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
Vvi4g2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g04544 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g4 Blo01g01484 . . . . . . Bma01g02238 . . Cma01g01777 Cma05g00116 . Car12g00229 . Cpe07g00209 . . . . . . . . . . . . . . . Cone20ag1268 Cone17ag0142 Cone16ag0715 Cone2ag0316 . . . . . . . . . . Bma01g00959 . . . . . Cma12g00246 Car01g01370 Car05g00100 Cpe11g00096 Cpe02g00508 . . . . . . . . . . . . . . . Csa02g02262 . .
Vvi4g5 . Blo12g01057 . Bda03g00159 . . . . Cmo05g00120 . . . . Car12g00229 Sed09g1609 Cpe07g00209 . Bhi04g00862 Tan02g2553 Cmetu03g1333 . Hepe10g0373 . Lcy13g1421 . . . . . . . . Cone7ag1308 . . . . . . . . . . . Bpe04g00141 . . . . . . Cma12g00246 . . . . Bhi09g02568 . . . Hepe01g2213 Mch11g0761 . Cla08g01215 Cam08g1676 Cec08g1254 Cco08g1373 Clacu08g1374 . Cre08g1159 . Csa02g02262 . .
Vvi4g6 . . . . . . . . . . Cma01g01441 . Car09g00555 . . . Cpe06g00484 . . . . . . . . . . . . . . . . . . Lsi04g02322 Csa03g04542 Chy04g00161 . . . . . . . . . . Cmo01g01495 . Cma09g00627 . . . . Cpe02g00507 Bhi09g02568 . . . Hepe01g2213 Mch11g0761 . . . . . . . . . . . Cme04g00185
Vvi4g7 . . . . . . . . . . . . . Car12g00224 . Cpe07g00204 . Bhi04g00869 Tan06g0248 . . Hepe10g0379 . Lcy13g1433 . . . . . . . . . . . . . . . Blo17g00302 . . Bda13g01324 . . . Bma02g00080 . . . . Cma12g00241 . . . . . . . . . . . Cla08g01208 Cam08g1670 Cec08g1248 Cco08g1365 Clacu08g1367 . Cre08g1152 . Csa02g02253 . .
Vvi4g8 . . . . . . . . . . . . . Car12g00223 Sed01g1255 Cpe07g00203 . Bhi04g00871 Tan02g2544 Cmetu03g1530 . . . Lcy13g1434 . . . . . . . . . . . . . . . . Blo18g00311 Bda01g00940 . . . . . . . . . Cma12g00240 . . . . . . . . . . . Cla08g01207 Cam08g1669 Cec08g1247 Cco08g1364 Clacu08g1366 . Cre08g1151 . Csa02g02252 . .
Vvi4g9 . . . . . . . . . . Cma01g01442 . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g02321 Csa03g04541 Chy04g00162 . . . Bda01g00942 . . . . . . Cmo01g01496 . . . . . . Cpe02g00506 Bhi09g02566 Tan01g3920 . . . . . . . . . . . . . . . Cme04g00186
Vvi4g10 . . . . . . . . . . . . . . Sed02g1237 Cpe07g00202 . Bhi04g00872 Tan02g2543 Cmetu02g0241 . . . . . . . . . . . . . . . . . . . . . . Bda13g01323 . . . Bma02g00080 . . . . Cma12g00238 . . . . . . . . . . . Cla08g01206 Cam08g1667 Cec08g1245 Cco08g1363 Clacu08g1365 . Cre08g1150 . Csa02g02251 . .
Vvi4g11 . . . . . . Bma04g00134 . . . Cma01g01443 . Car09g00554 . . . Cpe06g00483 . . . . . . . . . . . . . . . . . . . Csa03g04540 Chy04g00163 . . . . . . . . . Sed12g1387 . . . . . . . Cpe02g00505 Bhi09g02562 Tan01g3912 Cmetu04g3043 . Hepe01g2211 Mch11g0759 . . . . . . . . . . . Cme04g00187
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 42787762 42792218 - Bda003091.1 Bda01g00940 940
1 42832505 42840184 + Bda003093.1 Bda01g00942 942
3 1314886 1317379 + Bda016101.1 Bda03g00159 159
13 35457289 35457961 - Bda000132.1 Bda13g01323 1323
13 35532568 35537177 - Bda000135.1 Bda13g01324 1324
4 21655263 21660970 - XM_039029358.1 Bhi04g00862 862
4 21940816 21945902 + XM_039028272.1 Bhi04g00869 869
4 21957943 21963904 - XM_039029563.1 Bhi04g00871 871
4 21986094 21989008 + XM_039028117.1 Bhi04g00872 872
9 69492768 69496054 - XM_039040972.1 Bhi09g02562 2562
9 69500006 69523887 - XM_039042016.1 Bhi09g02566 2566
9 69595311 69601406 + XM_039042569.1 Bhi09g02568 2568
1 54286886 54289370 + BLOR01484 Blo01g01484 1484
12 28372742 28385345 + BLOR05076 Blo12g01057 1057
17 3167608 3172009 - BLOR16123 Blo17g00302 302
18 3243548 3255645 + BLOR08799 Blo18g00311 311
1 9425944 9428603 + Bma001184.1 Bma01g00959 959
1 79515244 79517718 + Bma003092.1 Bma01g02238 2238
2 681884 691983 - Bma014536.1 Bma02g00080 80
4 1077493 1080697 - Bma018582.1 Bma04g00134 134
4 951974 954450 + Bpe014860.1 Bpe04g00141 141
8 22913697 22916422 - CaPI482276_08g016670.1 Cam08g1667 1667
8 22923433 22929820 + CaPI482276_08g016690.1 Cam08g1669 1669
8 22931712 22936751 - CaPI482276_08g016700.1 Cam08g1670 1670
8 22991886 22998453 + CaPI482276_08g016760.1 Cam08g1676 1676
1 12044130 12045141 + Carg10667-RA Car01g01370 1370
5 514479 515960 + Carg11905-RA Car05g00100 100
9 3132702 3136445 - Carg03036-RA Car09g00554 554
9 3138596 3144056 + Carg03037-RA Car09g00555 555
12 1502263 1507801 + Carg03830-RA Car12g00223 223
12 1508283 1514908 - Carg03831-RA Car12g00224 224
12 1542132 1547639 + Carg03836-RA Car12g00229 229
8 25551374 25554102 - CcPI632755_08g013630.1 Cco08g1363 1363
8 25561153 25569582 + CcPI632755_08g013640.1 Cco08g1364 1364
8 25570090 25575165 - CcPI632755_08g013650.1 Cco08g1365 1365
8 25638008 25644562 + CcPI632755_08g013730.1 Cco08g1373 1373
8 24392025 24395902 - CePI673135_08g012450.1 Cec08g1245 1245
8 24402966 24409274 + CePI673135_08g012470.1 Cec08g1247 1247
8 24411161 24416195 - CePI673135_08g012480.1 Cec08g1248 1248
8 24473203 24479788 + CePI673135_08g012540.1 Cec08g1254 1254
4 1427264 1432848 - Chy4G068790.1 Chy04g00161 161
4 1435331 1442902 + Chy4G068800.1 Chy04g00162 162
4 1447664 1450102 + Chy4G068810.1 Chy04g00163 163
8 23686643 23689393 - ClG42_08g0136500.10 Clacu08g1365 1365
8 23696373 23702753 + ClG42_08g0136600.10 Clacu08g1366 1366
8 23704569 23709629 - ClG42_08g0136700.10 Clacu08g1367 1367
8 23764734 23771310 + ClG42_08g0137400.10 Clacu08g1374 1374
8 24969192 24971914 - ClCG08G012100.2 Cla08g01206 1206
8 24978607 24985607 + ClCG08G012110.2 Cla08g01207 1207
8 24987320 24993573 - ClCG08G012120.1 Cla08g01208 1208
8 25050707 25055748 + ClCG08G012185.1 Cla08g01215 1215
1 10144088 10151031 - CmaCh01G014410.1 Cma01g01441 1441
1 10151083 10160613 + CmaCh01G014420.1 Cma01g01442 1442
1 10162705 10170138 + CmaCh01G014430.1 Cma01g01443 1443
1 11913439 11920667 + CmaCh01G017770.1 Cma01g01777 1777
5 503339 505006 + CmaCh05G001160.1 Cma05g00116 116
9 2948778 2959854 + CmaCh09G006270.1 Cma09g00627 627
12 1189275 1190914 - CmaCh12G002380.1 Cma12g00238 238
12 1197054 1202398 + CmaCh12G002400.1 Cma12g00240 240
12 1202025 1209680 - CmaCh12G002410.1 Cma12g00241 241
12 1233868 1238847 + CmaCh12G002460.1 Cma12g00246 246
4 1393639 1398629 - MELO3C003471.2.1 Cme04g00185 185
4 1400821 1409177 + MELO3C003472.2.1 Cme04g00186 186
4 1412872 1417058 + MELO3C003473.2.1 Cme04g00187 187
2 1137563 1141069 + PI0016210.1 Cmetu02g0241 241
3 3372173 3376846 + PI0022911.1 Cmetu03g1333 1333
3 3318391 3322906 + PI0014729.1 Cmetu03g1530 1530
4 31990051 31993409 - PI0015611.1 Cmetu04g3043 3043
1 11556825 11563238 - CmoCh01G014950.1 Cmo01g01495 1495
1 11563254 11571685 + CmoCh01G014960.1 Cmo01g01496 1496
5 511868 514184 + CmoCh05G001200.1 Cmo05g00120 120
2 1659786 1660437 - Conep02aG0032700.1 Cone2ag0316 316
7 9610040 9612918 + Conep07aG0134700.1 Cone7ag1308 1308
16 8331500 8332057 + Conep16aG0307600.1 Cone16ag0715 715
17 729920 730774 - Conep17aG0014300.1 Cone17ag0142 142
20 8291047 8291769 + Conep20aG0131200.1 Cone20ag1268 1268
2 2960084 2964533 - Cp4.1LG02g03650.1 Cpe02g00505 505
2 2966138 2974279 - Cp4.1LG02g03630.1 Cpe02g00506 506
2 2975112 2981707 + Cp4.1LG02g03680.1 Cpe02g00507 507
2 2984020 2987027 + Cp4.1LG02g03660.1 Cpe02g00508 508
6 2846433 2850090 - Cp4.1LG06g03740.1 Cpe06g00483 483
6 2851980 2859299 + Cp4.1LG06g03830.1 Cpe06g00484 484
7 1294205 1301765 - Cp4.1LG07g02420.1 Cpe07g00202 202
7 1302356 1307648 + Cp4.1LG07g02460.1 Cpe07g00203 203
7 1308199 1314853 - Cp4.1LG07g02400.1 Cpe07g00204 204
7 1341978 1349300 + Cp4.1LG07g02500.1 Cpe07g00209 209
11 515711 520241 - Cp4.1LG11g01050.1 Cpe11g00096 96
8 24720248 24729244 - CrPI670011_08g011500.1 Cre08g1150 1150
8 24730002 24736358 + CrPI670011_08g011510.1 Cre08g1151 1151
8 24738178 24743250 - CrPI670011_08g011520.1 Cre08g1152 1152
8 24800427 24807015 + CrPI670011_08g011590.1 Cre08g1159 1159
2 20189400 20191767 - CsaV3_2G030700.1 Csa02g02251 2251
2 20195595 20200786 + CsaV3_2G030710.1 Csa02g02252 2252
2 20201532 20206811 - CsaV3_2G030720.1 Csa02g02253 2253
2 20244647 20249330 + CsaV3_2G030810.1 Csa02g02262 2262
3 39564190 39566583 - CsaV3_3G048460.1 Csa03g04540 4540
3 39570880 39579062 - CsaV3_3G048470.1 Csa03g04541 4541
3 39580817 39586299 + CsaV3_3G048480.1 Csa03g04542 4542
3 39605940 39611248 + CsaV3_3G048500.1 Csa03g04544 4544
1 86795271 86797993 - Hsped.01g22110.1 Hepe01g2211 2211
1 86815217 86825344 + Hsped.01g22130.1 Hepe01g2213 2213
10 4103152 4107794 - Hsped.10g03730.1 Hepe10g0373 373
10 4148539 4153479 - Hsped.10g03790.1 Hepe10g0379 379
13 32626642 32634319 - Maker00034020 Lcy13g1421 1421
13 32824416 32829404 + Maker00034130 Lcy13g1433 1433
13 32831081 32835692 - Maker00034028 Lcy13g1434 1434
4 30410980 30420520 - Lsi04G023210.1 Lsi04g02321 2321
4 30422607 30428790 + Lsi04G023220.1 Lsi04g02322 2322
11 5111868 5115153 - MC11g0638 Mch11g0759 759
11 5127018 5132513 + MC11g0640 Mch11g0761 761
1 9324728 9330361 + Sed0024833.1 Sed01g1255 1255
2 49183391 49185726 - Sed0014472.2 Sed02g1237 1237
9 39580430 39587269 + Sed0013678.1 Sed09g1609 1609
12 11083730 11086857 - Sed0019866.3 Sed12g1387 1387
1 104063701 104066766 - Tan0001004.2 Tan01g3912 3912
1 104071105 104080234 - Tan0006002.4 Tan01g3920 3920
2 93949025 93954135 - Tan0007420.2 Tan02g2543 2543
2 93963897 93969126 + Tan0015131.1 Tan02g2544 2544
2 94076141 94081248 + Tan0003973.1 Tan02g2553 2553
6 2021579 2026749 - Tan0006533.5 Tan06g0248 248
4 16201 17540 + Vvi4g2 Vvi4g2 2
4 24524 25255 - Vvi4g3 Vvi4g3 3
4 55348 55990 + Vvi4g4 Vvi4g4 4
4 69280 78477 + Vvi4g5 Vvi4g5 5
4 81665 94722 - Vvi4g6 Vvi4g6 6
4 105731 111628 + Vvi4g7 Vvi4g7 7
4 112192 124427 - Vvi4g8 Vvi4g8 8
4 129855 154757 + Vvi4g9 Vvi4g9 9
4 155643 160125 + Vvi4g10 Vvi4g10 10
4 162910 165161 + Vvi4g11 Vvi4g11 11
       

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