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
Vvi18g280 . . . . . . . . . Cmo15g00700 . . . . . . . Bhi04g01923 Tan11g1287 . . Hepe02g2280 . . Cla08g00582 Cam08g0997 Cec08g0586 Cco08g0696 Clacu08g0706 . Cre08g0517 . . Cone17ag1278 Cone20ag0448 . . . . Blo17g00178 . . Bda13g01482 . Bpe14g00382 . Bma02g00218 . . . . . . Car15g00631 . . . . . . . . . . . . . . . . Lsi08g00428 . . .
Vvi18g281 . . . . . . . . Cmo04g02466 Cmo15g00701 . . . . Sed03g0792 . . Bhi04g01924 Tan11g1288 Cmetu03g2241 . Hepe02g2281 . Lcy10g1219 Cla08g00581 Cam08g0996 Cec08g0585 Cco08g0695 Clacu08g0705 . Cre08g0516 Cone4ag1397 . Cone17ag1277 Cone20ag0449 . . . . Blo17g00179 . . Bda13g01483 . Bpe14g00381 . Bma02g00219 . . . . . Car04g02283 Car15g00632 Cpe01g02045 . . . . . . . . . . . . . . . Lsi08g00427 . . .
Vvi18g282 . . . . . . . . . Cmo15g00703 . . . . Sed03g0794 . . Bhi04g01926 Tan11g1290 Cmetu03g0298 . Hepe02g2282 . Lcy10g1217 Cla08g00580 Cam08g0995 Cec08g0584 Cco08g0694 Clacu08g0704 . Cre08g0515 . . . Cone20ag0450 . . . Cme03g00572 Blo17g00180 . . . . Bpe14g00380 . Bma02g00220 . . . . . . Car15g00634 . . . . . . . . . . . . . . . . Lsi08g00426 . . .
Vvi18g283 . . . . . . . . Cmo04g02465 . . . . . . . . Bhi04g01928 Tan11g1292 . . Hepe02g2283 . . Cla08g00579 Cam08g0994 Cec08g0583 Cco08g0693 Clacu08g0703 . Cre08g0514 Cone4ag1396 Cone7ag1541 . . . . . Cme03g00573 . . . Bda13g01484 . Bpe14g00379 . Bma02g00221 . . . . . Car04g02282 . Cpe01g02044 . . . . . . . . . . . . . . . Lsi08g00423 . . .
Vvi18g284 . Blo12g00672 . . Bpe02g00072 . . Bma01g02646 Cmo04g02464 . . Cma09g00799 . . . . . Bhi04g01968 . . . Hepe03g1048 . . Cla08g00578 Cam08g0993 Cec08g0581 Cco08g0692 Clacu08g0702 . Cre08g0513 . . . . . Csa04g01808 . Cme03g00574 Blo17g00181 . . . . . . . . . Cmo09g00792 . . . Car09g00716 . . Bhi09g02666 . . . . Mch11g0824 . . . . . . . . Lsi08g00420 . . .
Vvi18g285 . . . Bda03g00533 . Bpe04g00487 . . . . . . . . . . . Bhi04g01971 . . . . . . . . . . . . . Cone4ag1395 Cone7ag1542 . . Lsi04g02384 . . Cme03g01505 . . . Bda13g01485 . . . . . . . . . . . . . . . . . . . . Cla11g01531 Cam11g1590 Cec11g1619 Cco11g1620 Clacu11g1749 Cmu11g1565 Cre11g1981 . . . Cme07g00859
Vvi18g286 . . . . . . . . Cmo04g02463 . . . . . . Cpe06g00635 . Bhi04g01972 . . . . . . . . . . . . . . . . . . Csa04g01903 . . . . . . . Bpe14g00378 . . . . . . . . . Cpe01g02043 . . . . . . . . . . . . . . . . . Chy07g00654 .
Vvi18g287 . . . Bda03g00532 . Bpe04g00486 . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1394 . . . Lsi04g02383 Csa04g01809 . . . . . . . . . . Sed12g1462 . . . . . . . . Bhi09g02664 Tan01g4020 Cmetu07g1621 . . . . Cla11g01529 Cam11g1589 Cec11g1618 Cco11g1619 Clacu11g1747 Cmu11g1564 Cre11g1980 . . Chy07g00655 Cme07g00860
Vvi18g288 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma12g00143 . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g289 . . . . . . . . Cmo04g02462 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo18g00187 . Bda01g01422 Bpe02g01636 . Bma01g00825 . . . . . . Car04g02280 . Cpe01g02042 . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 50158331 50161083 - Bda003667.1 Bda01g01422 1422
3 4429858 4431414 + Bda016502.1 Bda03g00532 532
3 4434334 4436050 + Bda016503.1 Bda03g00533 533
13 37749633 37752701 + Bda032811 Bda13g01482 1482
13 37759304 37760694 - Bda000327.1 Bda13g01483 1483
13 37767336 37768981 - Bda000328.2 Bda13g01484 1484
13 37769446 37771369 - Bda000329.1 Bda13g01485 1485
4 48450066 48454916 + XM_039030760.1 Bhi04g01923 1923
4 48457122 48459868 - XM_039028224.1 Bhi04g01924 1924
4 48476909 48485476 + XM_039028782.1 Bhi04g01926 1926
4 48485544 48490318 - XM_039028783.1 Bhi04g01928 1928
4 50552427 50559033 + XM_039030129.1 Bhi04g01968 1968
4 50622840 50635994 + XM_039030523.1 Bhi04g01971 1971
4 50717291 50722677 + XM_039030548.1 Bhi04g01972 1972
9 71584820 71585638 + XM_039042565.1 Bhi09g02664 2664
9 71600438 71604529 + XM_039040878.1 Bhi09g02666 2666
12 25021362 25027581 - BLOR04691 Blo12g00672 672
17 1833795 1837339 + BLOR15999 Blo17g00178 178
17 1838339 1847277 - BLOR16000 Blo17g00179 179
17 1841639 1844822 + BLOR16001 Blo17g00180 180
17 1847688 1849488 - BLOR16002 Blo17g00181 181
18 1798920 1805781 + BLOR08675 Blo18g00187 187
1 7764850 7767593 + Bma001044.1 Bma01g00825 825
1 83962891 83970206 + Bma003532.1 Bma01g02646 2646
2 2341624 2345103 + Bma014675.1 Bma02g00218 218
2 2345883 2347446 - Bma014676.2 Bma02g00219 219
2 2347976 2350817 + Bma014677.2 Bma02g00220 220
2 2351861 2353446 - Bma030860 Bma02g00221 221
2 562039 563688 - Bpe007924.1 Bpe02g00072 72
2 19172338 19175057 - Bpe009482.1 Bpe02g01636 1636
4 3058821 3060372 + Bpe025629 Bpe04g00486 486
4 3063383 3064835 + Bpe015170.1 Bpe04g00487 487
14 3578482 3580860 + Bpe007032.1 Bpe14g00378 378
14 3581314 3582905 + Bpe007033.1 Bpe14g00379 379
14 3583902 3586726 - Bpe007034.1 Bpe14g00380 380
14 3587685 3589250 + Bpe007035.1 Bpe14g00381 381
14 3589962 3593537 - Bpe024976 Bpe14g00382 382
8 16062190 16069276 + CaPI482276_08g009930.1 Cam08g0993 993
8 16093170 16098074 + CaPI482276_08g009940.1 Cam08g0994 994
8 16098643 16106145 - CaPI482276_08g009950.1 Cam08g0995 995
8 16109107 16111284 + CaPI482276_08g009960.1 Cam08g0996 996
8 16112220 16117043 - CaPI482276_08g009970.1 Cam08g0997 997
11 28631314 28636992 + CaPI482276_11g015890.1 Cam11g1589 1589
11 28644389 28647239 + CaPI482276_11g015900.1 Cam11g1590 1590
4 18346361 18350416 - Carg24449-RA Car04g02280 2280
4 18362955 18367400 + Carg24447-RA Car04g02282 2282
4 18367885 18370719 + Carg24445-RA Car04g02283 2283
9 4243046 4245586 - Carg17035-RA Car09g00716 716
15 3502536 3505927 + Carg01524-RA Car15g00631 631
15 3506690 3508620 - Carg01523-RA Car15g00632 632
15 3509839 3516203 + Carg01521-RA Car15g00634 634
8 18357870 18364839 + CcPI632755_08g006920.1 Cco08g0692 692
8 18433599 18438493 + CcPI632755_08g006930.1 Cco08g0693 693
8 18439115 18446620 - CcPI632755_08g006940.1 Cco08g0694 694
8 18449799 18451966 + CcPI632755_08g006950.1 Cco08g0695 695
8 18452921 18457709 - CcPI632755_08g006960.1 Cco08g0696 696
11 29007335 29013216 + CcPI632755_11g016190.1 Cco11g1619 1619
11 29020257 29023149 + CcPI632755_11g016200.1 Cco11g1620 1620
8 17235107 17241906 + CePI673135_08g005810.1 Cec08g0581 581
8 17264401 17269270 + CePI673135_08g005830.1 Cec08g0583 583
8 17269897 17277400 - CePI673135_08g005840.1 Cec08g0584 584
8 17280456 17283728 + CePI673135_08g005850.1 Cec08g0585 585
8 17283817 17288364 - CePI673135_08g005860.1 Cec08g0586 586
11 30458724 30463776 + CePI673135_11g016180.1 Cec11g1618 1618
11 30471817 30474702 + CePI673135_11g016190.1 Cec11g1619 1619
7 6254589 6257657 - Chy7G134840.1 Chy07g00654 654
7 6268559 6273022 - Chy7G134850.1 Chy07g00655 655
8 16778760 16785417 + ClG42_08g0070200.10 Clacu08g0702 702
8 16822871 16827721 + ClG42_08g0070300.10 Clacu08g0703 703
8 16828346 16835772 - ClG42_08g0070400.10 Clacu08g0704 704
8 16838452 16840494 + ClG42_08g0070500.10 Clacu08g0705 705
8 16841460 16846237 - ClG42_08g0070600.10 Clacu08g0706 706
11 28656209 28662209 + ClG42_11g0174700.10 Clacu11g1747 1747
11 28669297 28672210 + ClG42_11g0174900.10 Clacu11g1749 1749
8 17571583 17578384 + ClCG08G005550.1 Cla08g00578 578
8 17629480 17636080 + ClCG08G005560.2 Cla08g00579 579
8 17635550 17646114 - ClCG08G005570.2 Cla08g00580 580
8 17645799 17648176 + ClCG08G005580.1 Cla08g00581 581
8 17648755 17653686 - ClCG08G005590.1 Cla08g00582 582
11 28934840 28941636 + ClCG11G015660.2 Cla11g01529 1529
11 28947910 28951293 + ClCG11G015670.2 Cla11g01531 1531
9 3899192 3901755 - CmaCh09G007990.1 Cma09g00799 799
12 619268 621397 + CmaCh12G001430.1 Cma12g00143 143
3 8898536 8909838 + MELO3C010600.2.1 Cme03g00572 572
3 8909889 8913336 - MELO3C010599.2.1 Cme03g00573 573
3 8965872 8972615 + MELO3C010598.2.1 Cme03g00574 574
3 24293859 24296240 + MELO3C011368.2.1 Cme03g01505 1505
7 8550197 8553762 - MELO3C010471.2.1 Cme07g00859 859
7 8563927 8568668 - MELO3C010470.2.1 Cme07g00860 860
3 12619376 12630154 + PI0011344.1 Cmetu03g0298 298
3 12534403 12537130 - PI0010114.1 Cmetu03g2241 2241
7 19615981 19622379 + PI0003043.1 Cmetu07g1621 1621
4 18205007 18208061 - CmoCh04G024620.1 Cmo04g02462 2462
4 18212099 18216079 + CmoCh04G024630.1 Cmo04g02463 2463
4 18217217 18219644 + CmoCh04G024640.1 Cmo04g02464 2464
4 18221001 18224626 + CmoCh04G024650.1 Cmo04g02465 2465
4 18224660 18229086 + CmoCh04G024660.1 Cmo04g02466 2466
9 4054770 4057634 - CmoCh09G007920.1 Cmo09g00792 792
15 3410274 3414114 + CmoCh15G007000.1 Cmo15g00700 700
15 3413919 3416342 - CmoCh15G007010.1 Cmo15g00701 701
15 3416858 3423458 + CmoCh15G007030.1 Cmo15g00703 703
11 27909548 27915560 + CmPI595203_11g015640.1 Cmu11g1564 1564
11 27922639 27925557 + CmPI595203_11g015650.1 Cmu11g1565 1565
4 11237627 11240345 + Conep04aG0144300.1 Cone4ag1394 1394
4 11243721 11245515 + Conep04aG0144400.1 Cone4ag1395 1395
4 11245947 11247668 + Conep04aG0144500.1 Cone4ag1396 1396
4 11247907 11249628 + Conep04aG0144600.1 Cone4ag1397 1397
7 10637580 10638787 - Conep07aG0158700.1 Cone7ag1541 1541
7 10639328 10641296 - Conep07aG0158800.1 Cone7ag1542 1542
17 9190777 9191706 + Conep17aG0130800.1 Cone17ag1277 1277
17 9192663 9197570 - Conep17aG0130900.1 Cone17ag1278 1278
20 2286343 2290021 + Conep20aG0046300.1 Cone20ag0448 448
20 2290876 2293330 - Conep20aG0046400.1 Cone20ag0449 449
20 2294276 2300172 + Conep20aG0046500.1 Cone20ag0450 450
1 17340879 17345941 - Cp4.1LG01g20500.1 Cpe01g02042 2042
1 17350414 17357190 + Cp4.1LG01g20430.1 Cpe01g02043 2043
1 17358163 17362350 + Cp4.1LG01g20360.1 Cpe01g02044 2044
1 17363598 17366542 + Cp4.1LG01g20420.1 Cpe01g02045 2045
6 3930842 3933629 - Cp4.1LG06g06400.1 Cpe06g00635 635
8 17683883 17691113 + CrPI670011_08g005130.1 Cre08g0513 513
8 17723905 17728839 + CrPI670011_08g005140.1 Cre08g0514 514
8 17729463 17739236 - CrPI670011_08g005150.1 Cre08g0515 515
8 17739329 17741497 + CrPI670011_08g005160.1 Cre08g0516 516
8 17742391 17747175 - CrPI670011_08g005170.1 Cre08g0517 517
11 31555786 31561660 + CrPI670011_11g019800.1 Cre11g1980 1980
11 31568705 31571640 + CrPI670011_11g019810.1 Cre11g1981 1981
4 17728900 17732349 - CsaV3_4G028340.1 Csa04g01808 1808
4 17741608 17747847 - CsaV3_4G028350.1 Csa04g01809 1809
4 18776633 18780793 - CsaV3_4G029290.1 Csa04g01903 1903
2 65935787 65939908 + Hsped.02g22800.1 Hepe02g2280 2280
2 65942087 65944826 - Hsped.02g22810.1 Hepe02g2281 2281
2 65951528 65964046 + Hsped.02g22820.1 Hepe02g2282 2282
2 65965951 65969360 - Hsped.02g22830.1 Hepe02g2283 2283
3 57333836 57334261 - Hsped.03g10480.1 Hepe03g1048 1048
10 34819183 34823308 - Maker00008533 Lcy10g1217 1217
10 34832255 34834470 + Maker00008466 Lcy10g1219 1219
4 30972070 30972526 + Lsi04G023830.1 Lsi04g02383 2383
4 30985937 30989220 + Lsi04G023840.1 Lsi04g02384 2384
8 11705883 11711891 + Lsi08G004200.1 Lsi08g00420 420
8 11754962 11758496 + Lsi08G004230.1 Lsi08g00423 423
8 11779607 11787497 - Lsi08G004260.1 Lsi08g00426 426
8 11788790 11791532 + Lsi08G004270.1 Lsi08g00427 427
8 11792607 11797227 - Lsi08G004280.1 Lsi08g00428 428
11 5557448 5560490 + MC11g0692 Mch11g0824 824
3 4789795 4792974 - Sed0005970.1 Sed03g0792 792
3 4793985 4801657 + Sed0010827.2 Sed03g0794 794
12 14752438 14767495 - Sed0003401.2 Sed12g1462 1462
1 105149081 105155082 - Tan0016920.1 Tan01g4020 4020
11 10980403 10986226 + Tan0012405.2 Tan11g1287 1287
11 10987228 10989905 - Tan0017172.1 Tan11g1288 1288
11 10994486 11000415 + Tan0017322.1 Tan11g1290 1290
11 11001202 11004894 - Tan0010770.2 Tan11g1292 1292
18 3109636 3133801 + Vvi18g280 Vvi18g280 280
18 3134530 3146368 - Vvi18g281 Vvi18g281 281
18 3149242 3169300 + Vvi18g282 Vvi18g282 282
18 3170426 3174977 - Vvi18g283 Vvi18g283 283
18 3177009 3180121 - Vvi18g284 Vvi18g284 284
18 3180623 3189934 - Vvi18g285 Vvi18g285 285
18 3190005 3192536 - Vvi18g286 Vvi18g286 286
18 3197115 3198320 + Vvi18g287 Vvi18g287 287
18 3198720 3206947 - Vvi18g288 Vvi18g288 288
18 3209031 3213914 + Vvi18g289 Vvi18g289 289
       

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