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
Vvi3g276 . . . . . Bpe12g00145 . . . . Cma02g00296 . Car02g00176 . . . . . . . . . . . . . . . . . . . . . Cone10ag1215 . . . . . Blo13g00479 . . . . . Bma08g00722 . Cmo02g00291 . . . . . . Cpe05g01340 . . . . . . . . . . . . . . . . . .
Vvi3g277 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g278 . Blo15g00428 Bda06g00438 . . . . . . . . Cma20g00717 . Car20g00618 . . . . . . . . . . . . . . . . . Cone12ag1269 Cone8ag1323 . . Lsi10g00826 . . . . . . . . . . . . . Cmo20g00715 . . . . Cpe16g00348 . . . . . . . . . . . . . . . . . . Cme11g01284
Vvi3g279 . . . . . Bpe12g00146 . . Cmo19g00812 Cmo11g01781 . . . . . . Cpe15g00635 Bhi05g01598 . . . . . . Cla02g00356 Cam02g0364 Cec02g0365 Cco02g0372 Clacu02g0356 Cmu02g0353 Cre02g0683 . . . . . Csa07g00177 . Cme01g01155 . Blo13g00478 . . . . . Bma08g00721 . . . Cma11g01338 . Car11g01409 Car19g00608 . . . . . . . . . . . . . . . . Lsi11g01278 . Chy01g00604 .
Vvi3g280 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme01g01154 . . . . Bpe15g00787 . . Bma08g00719 . . . Cma11g01337 . . . . . . . . . . . . . . . . . . . . . Chy01g00602 .
Vvi3g281 . . . . . Bpe12g00148 . . Cmo19g00813 Cmo11g01783 . . . . Sed05g2177 Cpe04g00628 Cpe15g00637 Bhi05g01590 Tan02g0585 Cmetu01g0562 . . . . Cla02g00354 Cam02g0363 Cec02g0364 Cco02g0371 Clacu02g0354 Cmu02g0351 . Cone12ag1271 Cone8ag1325 . . . Csa07g00180 . . Blo04g00603 Blo13g00475 . Bda14g00644 . . Bma03g00635 . . . . . Cma19g00792 Car11g01410 Car19g00609 . . . . . . . . . . . . . . . . Lsi11g01279 . . .
Vvi3g282 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g283 . . . . . . . . . . Cma02g00297 . Car02g00177 Car20g00617 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo20g00714 . . . . Cpe16g00349 Cpe05g01339 . . . . . . . . . . . . . . . . . .
Vvi3g284 . . Bda06g00439 . Bpe07g00672 . . Bma12g00878 Cmo19g00814 . . . . Car20g00616 Sed08g2863 . Cpe15g00638 Bhi05g01589 Tan02g0583 Cmetu11g2392 . Hepe02g0374 . . Cla02g00353 Cam02g0362 Cec02g0363 Cco02g0370 Clacu02g0353 Cmu02g0350 Cre02g0682 Cone12ag1272 Cone8ag1326 Cone3ag1243 . Lsi10g00828 Csa07g00181 . Cme01g01152 . . . . . . . . . . Cmo20g00713 . Cma19g00793 . Car19g00610 Cpe16g00350 . . . . . . . . . . . . . . . Lsi11g01280 . Chy01g00600 .
Vvi3g285 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag1273 Cone8ag1327 Cone3ag1247 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 6458074 6460521 + Bda023683.1 Bda06g00438 438
6 6461659 6462693 + Bda023684.1 Bda06g00439 439
14 4830071 4833576 + Bda027401.1 Bda14g00644 644
5 52762107 52763362 - XM_039032986.1 Bhi05g01589 1589
5 52831815 52836416 + XM_039032167.1 Bhi05g01590 1590
5 52840192 52845635 + XM_039031961.1 Bhi05g01598 1598
4 5206603 5211800 + BLOR13515 Blo04g00603 603
13 25630692 25634138 - BLOR05756 Blo13g00475 475
13 25679192 25683070 + BLOR05759 Blo13g00478 478
13 25683582 25686001 - BLOR05760 Blo13g00479 479
15 6165272 6167714 - BLOR06822 Blo15g00428 428
3 5235540 5240709 + Bma016928.1 Bma03g00635 635
8 43038838 43042207 - Bma028083.1 Bma08g00719 719
8 43047075 43051976 + Bma028085.1 Bma08g00721 721
8 43052452 43054097 - Bma028086.1 Bma08g00722 722
12 39990988 39992022 + Bma008202.1 Bma12g00878 878
7 13407320 13408351 + Bpe021522.1 Bpe07g00672 672
12 1057670 1059424 + Bpe024875 Bpe12g00145 145
12 1059909 1063933 - Bpe005384.3 Bpe12g00146 146
12 1069015 1072379 + Bpe005385.1 Bpe12g00148 148
15 18123373 18126854 - Bpe001714.1 Bpe15g00787 787
2 4361008 4361862 - CaPI482276_02g003620.1 Cam02g0362 362
2 4372341 4380288 + CaPI482276_02g003630.1 Cam02g0363 363
2 4380350 4384208 + CaPI482276_02g003640.1 Cam02g0364 364
2 1052135 1055979 - Carg19765-RA Car02g00176 176
2 1059250 1062201 + Carg19766-RA Car02g00177 177
11 11538812 11544115 - Carg18122-RA Car11g01409 1409
11 11545648 11549758 - Carg18121-RA Car11g01410 1410
19 7573050 7578710 - Carg04089-RA Car19g00608 608
19 7579384 7583761 - Carg04090-RA Car19g00609 609
19 7584838 7586307 + Carg04091-RA Car19g00610 610
20 3450662 3451321 - Carg16136-RA Car20g00616 616
20 3452856 3454643 - Carg16137-RA Car20g00617 617
20 3457738 3460842 - Carg16138-RA Car20g00618 618
2 3362422 3363276 - CcPI632755_02g003700.1 Cco02g0370 370
2 3371336 3378860 + CcPI632755_02g003710.1 Cco02g0371 371
2 3379346 3386000 + CcPI632755_02g003720.1 Cco02g0372 372
2 3370239 3371093 - CePI673135_02g003630.1 Cec02g0363 363
2 3376534 3384948 + CePI673135_02g003640.1 Cec02g0364 364
2 3387253 3393117 + CePI673135_02g003650.1 Cec02g0365 365
1 4288939 4289814 - Chy1G006000.1 Chy01g00600 600
1 4295745 4299716 + Chy1G006020.1 Chy01g00602 602
1 4303522 4308547 + Chy1G006040.1 Chy01g00604 604
2 3238080 3238934 - ClG42_02g0035300.10 Clacu02g0353 353
2 3248111 3252128 + ClG42_02g0035400.10 Clacu02g0354 354
2 3256128 3259994 + ClG42_02g0035600.10 Clacu02g0356 356
2 3451511 3452365 - ClCG02G003500.1 Cla02g00353 353
2 3461237 3467427 + ClCG02G003510.2 Cla02g00354 354
2 3469473 3475470 + ClCG02G003530.1 Cla02g00356 356
2 1381399 1384249 - CmaCh02G002960.1 Cma02g00296 296
2 1384832 1389935 + CmaCh02G002970.1 Cma02g00297 297
11 8859880 8865719 + CmaCh11G013370.1 Cma11g01337 1337
11 8866342 8872394 + CmaCh11G013380.1 Cma11g01338 1338
19 7683142 7694534 - CmaCh19G007920.1 Cma19g00792 792
19 7695770 7696660 + CmaCh19G007930.1 Cma19g00793 793
20 3308472 3316142 - CmaCh20G007170.1 Cma20g00717 717
1 14796460 14797326 - MELO3C013258.2.1 Cme01g01152 1152
1 14832949 14837743 + MELO3C013259.2.1 Cme01g01154 1154
1 14839228 14846324 + MELO3C013260.2.1 Cme01g01155 1155
11 19590109 19594660 - MELO3C013694.2.1 Cme11g01284 1284
1 4590925 4595523 + PI0025264.1 Cmetu01g0562 562
11 16890796 16891307 - PI0015793.1 Cmetu11g2392 2392
2 1443650 1447037 - CmoCh02G002910.1 Cmo02g00291 291
11 12531540 12536268 - CmoCh11G017810.1 Cmo11g01781 1781
11 12538590 12544368 - CmoCh11G017830.1 Cmo11g01783 1783
19 8034606 8040979 - CmoCh19G008120.1 Cmo19g00812 812
19 8041502 8046143 - CmoCh19G008130.1 Cmo19g00813 813
19 8047935 8048825 + CmoCh19G008140.1 Cmo19g00814 814
20 3507341 3507976 - CmoCh20G007130.1 Cmo20g00713 713
20 3508905 3512838 - CmoCh20G007140.1 Cmo20g00714 714
20 3514411 3517376 - CmoCh20G007150.1 Cmo20g00715 715
2 3230757 3231611 - CmPI595203_02g003500.1 Cmu02g0350 350
2 3239498 3244799 + CmPI595203_02g003510.1 Cmu02g0351 351
2 3248829 3252693 + CmPI595203_02g003530.1 Cmu02g0353 353
3 31221835 31222797 + Conep03aG0175000.1 Cone3ag1243 1243
3 31282019 31286372 + Conep03aG0175400.1 Cone3ag1247 1247
8 10724588 10725885 + Conep08aG0136200.1 Cone8ag1323 1323
8 10728073 10731373 + Conep08aG0136400.1 Cone8ag1325 1325
8 10731700 10732674 + Conep08aG0136500.1 Cone8ag1326 1326
8 10741156 10744824 + Conep08aG0136600.1 Cone8ag1327 1327
10 9049143 9051899 + Conep10aG0125000.1 Cone10ag1215 1215
12 9729543 9732173 + Conep12aG0131000.1 Cone12ag1269 1269
12 9734072 9737513 + Conep12aG0131200.1 Cone12ag1271 1271
12 9737824 9738801 + Conep12aG0131300.1 Cone12ag1272 1272
12 9744882 9748458 + Conep12aG0131400.1 Cone12ag1273 1273
4 6501872 6513906 - Cp4.1LG04g04520.1 Cpe04g00628 628
5 9428402 9433579 - Cp4.1LG05g13390.1 Cpe05g01339 1339
5 9435483 9438851 + Cp4.1LG05g13370.1 Cpe05g01340 1340
15 7097437 7103883 - Cp4.1LG15g06420.1 Cpe15g00635 635
15 7104349 7109161 - Cp4.1LG15g06390.1 Cpe15g00637 637
15 7110257 7111273 + Cp4.1LG15g06370.1 Cpe15g00638 638
16 5253031 5256110 + Cp4.1LG16g03470.1 Cpe16g00348 348
16 5257552 5261305 + Cp4.1LG16g03460.1 Cpe16g00349 349
16 5262364 5263002 + Cp4.1LG16g03520.1 Cpe16g00350 350
2 3789111 3789965 - CrPI670011_02g006820.1 Cre02g0682 682
2 3795630 3810576 + CrPI670011_02g006830.1 Cre02g0683 683
7 1466029 1472687 - CsaV3_7G001770.1 Csa07g00177 177
7 1474267 1479028 - CsaV3_7G001800.1 Csa07g00180 180
7 1483919 1484794 + CsaV3_7G001810.1 Csa07g00181 181
2 3488423 3489310 - Hsped.02g03740.1 Hepe02g0374 374
10 11573842 11577884 + Lsi10G008260.1 Lsi10g00826 826
10 11636937 11637452 + Lsi10G008280.1 Lsi10g00828 828
11 21390931 21397393 - Lsi11G012780.1 Lsi11g01278 1278
11 21405224 21410177 - Lsi11G012790.1 Lsi11g01279 1279
11 21415643 21416497 + Lsi11G012800.1 Lsi11g01280 1280
5 34608647 34614254 + Sed0010207.1 Sed05g2177 2177
8 39829230 39829790 + Sed0007909.1 Sed08g2863 2863
2 5143356 5145340 - Tan0012909.1 Tan02g0583 583
2 5152147 5156737 + Tan0006566.1 Tan02g0585 585
3 2613670 2617041 + Vvi3g276 Vvi3g276 276
3 2617961 2619973 + Vvi3g277 Vvi3g277 277
3 2620299 2622993 - Vvi3g278 Vvi3g278 278
3 2630924 2639037 + Vvi3g279 Vvi3g279 279
3 2641394 2643174 + Vvi3g280 Vvi3g280 280
3 2643175 2645835 + Vvi3g281 Vvi3g281 281
3 2647250 2657766 + Vvi3g282 Vvi3g282 282
3 2657816 2659770 + Vvi3g283 Vvi3g283 283
3 2660981 2661950 + Vvi3g284 Vvi3g284 284
3 2667487 2673608 + Vvi3g285 Vvi3g285 285
       

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