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
Vvi18g460 . . Bda01g00896 Bda03g00477 . . . . Cmo05g00544 . . . . . Sed14g0990 Cpe06g00443 . Bhi04g00792 Tan02g2428 Cmetu05g0584 . Hepe10g0467 . Lcy13g1532 . . . . . . . . Cone7ag1259 Cone17ag1200 . Lsi04g02261 Csa03g04472 Chy04g00229 Cme03g01838 Blo17g00109 . . . Bpe02g01132 Bpe14g00468 . Bma02g00126 Sed06g1552 . Cmo09g00565 . Cma05g00516 Car05g00467 Car09g00510 Cpe11g00456 . Bhi09g02473 Tan01g3822 Cmetu04g1810 . Hepe01g2153 Mch11g0691 . Cla11g01406 Cam11g1463 Cec11g1491 Cco11g1487 Clacu11g1624 Cmu11g1441 Cre11g1860 Lsi08g00991 Csa02g02176 Chy03g01341 Cme04g00255
Vvi18g461 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g462 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g463 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g464 . . . . . . . . Cmo05g00546 . . . . . Sed08g0776 . . Bhi04g00794 Tan06g0276 Cmetu02g1119 . Hepe10g0465 . Lcy13g1529 Cla08g01136 Cam08g1594 Cec08g1164 Cco08g1291 Clacu08g1294 . Cre08g1076 Cone6ag1543 . Cone8ag0208 . . . . Cme03g01836 Blo17g00108 . . . . . . . . . . . Cma05g00517 Car05g00469 . Cpe11g00458 . . . . . . . . . . . . . . . Lsi08g00993 Csa02g02178 Chy03g01339 .
Vvi18g465 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1315 . . Cone20ag0535 . . . . Blo17g00107 . . Bda13g01375 . Bpe14g00469 . Bma02g00125 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g466 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g467 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g468 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g469 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 41939582 41940691 + Bda003034.1 Bda01g00896 896
3 4106656 4107570 - Bda016447.1 Bda03g00477 477
13 36367981 36371004 + Bda000195.1 Bda13g01375 1375
4 19726080 19727929 + XM_039028342.1 Bhi04g00792 792
4 19787682 19791189 - XM_039028377.1 Bhi04g00794 794
9 67074507 67121409 + XM_039040676.1 Bhi09g02473 2473
17 962407 980055 + BLOR15928 Blo17g00107 107
17 990962 994807 + BLOR15929 Blo17g00108 108
17 1003174 1004289 - BLOR15930 Blo17g00109 109
2 1168086 1175643 + Bma014580.1 Bma02g00125 125
2 1179072 1179890 - Bma014581.1 Bma02g00126 126
2 14920718 14921818 + Bpe008990.1 Bpe02g01132 1132
14 4197633 4198760 + Bpe007118.1 Bpe14g00468 468
14 4199550 4204532 - Bpe007119.1 Bpe14g00469 469
8 22094941 22097557 - CaPI482276_08g015940.1 Cam08g1594 1594
11 27356301 27357407 + CaPI482276_11g014630.1 Cam11g1463 1463
5 2660437 2661549 + Carg08209-RA Car05g00467 467
5 2664896 2667421 - Carg08211-RA Car05g00469 469
9 2858251 2859378 + Carg02992-RA Car09g00510 510
8 24698296 24700900 - CcPI632755_08g012910.1 Cco08g1291 1291
11 27697706 27698797 + CcPI632755_11g014870.1 Cco11g1487 1487
8 23524685 23527309 - CePI673135_08g011640.1 Cec08g1164 1164
11 29124728 29125834 + CePI673135_11g014910.1 Cec11g1491 1491
3 16365605 16367938 + Chy3G063190.1 Chy03g01339 1339
3 16373185 16374294 - Chy3G063210.1 Chy03g01341 1341
4 2068522 2069637 - Chy4G069470.1 Chy04g00229 229
8 22870912 22873533 - ClG42_08g0129400.10 Clacu08g1294 1294
11 27386321 27387427 + ClG42_11g0162400.10 Clacu11g1624 1624
8 24111993 24114616 - ClCG08G011380.2 Cla08g01136 1136
11 27613808 27614914 + ClCG11G014380.2 Cla11g01406 1406
5 2466092 2469264 + CmaCh05G005160.1 Cma05g00516 516
5 2470262 2474581 - CmaCh05G005170.1 Cma05g00517 517
3 26717567 26720091 + MELO3C011055.2.1 Cme03g01836 1836
3 26724285 26725872 - MELO3C011053.2.1 Cme03g01838 1838
4 2032880 2033934 - MELO3C003544.2.1 Cme04g00255 255
2 15093187 15097409 + PI0008702.1 Cmetu02g1119 1119
4 31318583 31319635 + PI0028163.1 Cmetu04g1810 1810
5 3259924 3261499 + PI0029086.1 Cmetu05g0584 584
5 2629998 2631110 + CmoCh05G005440.1 Cmo05g00544 544
5 2635259 2638316 - CmoCh05G005460.1 Cmo05g00546 546
9 2746010 2747113 + CmoCh09G005650.1 Cmo09g00565 565
11 26638108 26639214 + CmPI595203_11g014410.1 Cmu11g1441 1441
4 10806673 10815081 + Conep04aG0136100.1 Cone4ag1315 1315
6 12118169 12120977 + Conep06aG0160300.1 Cone6ag1543 1543
7 9355928 9357367 - Conep07aG0129600.1 Cone7ag1259 1259
8 1120557 1124969 + Conep08aG0021700.1 Cone8ag0208 208
17 8765006 8766459 - Conep17aG0123000.1 Cone17ag1200 1200
20 2934404 2937158 - Conep20aG0055100.1 Cone20ag0535 535
6 2558524 2559642 + Cp4.1LG06g04190.1 Cpe06g00443 443
11 2577518 2578630 + Cp4.1LG11g04420.1 Cpe11g00456 456
11 2582256 2585297 - Cp4.1LG11g04550.1 Cpe11g00458 458
8 23876423 23879045 - CrPI670011_08g010760.1 Cre08g1076 1076
11 30253030 30254136 + CrPI670011_11g018600.1 Cre11g1860 1860
2 19593571 19595884 + CsaV3_2G029950.1 Csa02g02176 2176
2 19600315 19603303 - CsaV3_2G029970.1 Csa02g02178 2178
3 38974361 38975996 + CsaV3_3G047780.1 Csa03g04472 4472
1 86167877 86169241 + Hsped.01g21530.1 Hepe01g2153 2153
10 5346171 5349359 + Hsped.10g04650.1 Hepe10g0465 465
10 5378464 5380244 - Hsped.10g04670.1 Hepe10g0467 467
13 34080971 34083737 + Maker00033933 Lcy13g1529 1529
13 34106007 34107176 - Maker00033894 Lcy13g1532 1532
4 29645465 29646580 + Lsi04G022610.1 Lsi04g02261 2261
8 18386724 18387833 + Lsi08G009910.1 Lsi08g00991 991
8 18400199 18403095 - Lsi08G009930.1 Lsi08g00993 993
11 4535758 4536801 + MC11g0582 Mch11g0691 691
6 40359322 40359894 - Sed0011285.1 Sed06g1552 1552
8 5922688 5926979 - Sed0019437.2 Sed08g0776 776
14 19254685 19255643 + Sed0023565.1 Sed14g0990 990
1 103088646 103090231 + Tan0020335.1 Tan01g3822 3822
2 92852365 92854225 + Tan0002106.1 Tan02g2428 2428
6 2183288 2186341 - Tan0003329.1 Tan06g0276 276
18 5020554 5021751 + Vvi18g460 Vvi18g460 460
18 5029706 5032279 + Vvi18g461 Vvi18g461 461
18 5035062 5040140 + Vvi18g462 Vvi18g462 462
18 5058486 5059001 + Vvi18g463 Vvi18g463 463
18 5062035 5076971 - Vvi18g464 Vvi18g464 464
18 5077427 5081480 - Vvi18g465 Vvi18g465 465
18 5092139 5102291 + Vvi18g466 Vvi18g466 466
18 5102793 5106770 + Vvi18g467 Vvi18g467 467
18 5107100 5110250 + Vvi18g468 Vvi18g468 468
18 5121694 5123760 + Vvi18g469 Vvi18g469 469
       

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