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
Vvi4g1332 Blo04g00920 . . . . . Bma09g00432 . . . Cma03g01112 . Car03g01005 . . . Cpe10g00321 . . . . . . . Cla01g01488 Cam01g1555 Cec04g1201 Cco04g1269 Clacu01g1581 Cmu01g1470 Cre04g1151 . . . . Lsi01g01173 . . Cme08g01140 Blo05g00528 . . Bda14g01013 . . . . . Cmo03g01102 . . . . . . . . . . . . . . . . . . . . . . Csa06g02737 . .
Vvi4g1333 . . Bda04g00384 . . . Bma09g00435 . . . . Cma07g00816 . Car07g00803 . Cpe19g00508 . . . . . . . . Cla01g01487 Cam01g1554 Cec04g1200 Cco04g1268 Clacu01g1580 Cmu01g1469 Cre04g1150 . . Cone6ag1261 . Lsi01g01174 . . Cme08g01141 . . . . . . . . . . Cmo07g00845 . . . . . . . . . . . . . . . . . . . . . Csa06g02736 . .
Vvi4g1334 . . . . . . . . . Cmo20g01055 . . . . . . . . . . . . . . . . . . . . . . Cone12ag0884 . . . . . . . . . . . . . . . . . . Cma20g01049 . . Cpe05g01042 Cpe16g00097 Bhi10g01727 . . . Hepe08g1213 . . Cla02g00028 Cam02g0029 Cec02g0029 Cco02g0025 Clacu02g0029 Cmu02g0029 Cre02g0371 Lsi10g00761 . . .
Vvi4g1335 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda14g00994 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1336 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0917 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1337 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1338 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1480 Cone20ag0005 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1339 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1340 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1341 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 50851084 50859492 + Bda019331.1 Bda04g00384 384
14 8145622 8159495 - Bda027795.3 Bda14g00994 994
14 8517804 8522910 - Bda033956 Bda14g01013 1013
10 43263673 43281251 + XM_039045220.1 Bhi10g01727 1727
4 10886248 10890911 - BLOR13832 Blo04g00920 920
5 9820584 9840435 - BLOR15490 Blo05g00528 528
9 37847548 37864130 + Bma029429.1 Bma09g00432 432
9 38081447 38089657 + Bma029437.1 Bma09g00435 435
1 29080695 29088845 + CaPI482276_01g015540.1 Cam01g1554 1554
1 29090874 29101800 + CaPI482276_01g015550.1 Cam01g1555 1555
2 1447999 1456153 - CaPI482276_02g000290.1 Cam02g0029 29
3 8373255 8387239 - Carg10517-RA Car03g01005 1005
7 4245847 4250145 - Carg05327-RA Car07g00803 803
2 319222 334821 - CcPI632755_02g000250.1 Cco02g0025 25
4 28020880 28029071 + CcPI632755_04g012680.1 Cco04g1268 1268
4 28031093 28041952 + CcPI632755_04g012690.1 Cco04g1269 1269
2 312939 321096 - CePI673135_02g000290.1 Cec02g0029 29
4 31563601 31571455 + CePI673135_04g012000.1 Cec04g1200 1200
4 31573855 31584794 + CePI673135_04g012010.1 Cec04g1201 1201
1 27872879 27881082 + ClG42_01g0158000.10 Clacu01g1580 1580
1 27883091 27893977 + ClG42_01g0158100.10 Clacu01g1581 1581
2 347389 363015 - ClG42_02g0002900.10 Clacu02g0029 29
1 29382894 29391134 + ClCG01G015110.2 Cla01g01487 1487
1 29393515 29404401 + ClCG01G015120.2 Cla01g01488 1488
2 335601 347254 - ClCG02G000270.1 Cla02g00028 28
3 7588871 7601746 - CmaCh03G011120.1 Cma03g01112 1112
7 3762699 3771178 - CmaCh07G008160.1 Cma07g00816 816
20 7801757 7807780 - CmaCh20G010490.1 Cma20g01049 1049
8 8033090 8044537 - MELO3C024599.2.1 Cme08g01140 1140
8 8046349 8053701 - MELO3C024598.2.1 Cme08g01141 1141
3 8912703 8922957 - CmoCh03G011020.1 Cmo03g01102 1102
7 3979399 3988416 - CmoCh07G008450.1 Cmo07g00845 845
20 9712398 9718651 - CmoCh20G010550.1 Cmo20g01055 1055
1 28216776 28224957 + CmPI595203_01g014690.1 Cmu01g1469 1469
1 28226967 28237869 + CmPI595203_01g014700.1 Cmu01g1470 1470
2 346770 354965 - CmPI595203_02g000290.1 Cmu02g0029 29
6 10054643 10061644 - Conep06aG0130900.1 Cone6ag1261 1261
8 8859270 8865717 - Conep08aG0094300.1 Cone8ag0917 917
12 7859811 7864996 + Conep12aG0091000.1 Cone12ag0884 884
17 9981709 9983717 + Conep17aG0152100.1 Cone17ag1480 1480
20 50892 54949 - Conep20aG0000500.1 Cone20ag0005 5
5 6875283 6881621 - Cp4.1LG05g10480.1 Cpe05g01042 1042
10 1856020 1875161 + Cp4.1LG10g03820.1 Cpe10g00321 321
16 1805167 1811996 + Cp4.1LG16g00920.1 Cpe16g00097 97
19 4333833 4344728 + Cp4.1LG19g04830.1 Cpe19g00508 508
2 867833 876005 - CrPI670011_02g003710.1 Cre02g0371 371
4 30094619 30102822 + CrPI670011_04g011500.1 Cre04g1150 1150
4 30104757 30115676 + CrPI670011_04g011510.1 Cre04g1151 1151
6 23905265 23912576 + CsaV3_6G041220.1 Csa06g02736 2736
6 23913724 23925625 + CsaV3_6G041230.1 Csa06g02737 2737
8 12634223 12640993 - Hsped.08g12130.1 Hepe08g1213 1213
1 9955085 9966891 - Lsi01G011730.1 Lsi01g01173 1173
1 9969099 9980424 - Lsi01G011740.1 Lsi01g01174 1174
10 10444186 10451052 + Lsi10G007610.1 Lsi10g00761 761
4 23417240 23454255 + Vvi4g1332 Vvi4g1332 1332
4 23459593 23532718 + Vvi4g1333 Vvi4g1333 1333
4 23532733 23545014 + Vvi4g1334 Vvi4g1334 1334
4 23547255 23557704 - Vvi4g1335 Vvi4g1335 1335
4 23569494 23589672 - Vvi4g1336 Vvi4g1336 1336
4 23591104 23592241 - Vvi4g1337 Vvi4g1337 1337
4 23597423 23600044 + Vvi4g1338 Vvi4g1338 1338
4 23600815 23604300 - Vvi4g1339 Vvi4g1339 1339
4 23610769 23623902 + Vvi4g1340 Vvi4g1340 1340
4 23624396 23627302 + Vvi4g1341 Vvi4g1341 1341
       

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