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
Vvi1g71 . . Bda01g02133 . . . . . . . . . . Car18g01030 . Cpe09g00209 . . . . . . . . . . . . . . . . Cone19ag0916 . Cone9ag0555 . . . . . . . . . Bpe02g02322 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g72 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0921 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g73 . . . . . Bpe10g00893 . Bma15g00137 . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0546 Cone9ag0556 . . . . Blo06g00924 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g74 . Blo16g01096 . Bda11g01187 Bpe13g01385 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0922 . . . . . . . . . . Bda11g01187 . . . Bma06g00727 . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01743 Chy09g00681 Cme09g00681
Vvi1g75 Blo01g00446 Blo16g01097 Bda01g02135 Bda11g01188 Bpe13g01386 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0547 Cone9ag0558 . . . . . . . Bda11g01188 . . Bma01g00115 Bma06g00726 . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01744 Chy09g00682 Cme09g00680
Vvi1g76 . . . Bda11g01189 Bpe13g01387 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0548 . . . . . . . . Bda11g01189 . . . Bma06g00725 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g77 Blo01g00445 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0918 . . . . . . . . . . . Bpe02g02324 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g78 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g79 . . . . . Bpe10g00892 . Bma15g00138 . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0919 . . . . . . Blo06g00922 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g80 Blo01g00444 . Bda01g02136 . . Bpe10g00891 . Bma15g00139 Cmo04g01769 Cmo18g01141 . Cma18g01120 . Car18g01032 Sed06g1491 Cpe09g00208 Cpe01g01494 Bhi07g01518 Tan04g1031 Cmetu10g0795 Lac13g0357 Hepe10g1779 . . Cla05g02409 Cam05g2586 Cec05g2618 Cco05g2658 Clacu05g2588 Cmu05g2442 Cre05g2559 . . Cone6ag0549 Cone9ag0559 Lsi04g00380 Csa05g02495 Chy10g01043 Cme10g00377 . Blo11g00790 . . . Bpe02g02325 Bma01g00114 . . . . Cma04g01688 . Car04g01725 . . Cpe07g00079 . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57322336 57323723 + Bda004464.1 Bda01g02133 2133
1 57327029 57332135 + Bda004466.1 Bda01g02135 2135
1 57335386 57338569 - Bda004467.2 Bda01g02136 2136
11 12234910 12236587 + Bda007686.1 Bda11g01187 1187
11 12237670 12245319 + Bda007687.1 Bda11g01188 1188
11 12246696 12249236 + Bda007688.1 Bda11g01189 1189
7 43804930 43812016 - XM_039035595.1 Bhi07g01518 1518
1 4914628 4917314 + BLOR00444 Blo01g00444 444
1 4917669 4920050 - BLOR00445 Blo01g00445 445
1 4921222 4927156 - BLOR00446 Blo01g00446 446
6 32470169 32472199 + BLOR17505 Blo06g00922 922
6 32476791 32478715 - BLOR17507 Blo06g00924 924
11 11962012 11966365 + BLOR03666 Blo11g00790 790
16 39450500 39452420 + BLOR21883 Blo16g01096 1096
16 39453575 39469392 + BLOR21884 Blo16g01097 1097
1 1154183 1157253 + Bma000278.1 Bma01g00114 114
1 1160504 1166108 - Bma000279.1 Bma01g00115 115
6 38214106 38216632 - Bma023710.3 Bma06g00725 725
6 38218978 38224343 - Bma023711.1 Bma06g00726 726
6 38225131 38226805 - Bma023712.1 Bma06g00727 727
15 1466216 1467893 + Bma013116.1 Bma15g00137 137
15 1469833 1471626 - Bma013117.3 Bma15g00138 138
15 1473680 1476873 - Bma013118.1 Bma15g00139 139
2 23855309 23856662 + Bpe010137.1 Bpe02g02322 2322
2 23865092 23867533 + Bpe010139.1 Bpe02g02324 2324
2 23867906 23871061 - Bpe010140.1 Bpe02g02325 2325
10 14642524 14645701 + Bpe003195.1 Bpe10g00891 891
10 14647711 14649831 + Bpe003196.1 Bpe10g00892 892
10 14653522 14655474 - Bpe003197.1 Bpe10g00893 893
13 19076161 19077781 + Bpe011046.2 Bpe13g01385 1385
13 19078643 19084021 + Bpe011047.1 Bpe13g01386 1386
13 19085504 19087942 + Bpe011048.1 Bpe13g01387 1387
5 33516264 33522937 - CaPI482276_05g025860.1 Cam05g2586 2586
4 9893722 9899628 + Carg14380-RA Car04g01725 1725
18 10653187 10657731 + Carg17299-RA Car18g01030 1030
18 10660439 10666186 - Carg17298-RA Car18g01032 1032
5 34630976 34637633 - CcPI632755_05g026580.1 Cco05g2658 2658
5 36959952 36963557 - CePI673135_05g026180.1 Cec05g2618 2618
9 8911301 8912263 + Chy9G163970.1 Chy09g00681 681
9 8921823 8942704 + Chy9G163980.1 Chy09g00682 682
10 15680747 15684321 + Chy10G182370.1 Chy10g01043 1043
5 33723685 33730393 - ClG42_05g0258800.10 Clacu05g2588 2588
5 35597924 35601962 - ClCG05G023880.2 Cla05g02409 2409
4 8494575 8500550 + CmaCh04G016880.1 Cma04g01688 1688
18 9092224 9098243 - CmaCh18G011200.1 Cma18g01120 1120
9 7607178 7625643 - MELO3C002919.2.1 Cme09g00680 680
9 7633397 7634727 - MELO3C002920.2.1 Cme09g00681 681
10 2411609 2418546 - MELO3C012134.2.1 Cme10g00377 377
10 19615078 19618682 + PI0010840.1 Cmetu10g0795 795
4 8929176 8935244 + CmoCh04G017690.1 Cmo04g01769 1769
18 11672334 11678273 - CmoCh18G011410.1 Cmo18g01141 1141
5 33461479 33467677 - CmPI595203_05g024420.1 Cmu05g2442 2442
6 2690099 2691828 + Conep06aG0055900.1 Cone6ag0546 546
6 2693370 2698410 + Conep06aG0056000.1 Cone6ag0547 547
6 2698891 2702977 + Conep06aG0056100.1 Cone6ag0548 548
6 2703891 2708625 - Conep06aG0056200.1 Cone6ag0549 549
9 2635339 2636923 + Conep09aG0056500.1 Cone9ag0555 555
9 2637863 2639913 + Conep09aG0056600.1 Cone9ag0556 556
9 2642495 2647971 + Conep09aG0056800.1 Cone9ag0558 558
9 2650303 2654771 - Conep09aG0056900.1 Cone9ag0559 559
13 8043267 8043722 - Conep13aG0094900.1 Cone13ag0921 921
13 8044287 8045717 + Conep13aG0095000.1 Cone13ag0922 922
19 7094997 7096794 + Conep19aG0094200.1 Cone19ag0916 916
19 7103230 7105587 + Conep19aG0094500.1 Cone19ag0918 918
19 7105597 7107818 - Conep19aG0094600.1 Cone19ag0919 919
1 8920530 8925207 + Cp4.1LG01g12320.1 Cpe01g01494 1494
7 383453 387888 + Cp4.1LG07g00790.1 Cpe07g00079 79
9 1207425 1213442 + Cp4.1LG09g02040.1 Cpe09g00208 208
9 1215730 1219810 - Cp4.1LG09g02160.1 Cpe09g00209 209
5 36815124 36821818 - CrPI670011_05g025590.1 Cre05g2559 2559
5 20718514 20720070 + CsaV3_5G025620.1 Csa05g01743 1743
5 20726416 20740934 + CsaV3_5G025630.1 Csa05g01744 1744
5 26624508 26632004 + CsaV3_5G033140.1 Csa05g02495 2495
10 54560578 54567789 + Hsped.10g17790.1 Hepe10g1779 1779
13 2557093 2560713 + Lag0040153.1 Lac13g0357 357
4 3734945 3741771 - Lsi04G003800.1 Lsi04g00380 380
6 39603900 39610634 - Sed0011907.1 Sed06g1491 1491
4 9145524 9152553 - Tan0004035.1 Tan04g1031 1031
1 726649 729085 + Vvi1g71 Vvi1g71 71
1 729266 731550 - Vvi1g72 Vvi1g72 72
1 731576 733548 + Vvi1g73 Vvi1g73 73
1 736945 738532 + Vvi1g74 Vvi1g74 74
1 741221 751123 + Vvi1g75 Vvi1g75 75
1 751778 759740 + Vvi1g76 Vvi1g76 76
1 760230 762137 + Vvi1g77 Vvi1g77 77
1 762705 763140 + Vvi1g78 Vvi1g78 78
1 763144 767420 - Vvi1g79 Vvi1g79 79
1 770019 779392 - Vvi1g80 Vvi1g80 80
       

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