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
Vvi18g390 . . . . . . . . . . . . . Car12g00139 Sed04g0136 . Cpe07g00127 Bhi04g00750 Tan02g2380 Cmetu03g1402 . Hepe10g0511 . Lcy13g1571 Cla08g01100 Cam08g1554 Cec08g1127 Cco08g1254 Clacu08g1256 . Cre08g1038 . . . . . . . Cme03g01514 . . . . . . . . . . . Cma12g00151 . . . . . . . . . . . . . . . . . . . Lsi08g00957 . Chy03g01023 .
Vvi18g391 . . . . . . . . . . . . . . . . Cpe07g00108 . . . . . . . . . . . . . . Cone4ag1349 Cone7ag1582 . . . . . . . . . . . . . . . . . Cma12g00128 . . . . . . . . . . . . . . . . . . . Lsi08g00930 . . .
Vvi18g392 . . . . . . . . Cmo05g00518 . . . . . . . . . . . . . . . . . . . . . . Cone4ag1348 Cone7ag1583 Cone17ag1227 . . . . . . . . . . . . . . . . . . . . Cpe11g00433 . . . . . . . . . . . . . . . . . . .
Vvi18g393 . Blo12g00702 . Bda03g00496 Bpe02g00100 Bpe04g00451 . Bma01g02620 . . Cma01g01421 Cma09g00648 . . . Cpe06g00508 . . . . . . . . . . . . . . . Cone4ag1347 Cone7ag1584 . . Lsi04g02348 Csa04g01848 . . . . Bda11g00760 . . . . . Sed12g1412 Cmo01g01471 Cmo09g00631 . . . Car09g00576 . Cpe02g00525 Bhi09g02612 Tan01g3963 Cmetu07g1933 . Hepe01g2241 Mch11g0789 . Cla11g01498 Cam11g1554 Cec11g1586 Cco11g1582 Clacu11g1712 Cmu11g1531 Cre11g1947 . . Chy07g00705 Cme07g00929
Vvi18g394 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g395 . . . . Bpe02g00101 . . Bma01g02618 . . Cma01g01424 Cma09g00647 . . . Cpe06g00507 . . . . . . . . . . . . . . . Cone4ag1346 Cone7ag1585 . . Lsi04g02346 Csa03g04567 . . . . . . . . . . Sed12g1410 Cmo01g01473 Cmo09g00630 . . . Car09g00574 . Cpe02g00523 Bhi09g02610 Tan01g3960 Cmetu04g1462 . Hepe01g2239 Mch11g0787 . Cla11g01497 Cam11g1553 Cec11g1585 Cco11g1581 Clacu11g1711 Cmu11g1530 Cre11g1946 . . . .
Vvi18g396 . Blo12g00703 . Bda03g00494 . Bpe04g00450 . . . . . Cma09g00646 . . . Cpe06g00506 . . . . . . . . . . . . . . . Cone4ag1345 Cone7ag1586 . . Lsi04g02345 Csa03g04566 . . . . . . . . . . Sed04g0529 . Cmo09g00629 . . . Car09g00573 . . Bhi09g02609 Tan01g3959 . . Hepe01g2238 Mch11g0785 . Cla11g01496 Cam11g1552 Cec11g1584 Cco11g1580 Clacu11g1710 Cmu11g1529 Cre11g1945 . . . .
Vvi18g397 . Blo12g00704 . Bda03g00493 Bpe02g00102 Bpe04g00449 . Bma01g02617 Cmo05g00519 Cmo12g00118 . . . Car12g00142 Sed04g0138 . Cpe07g00129 Bhi04g00751 Tan02g2382 Cmetu03g0542 . Hepe10g0507 . Lcy13g1569 Cla08g01103 Cam08g1556 Cec08g1129 Cco08g1256 Clacu08g1258 . Cre08g1040 Cone6ag1563 Cone9ag1483 . . . . . Cme03g01516 . . Bda11g00761 . . . . . . . . Cma12g00153 Cma05g00496 Car05g00443 . Cpe11g00434 . . . . . . . . . . . . . . . Lsi08g00959 . Chy03g01025 .
Vvi18g398 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g399 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 4214306 4215934 - Bda016462.1 Bda03g00493 493
3 4217288 4219737 + Bda016463.2 Bda03g00494 494
3 4230751 4233074 + Bda016465.1 Bda03g00496 496
11 7663267 7667578 - Bda005509.1 Bda11g00760 760
11 7684766 7686371 + Bda005510.1 Bda11g00761 761
4 18475841 18477110 + XM_039030159.1 Bhi04g00750 750
4 18580171 18583342 - XM_039028143.1 Bhi04g00751 751
9 70510620 70513902 + XM_039040699.1 Bhi09g02609 2609
9 70517827 70521936 - XM_039042078.1 Bhi09g02610 2610
9 70563534 70566910 + XM_039041077.1 Bhi09g02612 2612
12 25289387 25291693 - BLOR04721 Blo12g00702 702
12 25319742 25323248 - BLOR04722 Blo12g00703 703
12 25324460 25326119 + BLOR04723 Blo12g00704 704
1 83756986 83758584 - Bma003503.1 Bma01g02617 2617
1 83760184 83762916 - Bma030310 Bma01g02618 2618
1 83775818 83778174 + Bma003505.1 Bma01g02620 2620
2 739891 742162 - Bpe007951.1 Bpe02g00100 100
2 746217 754678 + Bpe007952.2 Bpe02g00101 101
2 756175 757785 + Bpe007953.2 Bpe02g00102 102
4 2880561 2882208 - Bpe015135.1 Bpe04g00449 449
4 2883665 2886073 + Bpe015136.1 Bpe04g00450 450
4 2896787 2899122 + Bpe015138.1 Bpe04g00451 451
8 21787725 21788738 + CaPI482276_08g015540.1 Cam08g1554 1554
8 21799278 21801905 - CaPI482276_08g015560.1 Cam08g1556 1556
11 28317367 28320595 + CaPI482276_11g015520.1 Cam11g1552 1552
11 28323083 28334595 - CaPI482276_11g015530.1 Cam11g1553 1553
11 28351347 28353732 + CaPI482276_11g015540.1 Cam11g1554 1554
5 2538868 2541211 - Carg08184-RA Car05g00443 443
9 3242585 3246122 + Carg03056-RA Car09g00573 573
9 3248619 3251831 - Carg03057-RA Car09g00574 574
9 3262512 3265143 + Carg03059-RA Car09g00576 576
12 803258 804283 + Carg20546-RA Car12g00139 139
12 808341 810110 - Carg20543-RA Car12g00142 142
8 24359996 24361015 + CcPI632755_08g012540.1 Cco08g1254 1254
8 24374198 24376818 - CcPI632755_08g012560.1 Cco08g1256 1256
11 28685237 28688465 + CcPI632755_11g015800.1 Cco11g1580 1580
11 28690613 28702121 - CcPI632755_11g015810.1 Cco11g1581 1581
11 28719239 28721626 + CcPI632755_11g015820.1 Cco11g1582 1582
8 23211236 23212249 + CePI673135_08g011270.1 Cec08g1127 1127
8 23222974 23225688 - CePI673135_08g011290.1 Cec08g1129 1129
11 30142820 30146046 + CePI673135_11g015840.1 Cec11g1584 1584
11 30148099 30159651 - CePI673135_11g015850.1 Cec11g1585 1585
11 30176679 30179101 + CePI673135_11g015860.1 Cec11g1586 1586
3 13817662 13818702 + Chy3G060030.1 Chy03g01023 1023
3 13825637 13828042 - Chy3G060050.1 Chy03g01025 1025
7 6906266 6908854 - Chy7G135350.1 Chy07g00705 705
8 22562441 22563454 + ClG42_08g0125600.10 Clacu08g1256 1256
8 22574069 22576728 - ClG42_08g0125800.10 Clacu08g1258 1258
11 28345080 28348309 + ClG42_11g0171000.10 Clacu11g1710 1710
11 28350242 28361570 - ClG42_11g0171100.10 Clacu11g1711 1711
11 28378095 28380481 + ClG42_11g0171200.10 Clacu11g1712 1712
8 23797282 23798295 + ClCG08G011030.1 Cla08g01100 1100
8 23808613 23811868 - ClCG08G011050.2 Cla08g01103 1103
11 28608753 28611982 + ClCG11G015300.1 Cla11g01496 1496
11 28613501 28626093 - ClCG11G015330.2 Cla11g01497 1497
11 28645230 28647840 + ClCG11G015350.1 Cla11g01498 1498
1 10016227 10019346 - CmaCh01G014210.1 Cma01g01421 1421
1 10028846 10034538 + CmaCh01G014240.1 Cma01g01424 1424
5 2350430 2353653 - CmaCh05G004960.1 Cma05g00496 496
9 3058412 3061992 + CmaCh09G006460.1 Cma09g00646 646
9 3064477 3070259 - CmaCh09G006470.1 Cma09g00647 647
9 3078336 3081202 + CmaCh09G006480.1 Cma09g00648 648
12 527480 528622 - CmaCh12G001280.1 Cma12g00128 128
12 661816 662841 + CmaCh12G001510.1 Cma12g00151 151
12 665254 668009 - CmaCh12G001530.1 Cma12g00153 153
3 24385857 24386903 + MELO3C011360.2.1 Cme03g01514 1514
3 24393358 24396403 - MELO3C011358.2.1 Cme03g01516 1516
7 9762216 9765609 - MELO3C010417.2.1 Cme07g00929 929
3 5018045 5021177 + PI0019773.1 Cmetu03g0542 542
3 5028361 5029422 - PI0024560.1 Cmetu03g1402 1402
4 32194993 32198669 - PI0020270.1 Cmetu04g1462 1462
7 19065325 19068931 + PI0008410.1 Cmetu07g1933 1933
1 11426484 11428966 - CmoCh01G014710.1 Cmo01g01471 1471
1 11440544 11444006 + CmoCh01G014730.1 Cmo01g01473 1473
5 2503542 2504519 + CmoCh05G005180.1 Cmo05g00518 518
5 2507075 2510204 - CmoCh05G005190.1 Cmo05g00519 519
9 3142182 3145815 + CmoCh09G006290.1 Cmo09g00629 629
9 3147727 3153645 - CmoCh09G006300.1 Cmo09g00630 630
9 3163422 3166048 + CmoCh09G006310.1 Cmo09g00631 631
12 713736 716634 - CmoCh12G001180.1 Cmo12g00118 118
11 27597330 27600559 + CmPI595203_11g015290.1 Cmu11g1529 1529
11 27602527 27613870 - CmPI595203_11g015300.1 Cmu11g1530 1530
11 27630407 27632829 + CmPI595203_11g015310.1 Cmu11g1531 1531
4 10977972 10980698 + Conep04aG0139300.1 Cone4ag1345 1345
4 10980815 10983052 - Conep04aG0139400.1 Cone4ag1346 1346
4 10995561 10997518 + Conep04aG0139500.1 Cone4ag1347 1347
4 10998439 10999519 - Conep04aG0139600.1 Cone4ag1348 1348
4 11001931 11002898 + Conep04aG0139700.1 Cone4ag1349 1349
6 12215389 12217245 - Conep06aG0162500.1 Cone6ag1563 1563
7 10842244 10843387 - Conep07aG0162900.1 Cone7ag1582 1582
7 10845210 10846274 + Conep07aG0163000.1 Cone7ag1583 1583
7 10847042 10849012 - Conep07aG0163100.1 Cone7ag1584 1584
7 10858371 10860615 + Conep07aG0163200.1 Cone7ag1585 1585
7 10861140 10862503 - Conep07aG0163300.1 Cone7ag1586 1586
9 10919767 10921654 - Conep09aG0152800.1 Cone9ag1483 1483
17 8887448 8888685 - Conep17aG0125800.1 Cone17ag1227 1227
2 3092834 3098142 - Cp4.1LG02g03480.1 Cpe02g00523 523
2 3109436 3112353 + Cp4.1LG02g03530.1 Cpe02g00525 525
6 3006284 3010026 + Cp4.1LG06g05010.1 Cpe06g00506 506
6 3011929 3017926 - Cp4.1LG06g05110.1 Cpe06g00507 507
6 3027491 3030540 + Cp4.1LG06g05020.1 Cpe06g00508 508
7 560503 579462 - Cp4.1LG07g01080.1 Cpe07g00108 108
7 719987 721012 + Cp4.1LG07g01260.1 Cpe07g00127 127
7 723891 726917 - Cp4.1LG07g01340.1 Cpe07g00129 129
11 2451581 2452567 + Cp4.1LG11g04240.1 Cpe11g00433 433
11 2455151 2458388 - Cp4.1LG11g04350.1 Cpe11g00434 434
8 23560489 23561508 + CrPI670011_08g010380.1 Cre08g1038 1038
8 23572385 23575025 - CrPI670011_08g010400.1 Cre08g1040 1040
11 31241908 31245138 + CrPI670011_11g019450.1 Cre11g1945 1945
11 31247430 31258913 - CrPI670011_11g019460.1 Cre11g1946 1946
11 31276765 31279153 + CrPI670011_11g019470.1 Cre11g1947 1947
3 39747135 39750871 + CsaV3_3G048720.1 Csa03g04566 4566
3 39751155 39755368 - CsaV3_3G048730.1 Csa03g04567 4567
4 18160546 18164105 - CsaV3_4G028740.1 Csa04g01848 1848
1 87036107 87039703 + Hsped.01g22380.1 Hepe01g2238 2238
1 87045277 87047986 - Hsped.01g22390.1 Hepe01g2239 2239
1 87075113 87078833 + Hsped.01g22410.1 Hepe01g2241 2241
10 5845072 5847667 + Hsped.10g05070.1 Hepe10g0507 507
10 5866636 5874456 - Hsped.10g05110.1 Hepe10g0511 511
13 34527402 34530235 + Maker00034011 Lcy13g1569 1569
13 34544543 34545553 - Maker00033805 Lcy13g1571 1571
4 30629074 30632798 + Lsi04G023450.1 Lsi04g02345 2345
4 30634184 30638051 - Lsi04G023460.1 Lsi04g02346 2346
4 30662000 30665918 + Lsi04G023480.1 Lsi04g02348 2348
8 17704811 17705953 - Lsi08G009300.1 Lsi08g00930 930
8 18075371 18076393 + Lsi08G009570.1 Lsi08g00957 957
8 18087814 18092186 - Lsi08G009590.1 Lsi08g00959 959
11 5291527 5295245 + MC11g0662 Mch11g0785 785
11 5296974 5300991 - MC11g0663 Mch11g0787 787
11 5317706 5321421 + MC11g0665 Mch11g0789 789
4 919519 921029 + Sed0013354.1 Sed04g0136 136
4 932449 935414 - Sed0017833.1 Sed04g0138 138
4 3926520 3931712 - Sed0004691.4 Sed04g0529 529
12 11546133 11550183 - Sed0007497.1 Sed12g1410 1410
12 11676245 11680960 + Sed0025375.1 Sed12g1412 1412
1 104396934 104400389 + Tan0012526.2 Tan01g3959 3959
1 104403135 104406947 - Tan0005528.1 Tan01g3960 3960
1 104437144 104440598 + Tan0000280.2 Tan01g3963 3963
2 92441296 92442575 + Tan0013540.1 Tan02g2380 2380
2 92455992 92458935 - Tan0008158.1 Tan02g2382 2382
18 4264863 4269301 + Vvi18g390 Vvi18g390 390
18 4269302 4275210 - Vvi18g391 Vvi18g391 391
18 4279191 4280442 + Vvi18g392 Vvi18g392 392
18 4283722 4287720 - Vvi18g393 Vvi18g393 393
18 4300742 4300844 - Vvi18g394 Vvi18g394 394
18 4306813 4310127 + Vvi18g395 Vvi18g395 395
18 4310331 4319333 - Vvi18g396 Vvi18g396 396
18 4325999 4329435 + Vvi18g397 Vvi18g397 397
18 4329434 4329641 + Vvi18g398 Vvi18g398 398
18 4332856 4337515 + Vvi18g399 Vvi18g399 399
       

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