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
Vvi18g1310 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1311 . . . Bda03g00411 . . . Bma01g02531 . . . Cma09g01190 . . . Cpe06g00958 . Bhi04g02161 . . . . . Lcy10g2153 Cla08g00308 . . . . . . . . . Cone20ag0684 . . . Cme03g00892 . . Bda11g00853 . . . . . . . Cmo09g01218 . . . Car09g01089 . . . . . . . . . . . . . . . . . . . .
Vvi18g1312 Blo01g01749 . . . . . . Bma01g02530 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1313 . . . . Bpe02g00194 . . Bma01g02529 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g00854 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1314 . . . . . . . Bma01g02527 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme03g00284 . . Bda11g00855 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1315 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1316 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme03g00284 . . Bda11g00856 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy03g00200 .
Vvi18g1317 . . . . . . . . . . . . . . Sed03g0506 . . Bhi04g01749 Tan11g1105 . . . . . Cla08g00749 Cam08g1176 Cec08g0766 Cco08g0874 Clacu08g0882 . Cre08g0684 . . . . . . . . . . . . . . . . . . . . . . . . . Bhi09g01546 . . . . . . . . . . . . . Lsi08g00572 . . .
Vvi18g1318 . . . . Bpe02g00199 . . Bma01g02522 Cmo04g02577 Cmo15g00583 . . . . Sed11g1376 Cpe06g00912 Cpe13g00698 Bhi04g01748 Tan11g1103 Cmetu03g1200 . Hepe02g2812 . . . . . . . . . Cone4ag1468 . Cone17ag0770 Cone20ag0365 . . . . . Blo18g00145 . Bda13g01418 Bpe02g01107 Bpe14g00439 . . . . . . . Car04g02369 Car15g00537 Cpe01g02131 . Bhi09g01545 Tan01g3069 . . . . . Cla09g00952 Cam09g1003 Cec09g1006 Cco09g1018 . . . . . Chy03g00490 .
Vvi18g1319 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 3543626 3554332 - Bda033487 Bda03g00411 411
11 8396251 8399434 - Bda005604.1 Bda11g00853 853
11 8426203 8441494 + Bda005606.1 Bda11g00854 854
11 8451393 8454990 + Bda005607.1 Bda11g00855 855
11 8457551 8459684 + Bda005608.1 Bda11g00856 856
13 36891944 36901071 + Bda000245.3 Bda13g01418 1418
4 42536334 42545592 + XM_039029591.1 Bhi04g01748 1748
4 42536334 42545592 + XM_039029590.1 Bhi04g01749 1749
4 59044431 59055726 + XM_039028711.1 Bhi04g02161 2161
9 41542168 41614520 - XM_039042168.1 Bhi09g01545 1545
9 41542168 41567214 - XM_039042170.1 Bhi09g01546 1546
1 57224568 57227912 - BLOR01749 Blo01g01749 1749
18 1334960 1343614 + BLOR08633 Blo18g00145 145
1 82844192 82846453 - Bma003402.1 Bma01g02522 2522
1 82885021 82887530 - Bma003407.1 Bma01g02527 2527
1 82950340 82953647 - Bma003410.1 Bma01g02529 2529
1 82995462 82998905 - Bma003412.1 Bma01g02530 2530
1 83013773 83019372 + Bma003413.1 Bma01g02531 2531
2 1356348 1364744 + Bpe008044.1 Bpe02g00194 194
2 1392602 1402202 + Bpe008049.1 Bpe02g00199 199
2 14685263 14691861 - Bpe008965.1 Bpe02g01107 1107
14 4023960 4033148 - Bpe007090.1 Bpe14g00439 439
8 18106796 18119692 + CaPI482276_08g011760.1 Cam08g1176 1176
9 10426438 10447245 - CaPI482276_09g010030.1 Cam09g1003 1003
4 19009626 19017266 - Carg15804-RA Car04g02369 2369
9 10183414 10185096 - Carg28174-RA Car09g01089 1089
15 2933162 2941636 + Carg01620-RA Car15g00537 537
8 20605752 20607330 + CcPI632755_08g008740.1 Cco08g0874 874
9 9723230 9749145 - CcPI632755_09g010180.1 Cco09g1018 1018
8 19384486 19396792 + CePI673135_08g007660.1 Cec08g0766 766
9 9731478 9765616 - CePI673135_09g010060.1 Cec09g1006 1006
3 1879497 1882796 - Chy3G051800.1 Chy03g00200 200
3 6782852 6794297 + Chy3G054700.1 Chy03g00490 490
8 18895412 18908288 + ClG42_08g0088200.10 Clacu08g0882 882
8 7302249 7311726 + ClCG08G003000.2 Cla08g00308 308
8 19793846 19806955 + ClCG08G007370.2 Cla08g00749 749
9 9987824 10008423 - ClCG09G010210.1 Cla09g00952 952
9 7646946 7653193 + CmaCh09G011900.1 Cma09g01190 1190
3 3604770 3608247 - MELO3C008319.2.1 Cme03g00284 284
3 16958995 16967399 + MELO3C026152.2.1 Cme03g00892 892
3 8564528 8572868 + PI0006147.1 Cmetu03g1200 1200
4 18846671 18853319 - CmoCh04G025770.1 Cmo04g02577 2577
9 9420581 9427062 - CmoCh09G012180.1 Cmo09g01218 1218
15 2815996 2823572 + CmoCh15G005830.1 Cmo15g00583 583
4 11569995 11576725 + Conep04aG0152000.1 Cone4ag1468 1468
17 5838533 5848430 + Conep17aG0078800.1 Cone17ag0770 770
20 1650262 1659826 + Conep20aG0037900.1 Cone20ag0365 365
20 4226198 4231593 - Conep20aG0070500.1 Cone20ag0684 684
1 17964962 17973321 - Cp4.1LG01g21280.1 Cpe01g02131 2131
6 6310863 6337473 - Cp4.1LG06g07430.1 Cpe06g00912 912
6 8196848 8203199 - Cp4.1LG06g09610.1 Cpe06g00958 958
13 6496126 6504654 - Cp4.1LG13g03850.1 Cpe13g00698 698
8 19802170 19815224 + CrPI670011_08g006840.1 Cre08g0684 684
2 77170629 77180603 - Hsped.02g28120.1 Hepe02g2812 2812
10 45530013 45530621 - Maker00039797 Lcy10g2153 2153
8 13969465 13981797 - Lsi08G005720.1 Lsi08g00572 572
3 3064893 3074094 - Sed0012813.4 Sed03g0506 506
11 29751461 29760426 - Sed0019934.2 Sed11g1376 1376
1 78417198 78426374 + Tan0014568.1 Tan01g3069 3069
11 8774714 8783518 + Tan0020360.3 Tan11g1103 1103
11 8774714 8783518 + Tan0020360.5 Tan11g1105 1105
18 18233327 18233812 - Vvi18g1310 Vvi18g1310 1310
18 18289692 18300956 + Vvi18g1311 Vvi18g1311 1311
18 18301047 18305241 - Vvi18g1312 Vvi18g1312 1312
18 18330211 18334024 + Vvi18g1313 Vvi18g1313 1313
18 18346655 18351161 + Vvi18g1314 Vvi18g1314 1314
18 18456153 18457526 + Vvi18g1315 Vvi18g1315 1315
18 18495149 18499455 + Vvi18g1316 Vvi18g1316 1316
18 18675719 18680201 - Vvi18g1317 Vvi18g1317 1317
18 18680236 18701933 - Vvi18g1318 Vvi18g1318 1318
18 18753631 18756450 - Vvi18g1319 Vvi18g1319 1319
       

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