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
Vvi4g532 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g533 . . . . . . . . . . . . . . Sed05g1725 . . Bhi04g00035 Tan02g2750 Cmetu01g0581 . Hepe10g0228 . Lcy13g1815 . . . . . . . . . . . . . . . Blo17g00008 . . . . . . Bma02g00013 . . . . . . . . . Bhi09g02973 . . . . Mch11g0521 . . . . . . . . . . . Cme07g00102
Vvi4g534 . . . Bda03g00085 . . . . . . . . . . Sed11g1156 . . Bhi04g00034 Tan02g2749 Cmetu03g1805 . . . Lcy13g1814 . . . . . . . . Cone7ag1676 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla08g01356 Cam08g1821 Cec08g1400 Cco08g1530 Clacu08g1516 . Cre08g1302 . . . .
Vvi4g535 . . Bda01g00757 . . . . . . . . . . . . . . Bhi04g00032 . . . . . Lcy13g1813 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi09g02972 . . . . . . . . . . . . . . . . Cme07g00099
Vvi4g536 . . . . . . . . . . Cma01g01481 . . . Sed11g1158 Cpe07g00309 . Bhi04g00031 Tan02g2746 Cmetu03g1252 . . . Lcy13g1812 . . . . . . . . . . . . . . . . . . Bda13g01248 . . . . Sed05g1724 Cmo01g01537 . . . . . . . Bhi09g02971 Tan01g3593 Cmetu07g0019 . . . . . . . . . . . . . . Cme07g00098
Vvi4g537 . . . . . . Bma04g00082 . . . Cma01g01482 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe04g00070 . . Sed13g1993 Cmo01g01538 . . . . . . . Bhi09g02969 Tan01g3596 Cmetu07g1020 . Hepe01g1987 Mch11g0524 . . . . . . . . . . . Cme07g00097
Vvi4g538 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed05g1722 . . . . . . . . Bhi09g02968 Tan01g3597 Cmetu07g0381 . Hepe01g1988 Mch11g0525 . . . . . . . . . . . Cme07g00096
Vvi4g539 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g540 . . Bda01g00755 . . . . . . . Cma01g01485 . . . Sed05g0848 . . Bhi04g00028 Tan02g2744 Cmetu03g1616 . Hepe10g0232 . . . . . . . . . . . . . . . . . . . . . . . . . Sed05g1721 Cmo01g01539 . . . . . . . Bhi09g02965 Tan01g3600 . . . . . . . . . . . . . . . Cme07g00094
Vvi4g541 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi09g02963 . . . Hepe01g1991 Mch11g0528 . . . . . . . . . . . Cme07g00092
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 34791738 34803087 - Bda002795.2 Bda01g00755 755
1 34821946 34824606 + Bda002798.1 Bda01g00757 757
3 847169 849777 - Bda016023.1 Bda03g00085 85
13 34925483 34928608 + Bda000056.1 Bda13g01248 1248
4 648909 654263 - XM_039028994.1 Bhi04g00028 28
4 679406 682451 - XM_039030692.1 Bhi04g00031 31
4 785664 789567 + XM_039028220.1 Bhi04g00032 32
4 790679 794324 - XM_039028071.1 Bhi04g00034 34
4 796701 797536 - XM_039029708.1 Bhi04g00035 35
9 77065371 77073085 - XM_039043745.1 Bhi09g02963 2963
9 77103515 77107708 - XM_039041941.1 Bhi09g02965 2965
9 77126647 77139689 - XM_039041880.1 Bhi09g02968 2968
9 77176606 77182087 + XM_039041808.1 Bhi09g02969 2969
9 77182523 77186888 - XM_039041809.1 Bhi09g02971 2971
9 77244854 77251033 + XM_039040726.1 Bhi09g02972 2972
9 77257090 77257847 - XM_039041396.1 Bhi09g02973 2973
17 57901 58155 + BLOR15829 Blo17g00008 8
2 246245 246514 + Bma014471.1 Bma02g00013 13
4 673102 675662 + Bma018532.1 Bma04g00082 82
4 553726 558025 + Bpe014793.1 Bpe04g00070 70
8 24294473 24304206 - CaPI482276_08g018210.1 Cam08g1821 1821
8 26951304 26961415 - CcPI632755_08g015300.1 Cco08g1530 1530
8 25806526 25817128 - CePI673135_08g014000.1 Cec08g1400 1400
8 25038173 25048058 - ClG42_08g0151600.10 Clacu08g1516 1516
8 26376314 26385505 - ClCG08G013590.2 Cla08g01356 1356
1 10426014 10429568 + CmaCh01G014810.1 Cma01g01481 1481
1 10430130 10434315 - CmaCh01G014820.1 Cma01g01482 1482
1 10450414 10455276 + CmaCh01G014850.1 Cma01g01485 1485
7 564535 572533 - MELO3C016990.2.1 Cme07g00092 92
7 577212 581588 - MELO3C016988.2.1 Cme07g00094 94
7 598604 606758 - MELO3C016987.2.1 Cme07g00096 96
7 607559 612930 + MELO3C016986.2.1 Cme07g00097 97
7 613818 617881 - MELO3C016985.2.1 Cme07g00098 98
7 629380 635205 + MELO3C016983.2.1 Cme07g00099 99
7 636879 637735 - MELO3C016981.2.1 Cme07g00102 102
1 6274950 6276501 - PI0006063.1 Cmetu01g0581 581
3 4477175 4480586 - PI0010496.1 Cmetu03g1252 1252
3 4461040 4466325 - PI0008037.2 Cmetu03g1616 1616
3 4493122 4497005 - PI0015107.3 Cmetu03g1805 1805
7 24160189 24164028 + PI0004607.1 Cmetu07g0019 19
7 24172702 24180798 + PI0001636.1 Cmetu07g0381 381
7 24165641 24171420 - PI0005771.1 Cmetu07g1020 1020
1 11859324 11863726 + CmoCh01G015370.1 Cmo01g01537 1537
1 11863539 11867684 - CmoCh01G015380.1 Cmo01g01538 1538
1 11883239 11888343 + CmoCh01G015390.1 Cmo01g01539 1539
7 11235356 11238128 + Conep07aG0172700.1 Cone7ag1676 1676
7 2008482 2011717 - Cp4.1LG07g03130.1 Cpe07g00309 309
8 26093240 26103027 - CrPI670011_08g013020.1 Cre08g1302 1302
1 84666817 84671892 - Hsped.01g19870.1 Hepe01g1987 1987
1 84672944 84682026 + Hsped.01g19880.1 Hepe01g1988 1988
1 84711618 84718613 + Hsped.01g19910.1 Hepe01g1991 1991
10 2421755 2423145 + Hsped.10g02280.1 Hepe10g0228 228
10 2468647 2473189 + Hsped.10g02320.1 Hepe10g0232 232
13 37073734 37076862 - Maker00034266 Lcy13g1812 1812
13 37095310 37099355 + Maker00033998 Lcy13g1813 1813
13 37101041 37105043 - Maker00034236 Lcy13g1814 1814
13 37112100 37112966 - Maker00034180 Lcy13g1815 1815
11 3348440 3348686 + MC11g0425 Mch11g0521 521
11 3358004 3363696 - MC11g0427 Mch11g0524 524
11 3365246 3373642 + MC11g0428 Mch11g0525 525
11 3396090 3402803 + MC11g0431 Mch11g0528 528
5 6729889 6734478 - Sed0006996.2 Sed05g0848 848
5 30987398 30992764 - Sed0024191.4 Sed05g1721 1721
5 31012231 31033038 - Sed0004204.1 Sed05g1722 1722
5 31035436 31039424 - Sed0005888.2 Sed05g1724 1724
5 31046231 31046934 - Sed0018228.1 Sed05g1725 1725
11 27493191 27497894 + Sed0007080.2 Sed11g1156 1156
11 27519907 27522901 + Sed0015470.1 Sed11g1158 1158
13 24757647 24763516 - Sed0014901.6 Sed13g1993 1993
1 100976852 100980950 + Tan0015474.1 Tan01g3593 3593
1 100981028 100986365 - Tan0008499.3 Tan01g3596 3596
1 100995679 101004400 + Tan0012341.1 Tan01g3597 3597
1 101022852 101028003 + Tan0011286.2 Tan01g3600 3600
2 95684812 95689714 - Tan0021244.1 Tan02g2744 2744
2 95721593 95724850 - Tan0017681.1 Tan02g2746 2746
2 95743952 95747904 - Tan0009918.2 Tan02g2749 2749
2 95754376 95755592 - Tan0003375.1 Tan02g2750 2750
4 5714445 5716985 + Vvi4g532 Vvi4g532 532
4 5719504 5720985 - Vvi4g533 Vvi4g533 533
4 5732352 5739585 + Vvi4g534 Vvi4g534 534
4 5740293 5744083 - Vvi4g535 Vvi4g535 535
4 5775820 5780538 + Vvi4g536 Vvi4g536 536
4 5783787 5809616 - Vvi4g537 Vvi4g537 537
4 5817196 5849576 + Vvi4g538 Vvi4g538 538
4 5852143 5852980 + Vvi4g539 Vvi4g539 539
4 5879264 5888462 + Vvi4g540 Vvi4g540 540
4 5890295 5930252 + Vvi4g541 Vvi4g541 541
       

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