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
Vvi1g41 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g42 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g43 . . . . . Bpe10g00898 . Bma15g00133 Cmo04g01786 Cmo18g01129 . Cma18g01107 . Car18g01021 . Cpe09g00220 Cpe01g01505 Bhi07g01495 Tan04g1007 . Lac13g0373 Hepe10g1793 . . Cla05g02393 . . Cco05g2641 Clacu05g2568 Cmu05g2425 Cre05g2542 Cone13ag0908 . Cone6ag0529 . Lsi04g00364 Csa05g02510 Chy10g01057 Cme10g00358 . . . . . . . . . . . Cma04g01700 . Car04g01737 . . . . . . . . . . . . . . . . . . . . .
Vvi1g44 . Blo16g01087 . Bda11g01178 Bpe13g01376 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01178 . . . Bma06g00737 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g45 . Blo16g01089 . Bda11g01180 Bpe13g01378 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone9ag0543 . . . . . . . Bda11g01180 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g46 Blo01g00452 Blo16g01090 . . . . . . Cmo04g01784 Cmo18g00599 . Cma18g01108 . Car18g01022 Sed06g1772 Cpe09g00219 Cpe01g01504 Bhi07g01497 Tan04g1010 Cmetu10g0153 Lac13g0372 Hepe10g1792 . . Cla05g02394 . . Cco05g2642 Clacu05g2571 Cmu05g2427 Cre05g2544 Cone13ag0909 Cone19ag0903 Cone6ag0530 Cone9ag0544 Lsi04g00365 . . Cme10g00360 . . . . . Bpe02g02316 Bma01g00121 Bma06g00735 . . . Cma04g01699 . Car04g01736 . . Cpe07g00085 . . . . . . . . . . . . . . . . . .
Vvi1g47 Blo01g00451 . Bda01g02129 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe02g02317 Bma01g00120 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g48 . . . . . . . . . . . . . . . Cpe09g00719 . . . . . . . . . . . . . . . . . . . . Csa05g02508 Chy10g01056 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g49 . . . . . . . . . Cmo18g01131 . Cma18g01109 . Car18g01023 . . . Bhi07g01498 Tan04g1012 Cmetu10g0215 Lac13g0371 Hepe10g1791 . . Cla05g02395 . . Cco05g2643 Clacu05g2572 Cmu05g2428 Cre05g2545 Cone13ag0910 . . . Lsi04g00366 . . Cme10g00361 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g50 . . . . . . Bma14g01664 . Cmo04g01783 Cmo18g01132 . Cma18g01110 . . Sed06g1771 Cpe09g00217 Cpe01g01503 Bhi07g01499 Tan04g1013 Cmetu10g0697 Lac13g0370 . . . Cla05g02396 . . Cco05g2644 Clacu05g2573 Cmu05g2429 Cre05g2546 . . . . Lsi04g00367 Csa05g02507 Chy10g01055 Cme10g00362 . Blo11g00793 . . . . . . . . . Cma04g01698 . Car04g01735 . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57290732 57294190 + Bda004460.1 Bda01g02129 2129
11 12170763 12173430 - Bda033139 Bda11g01178 1178
11 12185772 12189552 + Bda007678.1 Bda11g01180 1180
7 43509070 43513072 - XM_039035977.1 Bhi07g01495 1495
7 43560958 43563173 - XM_039036271.1 Bhi07g01497 1497
7 43568983 43573695 - XM_039035450.1 Bhi07g01498 1498
7 43589020 43590949 + XM_039037439.1 Bhi07g01499 1499
1 4964685 4968161 - BLOR00451 Blo01g00451 451
1 4968763 4979858 + BLOR00452 Blo01g00452 452
11 12066268 12067494 - BLOR03669 Blo11g00793 793
16 39395297 39398375 - BLOR21874 Blo16g01087 1087
16 39402415 39406561 + BLOR21876 Blo16g01089 1089
16 39407009 39418660 - BLOR21877 Blo16g01090 1090
1 1207096 1210563 - Bma000285.1 Bma01g00120 120
1 1212632 1213494 + Bma000286.1 Bma01g00121 121
6 38357061 38357327 + Bma023722.1 Bma06g00735 735
6 38367668 38371372 + Bma023724.1 Bma06g00737 737
14 35276334 35277280 - Bma012396.1 Bma14g01664 1664
15 1439352 1441877 - Bma013112.1 Bma15g00133 133
2 23819190 23820034 - Bpe010132.1 Bpe02g02316 2316
2 23822915 23826313 + Bpe010133.1 Bpe02g02317 2317
10 14670749 14673304 + Bpe003202.1 Bpe10g00898 898
13 18995789 18998651 - Bpe011036.1 Bpe13g01376 1376
13 19001666 19005411 + Bpe011038.1 Bpe13g01378 1378
4 9934707 9936686 - Carg14370-RA Car04g01735 1735
4 9939161 9940638 + Carg14369-RA Car04g01736 1736
4 9942890 9952886 + Carg14368-RA Car04g01737 1737
18 10605069 10611958 - Carg17309-RA Car18g01021 1021
18 10613031 10614458 - Carg17308-RA Car18g01022 1022
18 10615821 10620978 - Carg17307-RA Car18g01023 1023
5 34537830 34538240 - CcPI632755_05g026410.1 Cco05g2641 2641
5 34542774 34544023 - CcPI632755_05g026420.1 Cco05g2642 2642
5 34550158 34554051 - CcPI632755_05g026430.1 Cco05g2643 2643
5 34557964 34559603 + CcPI632755_05g026440.1 Cco05g2644 2644
10 15735866 15737607 - Chy10G182490.1 Chy10g01055 1055
10 15739628 15748395 + Chy10G182500.1 Chy10g01056 1056
10 15748401 15762701 + Chy10G182510.1 Chy10g01057 1057
5 33624418 33630078 - ClG42_05g0256800.10 Clacu05g2568 2568
5 33637268 33638521 - ClG42_05g0257100.10 Clacu05g2571 2571
5 33644545 33648441 - ClG42_05g0257200.10 Clacu05g2572 2572
5 33651368 33653002 + ClG42_05g0257300.10 Clacu05g2573 2573
5 35472487 35481333 - ClCG05G023720.1 Cla05g02393 2393
5 35488716 35490368 - ClCG05G023730.1 Cla05g02394 2394
5 35508534 35512784 - ClCG05G023740.2 Cla05g02395 2395
5 35515931 35517877 + ClCG05G023750.1 Cla05g02396 2396
4 8534942 8537282 - CmaCh04G016980.1 Cma04g01698 1698
4 8539338 8540832 + CmaCh04G016990.1 Cma04g01699 1699
4 8543525 8547403 + CmaCh04G017000.1 Cma04g01700 1700
18 9042666 9045883 - CmaCh18G011070.1 Cma18g01107 1107
18 9046835 9048242 - CmaCh18G011080.1 Cma18g01108 1108
18 9049595 9054703 - CmaCh18G011090.1 Cma18g01109 1109
18 9056594 9059098 + CmaCh18G011100.1 Cma18g01110 1110
10 2312043 2316251 - MELO3C012152.2.1 Cme10g00358 358
10 2322812 2324796 - MELO3C012149.2.1 Cme10g00360 360
10 2327877 2332158 - MELO3C012148.2.1 Cme10g00361 361
10 2333422 2335492 + MELO3C012147.2.1 Cme10g00362 362
10 19681846 19683472 + PI0013920.1 Cmetu10g0153 153
10 19673824 19677899 + PI0006121.1 Cmetu10g0215 215
10 19670074 19672206 - PI0024864.2 Cmetu10g0697 697
4 8970539 8972681 - CmoCh04G017830.1 Cmo04g01783 1783
4 8974978 8976550 + CmoCh04G017840.1 Cmo04g01784 1784
4 8978820 8982136 + CmoCh04G017860.1 Cmo04g01786 1786
18 5597727 5601988 - CmoCh18G005990.1 Cmo18g00599 599
18 11619723 11622972 - CmoCh18G011290.1 Cmo18g01129 1129
18 11626770 11631661 - CmoCh18G011310.1 Cmo18g01131 1131
18 11633536 11636908 + CmoCh18G011320.1 Cmo18g01132 1132
5 33362218 33367914 - CmPI595203_05g024250.1 Cmu05g2425 2425
5 33375109 33376362 - CmPI595203_05g024270.1 Cmu05g2427 2427
5 33382384 33386280 - CmPI595203_05g024280.1 Cmu05g2428 2428
5 33389187 33390822 + CmPI595203_05g024290.1 Cmu05g2429 2429
6 2630272 2632948 - Conep06aG0054100.1 Cone6ag0529 529
6 2634454 2636050 - Conep06aG0054200.1 Cone6ag0530 530
9 2595068 2598882 + Conep09aG0055300.1 Cone9ag0543 543
9 2599542 2601302 - Conep09aG0055400.1 Cone9ag0544 544
13 7993134 7995923 - Conep13aG0093600.1 Cone13ag0908 908
13 7997567 7999239 - Conep13aG0093700.1 Cone13ag0909 909
13 8001985 8005282 - Conep13aG0093800.1 Cone13ag0910 910
19 7037382 7039167 - Conep19aG0092900.1 Cone19ag0903 903
1 8968241 8970533 - Cp4.1LG01g12050.1 Cpe01g01503 1503
1 8973367 8976814 + Cp4.1LG01g12090.1 Cpe01g01504 1504
1 8978301 8990108 + Cp4.1LG01g12130.1 Cpe01g01505 1505
7 413020 415662 - Cp4.1LG07g00850.1 Cpe07g00085 85
9 1247400 1249976 - Cp4.1LG09g02190.1 Cpe09g00217 217
9 1257760 1259260 + Cp4.1LG09g02050.1 Cpe09g00219 219
9 1260406 1270441 + Cp4.1LG09g02110.1 Cpe09g00220 220
9 6540961 6543296 + Cp4.1LG09g07140.1 Cpe09g00719 719
5 36712905 36720323 - CrPI670011_05g025420.1 Cre05g2542 2542
5 36726620 36727870 - CrPI670011_05g025440.1 Cre05g2544 2544
5 36733977 36737881 - CrPI670011_05g025450.1 Cre05g2545 2545
5 36738097 36743551 + CrPI670011_05g025460.1 Cre05g2546 2546
5 26681191 26684162 - CsaV3_5G033260.1 Csa05g02507 2507
5 26685270 26689585 + CsaV3_5G033270.1 Csa05g02508 2508
5 26696560 26699585 + CsaV3_5G033290.1 Csa05g02510 2510
10 54663444 54667946 + Hsped.10g17910.1 Hepe10g1791 1791
10 54674031 54675735 + Hsped.10g17920.1 Hepe10g1792 1792
10 54685238 54693152 + Hsped.10g17930.1 Hepe10g1793 1793
13 2624609 2626341 - Lag0040166.1 Lac13g0370 370
13 2633022 2636872 + Lag0040167.1 Lac13g0371 371
13 2641911 2643167 + Lag0040168.1 Lac13g0372 372
13 2647247 2650053 + Lag0040169.1 Lac13g0373 373
4 3636285 3640670 - Lsi04G003640.1 Lsi04g00364 364
4 3646987 3648226 - Lsi04G003650.1 Lsi04g00365 365
4 3660619 3665444 - Lsi04G003660.1 Lsi04g00366 366
4 3669949 3671949 + Lsi04G003670.1 Lsi04g00367 367
6 42436198 42438663 - Sed0026741.1 Sed06g1771 1771
6 42444665 42446381 + Sed0007510.1 Sed06g1772 1772
4 8987347 8991309 - Tan0004084.5 Tan04g1007 1007
4 9001238 9003018 - Tan0000371.2 Tan04g1010 1010
4 9011679 9015295 - Tan0013180.2 Tan04g1012 1012
4 9029266 9031180 + Tan0004772.1 Tan04g1013 1013
1 496478 498561 + Vvi1g41 Vvi1g41 41
1 498866 500438 - Vvi1g42 Vvi1g42 42
1 501309 504875 - Vvi1g43 Vvi1g43 43
1 506834 513217 - Vvi1g44 Vvi1g44 44
1 515729 520849 + Vvi1g45 Vvi1g45 45
1 523826 526024 - Vvi1g46 Vvi1g46 46
1 529829 543820 + Vvi1g47 Vvi1g47 47
1 544466 549815 - Vvi1g48 Vvi1g48 48
1 550210 556153 - Vvi1g49 Vvi1g49 49
1 558160 562819 + Vvi1g50 Vvi1g50 50
       

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