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
Vvi3g326 . Blo15g00406 Bda06g00456 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla02g01046 . Cec02g1119 Cco02g1153 Clacu02g1100 Cmu02g1060 Cre02g1368 . . . .
Vvi3g327 . . . . Bpe07g00689 . . Bma12g00893 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme11g01016
Vvi3g328 . . . . . Bpe12g00163 . . . Cmo11g01384 Cma02g00311 Cma20g00695 Car02g00192 . . Cpe04g00295 . Bhi05g01087 . . . . . . Cla02g00624 Cam02g0658 Cec02g0661 Cco02g0685 Clacu02g0666 . Cre02g0979 . . . . . Csa07g00228 . Cme01g00073 Blo04g00616 Blo13g00456 . . Bpe15g00768 . Bma03g00653 Bma08g00825 . Cmo02g00305 Cmo20g00687 . . . . . Cpe05g01328 . . . . . . . Cla02g01045 Cam02g1113 Cec02g1118 Cco02g1152 Clacu02g1099 Cmu02g1059 Cre02g1367 Lsi11g01321 . Chy01g00080 Cme11g01011
Vvi3g329 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g330 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g331 . . . . Bpe07g00690 . . Bma12g00894 . . Cma02g00313 . Car02g00193 . . . . . . . . . . . . . . . . . . Cone12ag1281 . . . . . . . . . . . . . . . . Cmo02g00307 . . . . . . Cpe05g01327 . . . . . . . . . . . . . . . . . .
Vvi3g332 . . . . . Bpe12g00164 . . . . Cma02g00314 . Car02g00195 Car20g00595 Sed01g0615 . . Bhi05g01518 Tan02g0522 Cmetu05g1570 Lac12g0422 Hepe02g0332 . . Cla02g00315 Cam02g0322 Cec02g0323 Cco02g0325 Clacu02g0314 Cmu02g0313 Cre02g0645 Cone12ag1280 Cone8ag1351 Cone3ag1265 . . Csa07g00229 . . Blo04g00617 Blo13g00584 . . Bpe15g00922 . Bma03g00654 Bma08g00700 . Cmo02g00308 . . . . . . Cpe05g01326 . . . . . . . Cla02g01042 . . . . . . Lsi11g01322 . Chy01g00551 Cme11g01009
Vvi3g333 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g334 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g335 . Blo15g00756 Bda06g01081 . . . . . . . Cma02g00375 Cma20g00824 Car02g00242 Car20g00710 . . . . . . . . . . . . . . . . . . . . . Lsi10g00400 . Chy11g00351 . . . . . . . . . . Cmo02g00382 Cmo20g00835 . . . . Cpe16g00264 Cpe05g01280 Bhi10g01968 . . . Hepe08g0991 . . . . . . . . . . Csa02g01291 . Cme11g00153
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 6593573 6595036 - Bda023700.1 Bda06g00456 456
6 38325664 38332686 + Bda022850.1 Bda06g01081 1081
5 39347385 39350511 + XM_039033104.1 Bhi05g01087 1087
5 51656194 51659934 + XM_039030882.1 Bhi05g01518 1518
10 48981958 48989973 - XM_039045806.1 Bhi10g01968 1968
4 5370670 5389140 + BLOR13528 Blo04g00616 616
4 5380017 5385500 - BLOR13529 Blo04g00617 617
13 24966786 24969619 - BLOR05737 Blo13g00456 456
13 27955209 27956636 + BLOR19636 Blo13g00584 584
15 5802220 5820315 + BLOR06800 Blo15g00406 406
15 25683333 25698131 + BLOR07150 Blo15g00756 756
3 5355881 5358039 + Bma016947.1 Bma03g00653 653
3 5359052 5363608 - Bma016948.1 Bma03g00654 654
8 42416233 42419775 + Bma028054.1 Bma08g00700 700
8 46047913 46049179 + Bma028220.1 Bma08g00825 825
12 40260477 40261935 - Bma008221.1 Bma12g00893 893
12 40263406 40266682 - Bma008222.1 Bma12g00894 894
7 13527973 13529434 - Bpe026073 Bpe07g00689 689
7 13530435 13541476 - Bpe021537.1 Bpe07g00690 690
12 1235131 1237459 + Bpe005400.1 Bpe12g00163 163
12 1239026 1241301 - Bpe005401.1 Bpe12g00164 164
15 18017862 18019951 - Bpe001697.1 Bpe15g00768 768
15 19000299 19007296 - Bpe001843.1 Bpe15g00922 922
2 3976977 3980215 + CaPI482276_02g003220.1 Cam02g0322 322
2 7623423 7625865 + CaPI482276_02g006580.1 Cam02g0658 658
2 20668781 20672433 + CaPI482276_02g011130.1 Cam02g1113 1113
2 1152055 1156286 + Carg19782-RA Car02g00192 192
2 1156241 1159888 - Carg19783-RA Car02g00193 193
2 1163894 1169057 - Carg19785-RA Car02g00195 195
2 1638898 1644785 - Carg24146-RA Car02g00242 242
20 3339235 3346434 - Carg16115-RA Car20g00595 595
20 4098004 4104528 - Carg26794-RA Car20g00710 710
2 2971476 2974966 + CcPI632755_02g003250.1 Cco02g0325 325
2 6856973 6859403 + CcPI632755_02g006850.1 Cco02g0685 685
2 19822042 19825786 - CcPI632755_02g011520.1 Cco02g1152 1152
2 19850654 19854520 + CcPI632755_02g011530.1 Cco02g1153 1153
2 2970393 2974076 + CePI673135_02g003230.1 Cec02g0323 323
2 6760832 6763274 + CePI673135_02g006610.1 Cec02g0661 661
2 24601000 24604718 - CePI673135_02g011180.1 Cec02g1118 1118
2 24629572 24633402 + CePI673135_02g011190.1 Cec02g1119 1119
1 535322 540728 + Chy1G000800.1 Chy01g00080 80
1 3948107 3951241 + Chy1G005510.1 Chy01g00551 551
11 3201693 3208791 - Chy11G189310.1 Chy11g00351 351
2 2855122 2858359 + ClG42_02g0031400.10 Clacu02g0314 314
2 6645622 6648029 + ClG42_02g0066600.10 Clacu02g0666 666
2 20587954 20591641 - ClG42_02g0109900.10 Clacu02g1099 1099
2 20613695 20617437 + ClG42_02g0110000.10 Clacu02g1100 1100
2 3055696 3059495 + ClCG02G003120.1 Cla02g00315 315
2 6955198 6957605 + ClCG02G006190.2 Cla02g00624 624
2 21282575 21292335 + ClCG02G010650.1 Cla02g01042 1042
2 21342579 21347809 - ClCG02G010680.1 Cla02g01045 1045
2 21369239 21373439 + ClCG02G010690.1 Cla02g01046 1046
2 1479622 1483822 + CmaCh02G003110.1 Cma02g00311 311
2 1484404 1487617 - CmaCh02G003130.1 Cma02g00313 313
2 1488160 1498124 - CmaCh02G003140.1 Cma02g00314 314
2 1886998 1893505 - CmaCh02G003750.1 Cma02g00375 375
20 3184059 3188826 + CmaCh20G006950.1 Cma20g00695 695
20 3920382 3926180 - CmaCh20G008240.1 Cma20g00824 824
1 516480 519680 + MELO3C018473.2.1 Cme01g00073 73
11 1640794 1646698 + MELO3C023332.2.1 Cme11g00153 153
11 14508800 14514142 + MELO3C013470.2.1 Cme11g01009 1009
11 14525329 14530176 - MELO3C013472.2.1 Cme11g01011 1011
11 14563385 14567958 + MELO3C013473.2.1 Cme11g01016 1016
5 18162790 18167627 + PI0028301.1 Cmetu05g1570 1570
2 1544517 1548653 + CmoCh02G003050.1 Cmo02g00305 305
2 1549285 1552321 - CmoCh02G003070.1 Cmo02g00307 307
2 1552953 1561790 - CmoCh02G003080.1 Cmo02g00308 308
2 1951825 1957671 - CmoCh02G003820.1 Cmo02g00382 382
11 9670549 9679642 + CmoCh11G013840.1 Cmo11g01384 1384
20 3387479 3392714 + CmoCh20G006870.1 Cmo20g00687 687
20 4162691 4169119 - CmoCh20G008350.1 Cmo20g00835 835
2 2849032 2852268 + CmPI595203_02g003130.1 Cmu02g0313 313
2 20460515 20464178 - CmPI595203_02g010590.1 Cmu02g1059 1059
2 20486253 20489995 + CmPI595203_02g010600.1 Cmu02g1060 1060
3 31466501 31472228 - Conep03aG0177200.1 Cone3ag1265 1265
8 10839315 10846061 - Conep08aG0139000.1 Cone8ag1351 1351
12 9779893 9785588 + Conep12aG0132100.1 Cone12ag1280 1280
12 9785923 9789606 + Conep12aG0132200.1 Cone12ag1281 1281
4 3733287 3736173 + Cp4.1LG04g07890.1 Cpe04g00295 295
5 8929219 8934424 + Cp4.1LG05g12730.1 Cpe05g01280 1280
5 9319250 9324796 + Cp4.1LG05g13230.1 Cpe05g01326 1326
5 9325589 9332894 + Cp4.1LG05g13220.1 Cpe05g01327 1327
5 9331548 9336670 - Cp4.1LG05g13280.1 Cpe05g01328 1328
16 4642303 4648654 + Cp4.1LG16g02600.1 Cpe16g00264 264
2 3394175 3397848 + CrPI670011_02g006450.1 Cre02g0645 645
2 7179803 7182245 + CrPI670011_02g009790.1 Cre02g0979 979
2 21868891 21872671 - CrPI670011_02g013670.1 Cre02g1367 1367
2 21935937 21939840 + CrPI670011_02g013680.1 Cre02g1368 1368
2 12561316 12569367 + CsaV3_2G015070.1 Csa02g01291 1291
7 1802629 1808133 + CsaV3_7G002280.1 Csa07g00228 228
7 1809602 1813858 - CsaV3_7G002290.1 Csa07g00229 229
2 3179900 3184345 + Hsped.02g03320.1 Hepe02g0332 332
8 9382911 9389925 - Hsped.08g09910.1 Hepe08g0991 991
12 4718239 4723147 + Lag0014794.1 Lac12g0422 422
10 6085441 6092395 + Lsi10G004000.1 Lsi10g00400 400
11 21841481 21848747 + Lsi11G013210.1 Lsi11g01321 1321
11 21848293 21853312 - Lsi11G013220.1 Lsi11g01322 1322
1 4374200 4382261 + Sed0002453.5 Sed01g0615 615
2 4709971 4714692 + Tan0015759.1 Tan02g0522 522
3 3050205 3052674 - Vvi3g326 Vvi3g326 326
3 3056277 3059289 - Vvi3g327 Vvi3g327 327
3 3061224 3067402 + Vvi3g328 Vvi3g328 328
3 3067415 3068111 + Vvi3g329 Vvi3g329 329
3 3070549 3078772 + Vvi3g330 Vvi3g330 330
3 3078819 3096034 - Vvi3g331 Vvi3g331 331
3 3097458 3103030 - Vvi3g332 Vvi3g332 332
3 3104160 3112730 + Vvi3g333 Vvi3g333 333
3 3112734 3116384 + Vvi3g334 Vvi3g334 334
3 3116925 3136608 - Vvi3g335 Vvi3g335 335
       

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