 Cam05g2534 2534
5 33170168 33187870 + CaPI482276_05g025350.1 Cam05g2535 2535
4 9343028 9359228 + Carg01781-RA Car04g01619 1619
18 10423945 10429081 + Carg21531-RA Car18g00998 998
5 34265881 34270686 + CcPI632755_05g026020.1 Cco05g2602 2602
5 34273725 34290703 + CcPI632755_05g026030.1 Cco05g2603 2603
5 34291599 34292027 - CcPI632755_05g026040.1 Cco05g2604 2604
5 36602091 36607158 + CePI673135_05g025630.1 Cec05g2563 2563
5 36609203 36626181 + CePI673135_05g025640.1 Cec05g2564 2564
5 36627084 36627512 - CePI673135_05g025650.1 Cec05g2565 2565
10 15925655 15948944 - Chy10G182780.1 Chy10g01084 1084
5 33374992 33380043 + ClG42_05g0252900.10 Clacu05g2529 2529
5 33386124 33398575 + ClG42_05g0253100.10 Clacu05g2531 2531
5 33399465 33399893 - ClG42_05g0253200.10 Clacu05g2532 2532
5 35210036 35215378 + ClCG05G023380.2 Cla05g02364 2364
5 35217167 35233938 + ClCG05G023390.2 Cla05g02365 2365
5 35234477 35234878 - ClCG05G023400.1 Cla05g02366 2366
18 8887679 8893638 + CmaCh18G010750.1 Cma18g01075 1075
10 2134324 2138988 + MELO3C012180.2.1 Cme10g00325 325
10 2139977 2157025 + MELO3C012178.2.1 Cme10g00326 326
10 19892503 19908543 - PI0007536.1 Cmetu10g0984 984
10 19909201 19914419 - PI0022228.1 Cmetu10g1844 1844
4 8365140 8367315 + CmoCh04G016370.1 Cmo04g01637 1637
4 8370606 8371624 + CmoCh04G016380.1 Cmo04g01638 1638
4 8376170 8381808 + CmoCh04G016390.1 Cmo04g01639 1639
4 8381556 8383319 - CmoCh04G016400.1 Cmo04g01640 1640
15 4439953 4443380 - CmoCh15G008780.1 Cmo15g00878 878
18 11442586 11449083 + CmoCh18G010970.1 Cmo18g01097 1097
5 33110657 33118071 + CmPI595203_05g023890.1 Cmu05g2389 2389
5 33124158 33137512 + CmPI595203_05g023910.1 Cmu05g2391 2391
9 2441143 2444095 - Conep09aG0052100.1 Cone9ag0511 511
1 8368472 8384968 + Cp4.1LG01g13240.1 Cpe01g01391 1391
9 1433742 1438820 - Cp4.1LG09g02480.1 Cpe09g00248 248
5 36457823 36462878 + CrPI670011_05g025050.1 Cre05g2505 2505
5 36468992 36482835 + CrPI670011_05g025070.1 Cre05g2507 2507
5 26863119 26879356 - CsaV3_5G033620.1 Csa05g02543 2543
5 26880403 26885051 - CsaV3_5G033630.1 Csa05g02544 2544
10 55101124 55107049 - Hsped.10g18360.1 Hepe10g1836 1836
13 2968290 2974464 - Lag0040218.1 Lac13g0422 422
4 3316174 3321444 + Lsi04G003250.1 Lsi04g00325 325
4 3321980 3339158 + Lsi04G003260.1 Lsi04g00326 326
4 3339650 3340063 - Lsi04G003270.1 Lsi04g00327 327
6 42690958 42709115 - Sed0018972.1 Sed06g1824 1824
6 42710036 42716799 - Sed0002818.2 Sed06g1826 1826
4 8270454 8276312 + Tan0013780.1 Tan04g0938 938
4 8282585 8297131 + Tan0019477.1 Tan04g0939 939
1 15925061 15931368 + Vvi1g1011 Vvi1g1011 1011
1 15950499 15952634 - Vvi1g1012 Vvi1g1012 1012
1 16053499 16055307 + Vvi1g1013 Vvi1g1013 1013
1 16128793 16129261 + Vvi1g1014 Vvi1g1014 1014
1 16157068 16202539 - Vvi1g1015 Vvi1g1015 1015
1 16211716 16268751 - Vvi1g1016 Vvi1g1016 1016
1 16268849 16269733 + Vvi1g1017 Vvi1g1017 1017
1 16271823 16283640 - Vvi1g1018 Vvi1g1018 1018
1 16288423 16288864 + Vvi1g1019 Vvi1g1019 1019
1 16384422 16391085 + Vvi1g1020 Vvi1g1020 1020
       

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