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
Vvi5g1119 . . . . . . . . . . . Cma14g01497 . Car14g01329 . . Cpe03g01257 Bhi01g02631 Tan10g1238 . . . . Lcy11g1233 . . . . . . . . . . Cone11ag0627 . . . Cme07g01856 . Blo07g00101 Bda11g00470 . . Bpe13g00728 . . . . Cmo14g01532 . . . . . . . . . . . . . Cla07g01581 Cam07g1678 Cec07g1773 Cco07g1736 Clacu07g1662 Cmu07g1628 Cre07g2002 . . . .
Vvi5g1120 . . . . . . . . Cmo08g00091 . Cma06g01633 . Car06g01388 . . Cpe08g00095 . . . . . . . . . . . . . . . . Cone15ag0602 . . . . . . . . . . . . . . . Cmo06g01632 . . . Car08g00073 . . Cpe17g00997 . . . . . . . . . . . . . . . . . .
Vvi5g1121 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1122 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1123 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1124 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1125 . . . . . . . . . Cmo17g00564 . . . . . . . . . . . . . . Cla08g00416 Cam08g0855 Cec08g0431 Cco08g0541 Clacu08g0567 . Cre08g0391 . . . . . . . . . . . . . . . . . . . . Cma17g00580 . Car17g00538 Cpe12g00494 . . . . . . . . Cla07g01507 Cam07g1604 Cec07g1700 Cco07g1663 Clacu07g1594 Cmu07g1559 Cre07g1936 . . . .
Vvi5g1126 . . . . . . . . . Cmo17g00565 . . . . . . . . . . . . . . Cla08g00418 Cam08g0856 Cec08g0432 Cco08g0542 Clacu08g0568 . Cre08g0392 . . . . . . . . . . . . . . . . . . . . Cma17g00581 . Car17g00539 Cpe12g00495 . . . . . . . . . . . . . . . . . . .
Vvi5g1127 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1128 . . . Bda08g00071 Bpe04g00913 . . Bma05g01212 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 644632 645771 - Bda024468.1 Bda08g00071 71
11 4957493 4959248 + Bda005209.1 Bda11g00470 470
1 65342365 65351368 - XM_039049146.1 Bhi01g02631 2631
7 1480603 1486539 + BLOR18033 Blo07g00101 101
5 51528385 51529677 + Bma022403.1 Bma05g01212 1212
4 6104923 6106266 + Bpe015577.1 Bpe04g00913 913
13 13841875 13849600 - Bpe010425.1 Bpe13g00728 728
7 30709342 30713643 + CaPI482276_07g016040.1 Cam07g1604 1604
7 31398985 31407595 + CaPI482276_07g016780.1 Cam07g1678 1678
8 12009157 12014319 + CaPI482276_08g008550.1 Cam08g0855 855
8 12025363 12026357 + CaPI482276_08g008560.1 Cam08g0856 856
6 9979136 9986734 + Carg15488-RA Car06g01388 1388
8 428200 437601 - Carg04915-RA Car08g00073 73
14 11233748 11249183 + Carg22440-RA Car14g01329 1329
17 5002717 5007894 + Carg22620-RA Car17g00538 538
17 5011488 5012470 + Carg22619-RA Car17g00539 539
7 30682416 30686685 + CcPI632755_07g016630.1 Cco07g1663 1663
7 31385763 31394333 + CcPI632755_07g017360.1 Cco07g1736 1736
8 13956631 13961162 + CcPI632755_08g005410.1 Cco08g0541 541
8 13973098 13974213 + CcPI632755_08g005420.1 Cco08g0542 542
7 32591613 32595685 + CePI673135_07g017000.1 Cec07g1700 1700
7 33306843 33315364 + CePI673135_07g017730.1 Cec07g1773 1773
8 12433463 12438006 + CePI673135_08g004310.1 Cec08g0431 431
8 12449947 12450982 + CePI673135_08g004320.1 Cec08g0432 432
7 30561638 30565913 + ClG42_07g0159400.10 Clacu07g1594 1594
7 31247655 31256215 + ClG42_07g0166200.10 Clacu07g1662 1662
8 12243062 12248144 + ClG42_08g0056700.10 Clacu08g0567 567
8 12259053 12260054 + ClG42_08g0056800.10 Clacu08g0568 568
7 32300077 32305448 + ClCG07G015830.2 Cla07g01507 1507
7 33016757 33026257 + ClCG07G016570.2 Cla07g01581 1581
8 12704090 12710627 + ClCG08G004020.1 Cla08g00416 416
8 12723587 12724799 + ClCG08G004030.2 Cla08g00418 418
6 10167263 10173274 + CmaCh06G016330.1 Cma06g01633 1633
14 11331150 11337519 + CmaCh14G014970.1 Cma14g01497 1497
17 4805885 4810678 + CmaCh17G005800.1 Cma17g00580 580
17 4814173 4815082 + CmaCh17G005810.1 Cma17g00581 581
7 24025411 24033687 - MELO3C017685.2.1 Cme07g01856 1856
6 11381172 11387028 + CmoCh06G016320.1 Cmo06g01632 1632
8 470540 478747 - CmoCh08G000910.1 Cmo08g00091 91
14 12231707 12248378 + CmoCh14G015320.1 Cmo14g01532 1532
17 5800617 5804434 + CmoCh17G005640.1 Cmo17g00564 564
17 5808667 5809559 + CmoCh17G005650.1 Cmo17g00565 565
7 30813787 30818049 + CmPI595203_07g015590.1 Cmu07g1559 1559
7 31499440 31508001 + CmPI595203_07g016280.1 Cmu07g1628 1628
11 3984096 3988470 + Conep11aG0064400.1 Cone11ag0627 627
15 3094836 3100883 - Conep15aG0061500.1 Cone15ag0602 602
3 10180533 10197146 + Cp4.1LG03g12610.1 Cpe03g01257 1257
8 590640 598407 - Cp4.1LG08g05680.1 Cpe08g00095 95
12 4839182 4845410 + Cp4.1LG12g04960.1 Cpe12g00494 494
12 4848090 4849075 + Cp4.1LG12g04940.1 Cpe12g00495 495
17 7565477 7572404 - Cp4.1LG17g10030.1 Cpe17g00997 997
7 34822345 34826605 + CrPI670011_07g019360.1 Cre07g1936 1936
7 35508013 35516595 + CrPI670011_07g020020.1 Cre07g2002 2002
8 13013183 13017627 + CrPI670011_08g003910.1 Cre08g0391 391
8 13029409 13030479 + CrPI670011_08g003920.1 Cre08g0392 392
11 35050690 35055079 + Maker00005203 Lcy11g1233 1233
10 13525968 13547659 - Tan0016607.1 Tan10g1238 1238
5 20385239 20410166 + Vvi5g1119 Vvi5g1119 1119
5 20411466 20425543 - Vvi5g1120 Vvi5g1120 1120
5 20435026 20435134 + Vvi5g1121 Vvi5g1121 1121
5 20437925 20445323 - Vvi5g1122 Vvi5g1122 1122
5 20457098 20457704 + Vvi5g1123 Vvi5g1123 1123
5 20464717 20481062 - Vvi5g1124 Vvi5g1124 1124
5 20493928 20499367 + Vvi5g1125 Vvi5g1125 1125
5 20506905 20508157 + Vvi5g1126 Vvi5g1126 1126
5 20536234 20592925 + Vvi5g1127 Vvi5g1127 1127
5 20613135 20614458 + Vvi5g1128 Vvi5g1128 1128
       

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