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
Vvi19g94 . . . . Bpe09g00262 . . Bma13g00926 . Cmo04g00715 . . . Car09g00591 . Cpe06g00521 . . . . . . . . Cla11g01701 Cam11g1767 Cec11g1787 Cco11g1792 Clacu11g1926 Cmu11g1737 Cre11g2145 Cone6ag0199 Cone9ag0229 . . . Csa04g02272 Chy07g00013 . . Blo10g00729 . Bda12g00816 . . . . . . Cmo09g00649 Cma04g00669 . . . . Cpe01g00603 . . . . . . . . . . . . . . . Csa04g00812 . .
Vvi19g95 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g96 . . Bda07g00331 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g97 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g98 Blo03g00702 Blo03g01562 . Bda09g00544 . Bpe08g00992 . . Cmo16g00469 Cmo04g00717 . . . Car09g00748 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe11g00443 . . Bma14g00271 . . Cmo09g00827 Cma04g00671 Cma16g00434 . . Cpe14g00367 Cpe01g00605 . . . . . . . . . . . . . . . Csa04g00810 . .
Vvi19g99 . . . . . . . Bma13g00927 Cmo16g00470 Cmo04g00718 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo10g00730 . . . . . . . . . Cma04g00672 Cma16g00435 . . Cpe14g00368 Cpe01g00606 . . . . . . . . . . . . . . . . . .
Vvi19g100 . . . . . . Bma10g00455 . Cmo16g00472 Cmo04g00719 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma04g00673 Cma16g00437 . . Cpe14g00369 Cpe01g00607 . . . . . . . . . . . . . . . Csa04g00808 . .
Vvi19g101 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g102 . . . . . . . . . Cmo04g00615 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo10g00731 . Bda12g00817 . . . . . . . Cma04g00576 . . . . Cpe01g00520 . . . . . . . . . . . . . . . Csa04g00807 . .
Vvi19g103 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 4407928 4419546 + Bda025417.1 Bda07g00331 331
9 7137656 7140493 + Bda031150.1 Bda09g00544 544
12 37562884 37564266 + Bda009327.1 Bda12g00816 816
12 37582162 37592752 - Bda009328.2 Bda12g00817 817
3 29793301 29795547 + BLOR11883 Blo03g00702 702
3 43420393 43421869 + BLOR12743 Blo03g01562 1562
10 22964555 22965946 + BLOR02519 Blo10g00729 729
10 22973311 22980921 + BLOR02520 Blo10g00730 730
10 22984667 22986551 - BLOR02521 Blo10g00731 731
10 5125538 5126501 + Bma004125.1 Bma10g00455 455
13 39705768 39706445 + Bma010004.1 Bma13g00926 926
13 39739283 39751540 + Bma010005.1 Bma13g00927 927
14 3237476 3240080 + Bma010685.1 Bma14g00271 271
8 12262169 12264929 - Bpe023116.1 Bpe08g00992 992
9 1922042 1923433 - Bpe023933.1 Bpe09g00262 262
11 3352215 3354796 - Bpe003814.1 Bpe11g00443 443
11 30219110 30220465 - CaPI482276_11g017670.1 Cam11g1767 1767
9 3345356 3348921 + Carg03074-RA Car09g00591 591
9 4445775 4447517 + Carg17070-RA Car09g00748 748
11 30629928 30631283 - CcPI632755_11g017920.1 Cco11g1792 1792
11 32077971 32080450 - CePI673135_11g017870.1 Cec11g1787 1787
7 140402 141757 - Chy7G128430.1 Chy07g00013 13
11 30254788 30258980 - ClG42_11g0192600.10 Clacu11g1926 1926
11 30600012 30602038 - ClCG11G017350.2 Cla11g01701 1701
4 2930865 2935007 + CmaCh04G005760.1 Cma04g00576 576
4 3411419 3412825 + CmaCh04G006690.1 Cma04g00669 669
4 3417776 3420554 + CmaCh04G006710.1 Cma04g00671 671
4 3421256 3429364 + CmaCh04G006720.1 Cma04g00672 672
4 3429067 3431030 - CmaCh04G006730.1 Cma04g00673 673
16 2165009 2170144 + CmaCh16G004340.1 Cma16g00434 434
16 2170707 2174407 + CmaCh16G004350.1 Cma16g00435 435
16 2177971 2180891 - CmaCh16G004370.1 Cma16g00437 437
4 3063996 3068077 + CmoCh04G006150.1 Cmo04g00615 615
4 3555493 3556899 + CmoCh04G007150.1 Cmo04g00715 715
4 3562533 3565212 + CmoCh04G007170.1 Cmo04g00717 717
4 3565802 3574637 + CmoCh04G007180.1 Cmo04g00718 718
4 3574363 3576590 - CmoCh04G007190.1 Cmo04g00719 719
9 3243929 3245365 + CmoCh09G006490.1 Cmo09g00649 649
9 4259257 4261405 + CmoCh09G008270.1 Cmo09g00827 827
16 2239375 2241916 + CmoCh16G004690.1 Cmo16g00469 469
16 2241977 2249330 + CmoCh16G004700.1 Cmo16g00470 470
16 2259431 2261109 - CmoCh16G004720.1 Cmo16g00472 472
11 29507913 29512105 - CmPI595203_11g017370.1 Cmu11g1737 1737
6 943483 947004 - Conep06aG0020100.1 Cone6ag0199 199
9 969320 972654 - Conep09aG0023200.1 Cone9ag0229 229
1 2990947 2995093 + Cp4.1LG01g01590.1 Cpe01g00520 520
1 3481908 3483314 + Cp4.1LG01g00740.1 Cpe01g00603 603
1 3489086 3492088 + Cp4.1LG01g00710.1 Cpe01g00605 605
1 3492717 3502719 + Cp4.1LG01g00760.1 Cpe01g00606 606
1 3500507 3502864 - Cp4.1LG01g00460.1 Cpe01g00607 607
6 3115219 3116145 + Cp4.1LG06g05270.1 Cpe06g00521 521
14 2228867 2231614 + Cp4.1LG14g03580.1 Cpe14g00367 367
14 2232735 2238866 + Cp4.1LG14g03610.1 Cpe14g00368 368
14 2239101 2258877 - Cp4.1LG14g03540.1 Cpe14g00369 369
11 33162151 33163506 - CrPI670011_11g021450.1 Cre11g2145 2145
4 5651985 5656344 + CsaV3_4G008070.1 Csa04g00807 807
4 5663802 5665279 + CsaV3_4G008080.1 Csa04g00808 808
4 5671957 5674648 - CsaV3_4G008100.1 Csa04g00810 810
4 5683361 5686943 - CsaV3_4G008120.1 Csa04g00812 812
4 23333240 23338069 - CsaV3_4G032980.1 Csa04g02272 2272
19 1082308 1086930 + Vvi19g94 Vvi19g94 94
19 1119848 1123813 + Vvi19g95 Vvi19g95 95
19 1126916 1130047 - Vvi19g96 Vvi19g96 96
19 1247634 1250651 - Vvi19g97 Vvi19g97 97
19 1293570 1301426 + Vvi19g98 Vvi19g98 98
19 1302567 1319687 + Vvi19g99 Vvi19g99 99
19 1320869 1322474 - Vvi19g100 Vvi19g100 100
19 1322473 1323002 - Vvi19g101 Vvi19g101 101
19 1328455 1335388 - Vvi19g102 Vvi19g102 102
19 1337603 1338174 + Vvi19g103 Vvi19g103 103
       

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