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
Vvi19g444 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g445 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g446 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g447 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g448 . Blo03g01437 . . . . . . . . . Cma09g00928 . . . . . Bhi09g01941 . . . Hepe01g1307 Mch11g1155 . . . . . . . . . Cone9ag0100 . . . . Chy04g00994 . . . . . . . . . . . Cmo09g00924 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g449 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma04g00986 . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g450 . . . . . . Bma10g00535 Bma13g01030 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda05g00735 Bda12g00891 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g451 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g452 . Blo03g01438 Bda07g00342 . Bpe09g00191 . . Bma13g01031 Cmo16g00914 . Cma01g01148 Cma09g00931 . . . . . Bhi09g01937 . . . . Mch11g1159 . Cla10g00532 Cam10g0530 Cec10g0548 Cco10g0537 Clacu10g0553 Cmu10g1378 Cre10g0781 . . . . . Csa03g00539 Chy04g00990 Cme06g02295 . Blo10g00807 . Bda12g00892 . . . Bma14g00353 Sed14g1362 Cmo01g01200 Cmo09g00928 . . . . . . Bhi11g00652 Tan01g1675 Cmetu04g0112 . Hepe07g1169 Mch10g1199 . Cla05g01530 Cam05g1639 Cec05g1643 Cco05g1676 Clacu05g1630 Cmu05g1526 . . . . .
Vvi19g453 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 55730172 55737782 + Bda021879.1 Bda05g00735 735
7 4475844 4477217 + Bda025428.1 Bda07g00342 342
12 39631582 39635945 + Bda009424.1 Bda12g00891 891
12 39674882 39675799 + Bda009426.1 Bda12g00892 892
9 53907382 53910036 - XM_039041633.1 Bhi09g01937 1937
9 54027335 54033586 - XM_039042324.1 Bhi09g01941 1941
11 15192849 15194754 - XM_039048247.1 Bhi11g00652 652
3 40954132 40959652 + BLOR12618 Blo03g01437 1437
3 40965481 40966395 + BLOR12619 Blo03g01438 1438
10 25482066 25482980 + BLOR02597 Blo10g00807 807
10 6496208 6500999 - Bma004232.1 Bma10g00535 535
13 42892035 42897663 + Bma010158.1 Bma13g01030 1030
13 42926099 42927016 + Bma010160.1 Bma13g01031 1031
14 4327310 4328455 - Bma010773.1 Bma14g00353 353
9 1327392 1328309 - Bpe023858.1 Bpe09g00191 191
5 23750913 23753260 - CaPI482276_05g016390.1 Cam05g1639 1639
10 7806757 7807902 - CaPI482276_10g005300.1 Cam10g0530 530
5 23796631 23799116 - CcPI632755_05g016760.1 Cco05g1676 1676
10 6404602 6406676 - CcPI632755_10g005370.1 Cco10g0537 537
5 26678391 26681308 - CePI673135_05g016430.1 Cec05g1643 1643
10 6647517 6648662 - CePI673135_10g005480.1 Cec10g0548 548
4 14589293 14590210 - Chy4G077080.1 Chy04g00990 990
4 14664195 14670070 - Chy4G077120.1 Chy04g00994 994
5 23853235 23856251 - ClG42_05g0163000.10 Clacu05g1630 1630
10 6650493 6651638 - ClG42_10g0055300.10 Clacu10g0553 553
5 25202788 25204161 - ClCG05G014715.1 Cla05g01530 1530
10 7066009 7067154 - ClCG10G005685.1 Cla10g00532 532
1 8393512 8395800 - CmaCh01G011480.1 Cma01g01148 1148
4 5067266 5093612 + CmaCh04G009860.1 Cma04g00986 986
9 4635160 4641647 + CmaCh09G009280.1 Cma09g00928 928
9 4652362 4653507 + CmaCh09G009310.1 Cma09g00931 931
6 30218377 30220840 - MELO3C025417.2.1 Cme06g02295 2295
4 2658271 2660859 + PI0026097.1 Cmetu04g0112 112
1 9723714 9725450 - CmoCh01G012000.1 Cmo01g01200 1200
9 4835313 4842493 + CmoCh09G009240.1 Cmo09g00924 924
9 4851657 4852802 + CmoCh09G009280.1 Cmo09g00928 928
16 5507583 5510038 - CmoCh16G009140.1 Cmo16g00914 914
5 23570615 23573727 - CmPI595203_05g015260.1 Cmu05g1526 1526
10 6772187 6773332 - CmPI595203_10g013780.1 Cmu10g1378 1378
9 435334 439481 - Conep09aG0010000.1 Cone9ag0100 100
10 7656887 7658032 - CrPI670011_10g007810.1 Cre10g0781 781
3 4513090 4514586 - CsaV3_3G005390.1 Csa03g00539 539
1 78271018 78277136 - Hsped.01g13070.1 Hepe01g1307 1307
7 26828912 26829085 + Hsped.07g11690.1 Hepe07g1169 1169
10 9421515 9423334 + MC10g_new0189 Mch10g1199 1199
11 8120430 8125628 + MC11g0954 Mch11g1155 1155
11 8145349 8147865 + MC11g_new0203 Mch11g1159 1159
14 22467314 22469727 - Sed0025342.1 Sed14g1362 1362
1 17811546 17812691 + Tan0017377.1 Tan01g1675 1675
19 5759971 5763303 - Vvi19g444 Vvi19g444 444
19 5763310 5766600 - Vvi19g445 Vvi19g445 445
19 5768651 5779409 - Vvi19g446 Vvi19g446 446
19 5799684 5805676 + Vvi19g447 Vvi19g447 447
19 5812017 5816845 + Vvi19g448 Vvi19g448 448
19 5851477 5864139 - Vvi19g449 Vvi19g449 449
19 5864697 5871371 - Vvi19g450 Vvi19g450 450
19 5891332 5892292 - Vvi19g451 Vvi19g451 451
19 5915391 5917479 + Vvi19g452 Vvi19g452 452
19 5927649 5928430 - Vvi19g453 Vvi19g453 453
       

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