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
Vvi3g356 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g357 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo04g00516 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g358 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g359 Blo02g00807 . . . . . . . Cmo19g00849 . Cma02g00387 Cma20g00840 . Car20g00727 Sed05g2098 . Cpe15g00669 Bhi05g01515 Tan02g0519 Cmetu01g0280 Lac12g0419 Hepe02g0330 . . Cla02g00313 Cam02g0320 Cec02g0321 Cco02g0323 Clacu02g0312 Cmu02g0311 Cre02g0643 Cone12ag1278 Cone8ag1355 . Cone10ag0975 Lsi10g00383 Csa07g00231 Chy11g00368 . Blo04g00618 . . Bda14g00659 Bpe15g00765 . . . Sed01g0294 Cmo02g00394 Cmo20g00850 . Cma19g00833 . Car19g00646 Cpe16g00250 Cpe05g01269 Bhi10g01989 Tan05g1287 Cmetu11g1343 . Hepe08g1004 . . . . . . . . . Lsi11g01326 Csa02g01275 Chy01g00549 Cme11g00128
Vvi3g360 . . . . . . . . . . Cma02g00389 . Car02g00252 . . . . . . . . . . . . . . . . . . . . . . Lsi10g00382 . Chy11g00369 . . . . . . . . . . Cmo02g00396 . . . . . . Cpe05g01268 . . . . . . . . . . . . . . . Csa02g01274 . Cme11g00127
Vvi3g361 . Blo15g00705 . . Bpe07g00423 . . Bma12g00506 . . . . Car02g00253 Car20g00728 . . . . . . . . . . . . . . . . . . . Cone3ag1168 Cone10ag0973 Lsi10g00381 . Chy11g00370 . Blo04g00514 . . . . . . . Sed05g3614 . Cmo20g00852 . . . . Cpe16g00249 Cpe05g01267 Bhi10g01991 Tan05g1289 Cmetu11g1174 . Hepe08g1005 . . . . . . . . . . Csa02g01273 . Cme11g00126
Vvi3g362 . . . . . . . . . . Cma02g00390 Cma20g00843 . Car20g00729 . . . . . . . . . . . . . . . . . Cone12ag1159 Cone8ag1208 . Cone10ag0972 Lsi10g00380 . Chy11g00371 . . . . . . . . . Sed01g0296 Cmo02g00397 Cmo20g00853 . . . . Cpe16g00248 Cpe05g01266 Bhi10g01993 Tan05g1292 Cmetu11g1816 . . . . . . . . . . . . Csa02g01269 . Cme11g00125
Vvi3g363 Blo02g00806 . . Bda08g00942 . . Bma05g00441 . . . Cma02g00391 . Car02g00254 Car20g00730 . . . . . . . . . . . . . . . . . Cone12ag1158 Cone8ag1207 . . Lsi10g00379 . Chy11g00372 . . . . . . . . . Sed01g0297 Cmo02g00398 Cmo20g00854 . . . . Cpe16g00247 Cpe05g01265 Bhi10g01995 Tan05g1293 Cmetu11g1187 . Hepe08g1009 . . . . . . . . . . Csa02g01268 . Cme11g00124
Vvi3g364 . . . . . . . . . . . . . . Sed04g3917 . . Bhi05g01246 Tan02g0783 Cmetu01g1193 . Hepe02g0490 . . . . . . . . . . . . Cone10ag0970 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g365 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 17629521 17636082 + Bda029588.2 Bda08g00942 942
14 4953633 4957054 - Bda027417.1 Bda14g00659 659
5 45261297 45271166 + XM_039031758.1 Bhi05g01246 1246
5 51614466 51619516 + XM_039032294.1 Bhi05g01515 1515
10 49717483 49721832 + XM_039046847.1 Bhi10g01989 1989
10 49726345 49730571 - XM_039044392.1 Bhi10g01991 1991
10 49877560 49880578 + XM_039044465.1 Bhi10g01993 1993
10 49882882 49889581 + XM_039045520.1 Bhi10g01995 1995
2 27868524 27884895 - BLOR10536 Blo02g00806 806
2 28108614 28123332 - BLOR10537 Blo02g00807 807
4 4377456 4390429 + BLOR13426 Blo04g00514 514
4 4404930 4408560 + BLOR13428 Blo04g00516 516
4 5390090 5393545 - BLOR13530 Blo04g00618 618
15 22416807 22419460 + BLOR07099 Blo15g00705 705
5 14674777 14681389 - Bma021293.1 Bma05g00441 441
12 15979407 15982840 - Bma007570.2 Bma12g00506 506
7 4723829 4726466 - Bpe021247.1 Bpe07g00423 423
15 18003728 18007114 + Bpe001694.1 Bpe15g00765 765
2 3960757 3965368 + CaPI482276_02g003200.1 Cam02g0320 320
2 1718194 1726355 + Carg24156-RA Car02g00252 252
2 1726412 1729830 - Carg24157-RA Car02g00253 253
2 1737841 1740795 + Carg22939-RA Car02g00254 254
19 7780659 7785292 - Carg04127-RA Car19g00646 646
20 4240570 4244589 + Carg26474-RA Car20g00727 727
20 4246291 4249929 - Carg26475-RA Car20g00728 728
20 4254962 4258171 + Carg26476-RA Car20g00729 729
20 4258745 4264117 + Carg26477-RA Car20g00730 730
2 2955526 2960056 + CcPI632755_02g003230.1 Cco02g0323 323
2 2953336 2957839 + CePI673135_02g003210.1 Cec02g0321 321
1 3933251 3937294 + Chy1G005490.1 Chy01g00549 549
11 3396796 3400750 + Chy11G189480.1 Chy11g00368 368
11 3402169 3404176 + Chy11G189490.1 Chy11g00369 369
11 3404939 3409494 - Chy11G189500.1 Chy11g00370 370
11 3426017 3434209 + Chy11G189510.1 Chy11g00371 371
11 3434718 3435191 + Chy11G189520.1 Chy11g00372 372
2 2839057 2843578 + ClG42_02g0031200.10 Clacu02g0312 312
2 3037546 3042237 + ClCG02G003100.2 Cla02g00313 313
2 1964800 1970729 + CmaCh02G003870.1 Cma02g00387 387
2 1971457 1973887 + CmaCh02G003890.1 Cma02g00389 389
2 1982151 1985250 + CmaCh02G003900.1 Cma02g00390 390
2 1986602 1992247 + CmaCh02G003910.1 Cma02g00391 391
19 7892522 7896690 - CmaCh19G008330.1 Cma19g00833 833
20 4022751 4026858 + CmaCh20G008400.1 Cma20g00840 840
20 4038993 4043313 + CmaCh20G008430.1 Cma20g00843 843
11 1166599 1172596 - MELO3C023306.2.1 Cme11g00124 124
11 1176104 1180208 - MELO3C023307.2.1 Cme11g00125 125
11 1195145 1200536 + MELO3C023308.2.1 Cme11g00126 126
11 1225962 1227405 - MELO3C023309.2.1 Cme11g00127 127
11 1228776 1233932 - MELO3C023310.2.1 Cme11g00128 128
1 4200094 4205089 + PI0025839.1 Cmetu01g0280 280
1 5935383 5944330 - PI0020112.1 Cmetu01g1193 1193
11 27550465 27554969 + PI0013001.1 Cmetu11g1174 1174
11 27517995 27524511 - PI0028490.1 Cmetu11g1187 1187
11 27559271 27564597 - PI0002417.1 Cmetu11g1343 1343
11 27526606 27531241 - PI0021229.1 Cmetu11g1816 1816
2 2034173 2038198 + CmoCh02G003940.1 Cmo02g00394 394
2 2039142 2043290 + CmoCh02G003960.1 Cmo02g00396 396
2 2050793 2053865 + CmoCh02G003970.1 Cmo02g00397 397
2 2054833 2060863 + CmoCh02G003980.1 Cmo02g00398 398
19 8242323 8247235 - CmoCh19G008490.1 Cmo19g00849 849
20 4274588 4278651 + CmoCh20G008500.1 Cmo20g00850 850
20 4280918 4284937 - CmoCh20G008520.1 Cmo20g00852 852
20 4290438 4293973 + CmoCh20G008530.1 Cmo20g00853 853
20 4295001 4300847 + CmoCh20G008540.1 Cmo20g00854 854
2 2832983 2837484 + CmPI595203_02g003110.1 Cmu02g0311 311
3 30353225 30357253 + Conep03aG0167300.1 Cone3ag1168 1168
8 10253429 10257453 - Conep08aG0124400.1 Cone8ag1207 1207
8 10257973 10260458 - Conep08aG0124500.1 Cone8ag1208 1208
8 10857989 10861027 - Conep08aG0139400.1 Cone8ag1355 1355
10 6524150 6526384 + Conep10aG0099600.1 Cone10ag0970 970
10 6529397 6532035 - Conep10aG0099800.1 Cone10ag0972 972
10 6543876 6548472 + Conep10aG0099900.1 Cone10ag0973 973
10 6554462 6558295 - Conep10aG0100100.1 Cone10ag0975 975
12 9226188 9229406 - Conep12aG0119700.1 Cone12ag1158 1158
12 9229794 9232217 - Conep12aG0119800.1 Cone12ag1159 1159
12 9772015 9774786 + Conep12aG0131900.1 Cone12ag1278 1278
5 8829342 8835586 - Cp4.1LG05g12610.1 Cpe05g01265 1265
5 8836479 8839661 - Cp4.1LG05g12590.1 Cpe05g01266 1266
5 8844048 8851513 + Cp4.1LG05g12560.1 Cpe05g01267 1267
5 8844542 8850453 - Cp4.1LG05g12580.1 Cpe05g01268 1268
5 8850981 8854912 - Cp4.1LG05g12620.1 Cpe05g01269 1269
15 7312775 7316943 - Cp4.1LG15g06700.1 Cpe15g00669 669
16 4508117 4514164 - Cp4.1LG16g02560.1 Cpe16g00247 247
16 4515698 4519446 - Cp4.1LG16g02540.1 Cpe16g00248 248
16 4523327 4527700 + Cp4.1LG16g02500.1 Cpe16g00249 249
16 4527921 4532774 - Cp4.1LG16g02590.1 Cpe16g00250 250
2 3378170 3382683 + CrPI670011_02g006430.1 Cre02g0643 643
2 12370721 12376985 - CsaV3_2G014840.1 Csa02g01268 1268
2 12382374 12387110 - CsaV3_2G014850.1 Csa02g01269 1269
2 12403883 12406567 + CsaV3_2G014890.1 Csa02g01273 1273
2 12406841 12409323 - CsaV3_2G014900.1 Csa02g01274 1274
2 12410284 12415449 - CsaV3_2G014910.1 Csa02g01275 1275
7 1821014 1825888 - CsaV3_7G002310.1 Csa07g00231 231
2 3166555 3171162 + Hsped.02g03300.1 Hepe02g0330 330
2 4794399 4798778 - Hsped.02g04900.1 Hepe02g0490 490
8 9575851 9582106 + Hsped.08g10040.1 Hepe08g1004 1004
8 9580993 9592573 - Hsped.08g10050.1 Hepe08g1005 1005
8 9616798 9622411 + Hsped.08g10090.1 Hepe08g1009 1009
12 4701547 4705425 + Lag0014791.1 Lac12g0419 419
10 5791799 5798326 - Lsi10G003790.1 Lsi10g00379 379
10 5801418 5803508 - Lsi10G003800.1 Lsi10g00380 380
10 5825741 5836344 + Lsi10G003810.1 Lsi10g00381 381
10 5833990 5835985 - Lsi10G003820.1 Lsi10g00382 382
10 5837261 5844213 - Lsi10G003830.1 Lsi10g00383 383
11 21866736 21871831 - Lsi11G013260.1 Lsi11g01326 1326
1 2260824 2266417 + Sed0003264.2 Sed01g0294 294
1 2270477 2272290 + Sed0002809.1 Sed01g0296 296
1 2274099 2280372 + Sed0008343.1 Sed01g0297 297
4 47298805 47303744 - Sed0018862.1 Sed04g3917 3917
5 34132346 34138199 - Sed0020665.1 Sed05g2098 2098
5 44459821 44462944 - Sed0007775.1 Sed05g3614 3614
2 4679369 4683795 + Tan0022307.1 Tan02g0519 519
2 7468224 7478500 - Tan0000006.1 Tan02g0783 783
5 14663192 14668145 + Tan0008787.1 Tan05g1287 1287
5 14676658 14679555 - Tan0011475.1 Tan05g1289 1289
5 15085814 15087817 + Tan0018000.1 Tan05g1292 1292
5 15091260 15097008 + Tan0014576.1 Tan05g1293 1293
3 3311528 3311907 - Vvi3g356 Vvi3g356 356
3 3311926 3325896 - Vvi3g357 Vvi3g357 357
3 3334415 3347343 + Vvi3g358 Vvi3g358 358
3 3353228 3358041 + Vvi3g359 Vvi3g359 359
3 3358095 3360699 + Vvi3g360 Vvi3g360 360
3 3360708 3368408 - Vvi3g361 Vvi3g361 361
3 3383812 3388437 + Vvi3g362 Vvi3g362 362
3 3389325 3396811 + Vvi3g363 Vvi3g363 363
3 3396906 3400842 - Vvi3g364 Vvi3g364 364
3 3404383 3408097 + Vvi3g365 Vvi3g365 365
       

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