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
Vvi18g370 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g371 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g02349 Csa04g01847 . . . . . . . . Bma01g00871 . . . . . . . . . Cpe02g00526 . . . . . . . Cla11g01499 Cam11g1556 Cec11g1587 Cco11g1584 Clacu11g1713 Cmu11g1533 Cre11g1949 . . . .
Vvi18g372 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g373 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g374 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g375 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma02g00267 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g376 . Blo12g00696 . Bda03g00503 Bpe02g00093 Bpe04g00458 . Bma01g02624 . . . Cma09g00649 . . . . . . . . . . . . . . . . . . . . . . . . Csa04g01846 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g377 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g378 . . . . Bpe02g00094 . . Bma01g02623 . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1235 Cone20ag0489 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g379 . Blo12g00697 . Bda03g00502 Bpe02g00095 Bpe04g00457 . . Cmo05g00507 Cmo12g00113 . . . Car12g00133 Sed04g0127 . Cpe07g00120 Bhi04g00736 Tan02g2367 Cmetu03g1991 . Hepe10g0520 . Lcy13g1582 Cla08g01092 Cam08g1545 Cec08g1119 Cco08g1246 Clacu08g1247 . Cre08g1029 . . Cone17ag1234 Cone20ag0491 . . . Cme03g01505 . Blo18g00213 . Bda01g01393 Bpe02g01607 . . . . . . Cma12g00143 Cma05g00485 Car05g00432 . Cpe11g00424 . . . . . . . . . . . . . . . Lsi08g00948 . Chy03g01015 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 49837530 49839405 + Bda003636.1 Bda01g01393 1393
3 4266491 4267501 - Bda016471.1 Bda03g00502 502
3 4268817 4269379 + Bda016472.1 Bda03g00503 503
4 18002468 18004675 + XM_039029801.1 Bhi04g00736 736
12 25222281 25222826 - BLOR04715 Blo12g00696 696
12 25243808 25244884 + BLOR04716 Blo12g00697 697
18 2085075 2086936 - BLOR08701 Blo18g00213 213
1 8168212 8171703 - Bma001093.1 Bma01g00871 871
1 83803687 83806194 + Bma003508.1 Bma01g02623 2623
1 83807041 83807765 + Bma003509.1 Bma01g02624 2624
2 2875122 2899468 + Bma014724.12 Bma02g00267 267
2 699733 700290 - Bpe007944.1 Bpe02g00093 93
2 701504 704574 - Bpe007945.1 Bpe02g00094 94
2 706286 707184 + Bpe007946.1 Bpe02g00095 95
2 18968958 18970859 + Bpe009453.1 Bpe02g01607 1607
4 2927298 2928304 - Bpe015144.1 Bpe04g00457 457
4 2929525 2930092 + Bpe015145.1 Bpe04g00458 458
8 21665197 21667193 + CaPI482276_08g015450.1 Cam08g1545 1545
11 28362295 28366001 + CaPI482276_11g015560.1 Cam11g1556 1556
5 2476615 2478696 + Carg09226-RA Car05g00432 432
12 759050 760922 + Carg20552-RA Car12g00133 133
8 24228614 24230615 + CcPI632755_08g012460.1 Cco08g1246 1246
11 28730051 28733773 + CcPI632755_11g015840.1 Cco11g1584 1584
8 23075748 23077732 + CePI673135_08g011190.1 Cec08g1119 1119
11 30181370 30191379 + CePI673135_11g015870.1 Cec11g1587 1587
3 13707007 13708829 + Chy3G059950.1 Chy03g01015 1015
8 22435780 22437777 + ClG42_08g0124700.10 Clacu08g1247 1247
11 28382739 28392701 + ClG42_11g0171300.10 Clacu11g1713 1713
8 23665453 23667803 + ClCG08G010950.2 Cla08g01092 1092
11 28656522 28660075 + ClCG11G015360.1 Cla11g01499 1499
5 2282997 2286110 + CmaCh05G004850.1 Cma05g00485 485
9 3088403 3089264 - CmaCh09G006490.1 Cma09g00649 649
12 619268 621397 + CmaCh12G001430.1 Cma12g00143 143
3 24293859 24296240 + MELO3C011368.2.1 Cme03g01505 1505
3 5121185 5123588 - PI0020086.1 Cmetu03g1991 1991
5 2443225 2445262 + CmoCh05G005070.1 Cmo05g00507 507
12 664390 666801 + CmoCh12G001130.1 Cmo12g00113 113
11 27641386 27645078 + CmPI595203_11g015330.1 Cmu11g1533 1533
17 8941127 8943484 - Conep17aG0126500.1 Cone17ag1234 1234
17 8945875 8948114 + Conep17aG0126600.1 Cone17ag1235 1235
20 2611244 2613468 - Conep20aG0050400.1 Cone20ag0489 489
20 2624223 2626400 + Conep20aG0050600.1 Cone20ag0491 491
2 3113853 3119074 + Cp4.1LG02g03570.1 Cpe02g00526 526
7 672932 675159 + Cp4.1LG07g01110.1 Cpe07g00120 120
11 2389903 2392488 + Cp4.1LG11g04260.1 Cpe11g00424 424
8 23432604 23434600 + CrPI670011_08g010290.1 Cre08g1029 1029
11 31287786 31291491 + CrPI670011_11g019490.1 Cre11g1949 1949
4 18115964 18117426 + CsaV3_4G028720.1 Csa04g01846 1846
4 18135773 18145219 - CsaV3_4G028730.1 Csa04g01847 1847
10 6035948 6038958 - Hsped.10g05200.1 Hepe10g0520 520
13 34691274 34693747 - Maker00034118 Lcy13g1582 1582
4 30676981 30682294 + Lsi04G023490.1 Lsi04g02349 2349
8 17942564 17945082 + Lsi08G009480.1 Lsi08g00948 948
4 801878 804592 + Sed0010701.1 Sed04g0127 127
2 92297837 92300784 + Tan0019721.1 Tan02g2367 2367
18 4068935 4069717 - Vvi18g370 Vvi18g370 370
18 4069910 4071971 + Vvi18g371 Vvi18g371 371
18 4072110 4072857 - Vvi18g372 Vvi18g372 372
18 4076660 4078865 + Vvi18g373 Vvi18g373 373
18 4087209 4096373 + Vvi18g374 Vvi18g374 374
18 4097929 4113909 - Vvi18g375 Vvi18g375 375
18 4121976 4123291 - Vvi18g376 Vvi18g376 376
18 4130504 4130666 + Vvi18g377 Vvi18g377 377
18 4130709 4134329 - Vvi18g378 Vvi18g378 378
18 4137997 4140727 + Vvi18g379 Vvi18g379 379
       

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