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
Vvi19g84 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g85 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g86 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g87 . . Bda07g00348 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g88 . . . Bda09g00549 . . . . . . . . . Car09g00594 Sed04g2474 Cpe06g00523 . Bhi09g03537 Tan01g4293 Cmetu07g0160 . Hepe01g1455 Mch11g0994 . Cla11g01695 Cam11g1762 Cec11g1782 Cco11g1786 Clacu11g1921 Cmu11g1732 Cre11g2140 . Cone9ag0234 . . Lsi04g01993 Csa04g02266 Chy07g00008 Cme07g00516 . . . . . . . . . . Cmo09g00653 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g89 Blo03g00704 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0202 Cone9ag0233 . . . . . . . . . . Bpe11g00441 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g90 . . . . . Bpe08g00987 . . . . Cma01g01250 . . . . . . . . . . . . . . . . . . . . Cone6ag0201 Cone9ag0232 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g91 Blo03g00703 . . Bda09g00548 Bpe09g00264 Bpe08g00988 . Bma13g00925 Cmo16g00465 . . . Car01g01074 . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo10g00727 . Bda12g00815 Bpe11g00442 . . Bma14g00272 . Cmo01g01308 . Cma04g00665 Cma16g00432 . . Cpe14g00364 Cpe01g00600 . . . . . . . . . . . . . . . Csa04g00814 . .
Vvi19g92 . . . Bda09g00547 . Bpe08g00989 . . . Cmo04g00713 . . . . . . Cpe02g00663 . . . . . . . . . . . . . . Cone6ag0200 Cone9ag0231 . . . . . . . . . . . . . . . . . Cma04g00666 . . . . Cpe01g00601 . . . . . . . . . . . . . . . Csa04g00813 . .
Vvi19g93 . . . . . . . . Cmo16g00466 Cmo04g00714 . . . . Sed04g2463 . . Bhi09g03527 Tan01g4304 Cmetu07g0033 . Hepe01g1449 Mch11g1000 . . . . . . . . . Cone9ag0230 . . Lsi04g02001 . . Cme07g00526 . Blo10g00728 . . . . . . . . . Cma04g00668 Cma16g00433 . Car16g00396 Cpe14g00365 Cpe01g00602 . . . . . . . . . . . . . . . . Chy07g00974 Cme07g01348
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 4511629 4518604 - Bda025436.1 Bda07g00348 348
9 7172541 7175893 + Bda031154.1 Bda09g00547 547
9 7177011 7179666 + Bda031155.1 Bda09g00548 548
9 7194033 7196129 + Bda031157.1 Bda09g00549 549
12 37552933 37554830 - Bda009326.1 Bda12g00815 815
9 88810237 88814243 + XM_039041253.1 Bhi09g03527 3527
9 89078602 89081676 + XM_039042356.1 Bhi09g03537 3537
3 29796179 29798551 + BLOR11884 Blo03g00703 703
3 29825808 29833108 - BLOR11885 Blo03g00704 704
10 22926813 22928903 - BLOR02517 Blo10g00727 727
10 22934990 22936930 + BLOR02518 Blo10g00728 728
13 39686888 39688909 - Bma010003.1 Bma13g00925 925
14 3241613 3243966 + Bma030648 Bma14g00272 272
8 12237667 12243120 + Bpe023111.1 Bpe08g00987 987
8 12243648 12246232 - Bpe023112.1 Bpe08g00988 988
8 12247243 12250573 - Bpe023113.1 Bpe08g00989 989
9 1940592 1942511 + Bpe023935.1 Bpe09g00264 264
11 3338832 3345922 + Bpe024756 Bpe11g00441 441
11 3348547 3350841 - Bpe003813.1 Bpe11g00442 442
11 30177974 30180082 - CaPI482276_11g017620.1 Cam11g1762 1762
1 10046518 10049859 - Carg14738-RA Car01g01074 1074
9 3356329 3359012 + Carg03077-RA Car09g00594 594
16 2431033 2433433 + Carg11363-RA Car16g00396 396
11 30584438 30586545 - CcPI632755_11g017860.1 Cco11g1786 1786
11 32032120 32041203 - CePI673135_11g017820.1 Cec11g1782 1782
7 102994 105041 - Chy7G128380.1 Chy07g00008 8
7 14374145 14374647 + Chy7G138040.1 Chy07g00974 974
11 30216700 30218808 - ClG42_11g0192100.10 Clacu11g1921 1921
11 30555338 30557905 - ClCG11G017270.1 Cla11g01695 1695
1 9004048 9008809 + CmaCh01G012500.1 Cma01g01250 1250
4 3393153 3396749 - CmaCh04G006650.1 Cma04g00665 665
4 3396771 3403990 - CmaCh04G006660.1 Cma04g00666 666
4 3404282 3407463 + CmaCh04G006680.1 Cma04g00668 668
16 2151472 2157962 - CmaCh16G004320.1 Cma16g00432 432
16 2159109 2162650 + CmaCh16G004330.1 Cma16g00433 433
7 4340081 4342521 - MELO3C025659.2.1 Cme07g00516 516
7 4410642 4414056 - MELO3C025649.2.1 Cme07g00526 526
7 19029462 19031423 + MELO3C016113.2.1 Cme07g01348 1348
7 21486798 21490418 - PI0024500.1 Cmetu07g0033 33
7 21441110 21444635 - PI0002125.1 Cmetu07g0160 160
1 10372501 10377542 - CmoCh01G013080.1 Cmo01g01308 1308
4 3539679 3546547 - CmoCh04G007130.1 Cmo04g00713 713
4 3547566 3551237 + CmoCh04G007140.1 Cmo04g00714 714
9 3256928 3259574 + CmoCh09G006530.1 Cmo09g00653 653
16 2228534 2232356 - CmoCh16G004650.1 Cmo16g00465 465
16 2233835 2236999 + CmoCh16G004660.1 Cmo16g00466 466
11 29469762 29471870 - CmPI595203_11g017320.1 Cmu11g1732 1732
6 950710 952951 + Conep06aG0020200.1 Cone6ag0200 200
6 953264 956217 - Conep06aG0020300.1 Cone6ag0201 201
6 956534 960409 - Conep06aG0020400.1 Cone6ag0202 202
9 973824 974589 - Conep09aG0023300.1 Cone9ag0230 230
9 975305 977805 + Conep09aG0023400.1 Cone9ag0231 231
9 980194 983087 - Conep09aG0023500.1 Cone9ag0232 232
9 983508 987200 - Conep09aG0023600.1 Cone9ag0233 233
9 987510 989392 + Conep09aG0023700.1 Cone9ag0234 234
1 3462923 3467517 - Cp4.1LG01g00630.1 Cpe01g00600 600
1 3468372 3473606 - Cp4.1LG01g00640.1 Cpe01g00601 601
1 3474319 3477993 + Cp4.1LG01g00720.1 Cpe01g00602 602
2 4173749 4177904 + Cp4.1LG02g02130.1 Cpe02g00663 663
6 3125310 3128009 + Cp4.1LG06g05210.1 Cpe06g00523 523
14 2215426 2221810 - Cp4.1LG14g03530.1 Cpe14g00364 364
14 2223180 2227267 + Cp4.1LG14g03600.1 Cpe14g00365 365
11 33113301 33122734 - CrPI670011_11g021400.1 Cre11g2140 2140
4 5698723 5703777 + CsaV3_4G008130.1 Csa04g00813 813
4 5708941 5712977 + CsaV3_4G008140.1 Csa04g00814 814
4 23295080 23297158 - CsaV3_4G032920.1 Csa04g02266 2266
1 79707287 79711647 + Hsped.01g14490.1 Hepe01g1449 1449
1 79779859 79782119 + Hsped.01g14550.1 Hepe01g1455 1455
4 27032680 27035452 - Lsi04G019930.1 Lsi04g01993 1993
4 27136086 27145389 - Lsi04G020010.1 Lsi04g02001 2001
11 6907365 6910456 - MC11g0813 Mch11g0994 994
11 6944388 6947452 - MC11g0818 Mch11g1000 1000
4 37799556 37803070 + Sed0025313.1 Sed04g2463 2463
4 37880069 37883086 + Sed0018751.1 Sed04g2474 2474
1 107803733 107806676 - Tan0000091.1 Tan01g4293 4293
1 107937892 107940856 - Tan0021544.1 Tan01g4304 4304
19 955251 960645 - Vvi19g84 Vvi19g84 84
19 968092 977755 + Vvi19g85 Vvi19g85 85
19 979170 997624 + Vvi19g86 Vvi19g86 86
19 1012163 1014463 + Vvi19g87 Vvi19g87 87
19 1015624 1018257 - Vvi19g88 Vvi19g88 88
19 1020157 1034257 + Vvi19g89 Vvi19g89 89
19 1034869 1045969 + Vvi19g90 Vvi19g90 90
19 1048081 1053505 - Vvi19g91 Vvi19g91 91
19 1054216 1059738 - Vvi19g92 Vvi19g92 92
19 1061569 1067005 + Vvi19g93 Vvi19g93 93
       

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