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
Vvi5g239 . . . . . . . . . . . . . . . . Cpe03g01307 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g240 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00399 Cam06g0420 Cec06g0428 Cco06g0428 Clacu06g0407 Cmu06g0407 Cre06g1186 . . . . . . . . . . . . . . . . . . . . . . . Cpe12g00345 . Bhi12g01987 . . . . . . . . . . . . . . . . .
Vvi5g241 . . Bda03g00830 . Bpe04g01136 . Bma04g00729 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi05g01396 . . Cme06g00822 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g242 . . . . . . . . . . . . . . Sed02g0487 . . Bhi01g01119 Tan10g1105 Cmetu06g2035 . . . . . . . . . . . Cone14ag0686 . . . . . . . . . . . . . . . . Cmo06g01578 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g243 . . . . . . . . . . . Cma14g01567 . Car14g01382 Sed12g0749 . Cpe03g01310 Bhi01g01120 Tan10g1106 Cmetu06g0325 . Hepe05g1352 . . . . . . . . . . . . . Lsi05g01393 . . Cme06g00824 . . . . . . . . . . Cmo14g01602 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g244 Blo01g00025 . . . . . . Bma05g00987 . . . . Car06g01297 . . Cpe08g00117 . . . . . . . . Cla06g00398 Cam06g0419 Cec06g0427 Cco06g0427 Clacu06g0406 Cmu06g0406 Cre06g1185 . Cone15ag0698 . . . . . . . Blo07g00066 Bda11g00439 . Bpe05g00795 Bpe13g00757 . Bma06g01400 . . . . . . . Cpe12g00346 . Bhi12g01988 . . . . . Lcy12g0897 . . . . . . . . . . .
Vvi5g245 . . . . . . . . Cmo08g01236 Cmo17g00349 . Cma14g01565 . Car14g01381 . . Cpe03g01309 . . . . . . . . . . . . . . Cone14ag0685 Cone15ag0697 . . . . Chy11g01557 . . . . . . . . . . . Cmo14g01600 Cma08g01266 Cma17g00358 . Car17g00331 . . . . . . . . . . . . . . . . . . . Cme11g02068
Vvi5g246 . . . . . . . . . . . Cma14g01563 . Car14g01380 Sed02g1116 . Cpe03g01308 Bhi01g01121 Tan10g1110 Cmetu06g2692 . Hepe05g1350 . Lcy11g1311 . . . . . . . . . . . Lsi05g01392 . . Cme06g00825 . . . . . . . . . . Cmo14g01599 . . Car08g01105 . Cpe12g00279 . . . . . . . . . . . . . . . . . . .
Vvi5g247 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g248 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 7120273 7121134 + Bda016817.1 Bda03g00830 830
11 4658516 4664558 + Bda005183.1 Bda11g00439 439
1 21813063 21814572 + XM_039021406.1 Bhi01g01119 1119
1 21824352 21827158 + XM_039048088.1 Bhi01g01120 1120
1 21831105 21834054 - XM_039025226.1 Bhi01g01121 1121
12 62473273 62503637 - XM_039018707.1 Bhi12g01987 1987
12 62568156 62587317 + XM_039019743.1 Bhi12g01988 1988
1 349007 359400 - BLOR00025 Blo01g00025 25
7 962245 971512 + BLOR17998 Blo07g00066 66
4 7620406 7621268 + Bma019237.1 Bma04g00729 729
5 48362815 48374185 - Bma022138.1 Bma05g00987 987
6 50772833 50780732 + Bma024515.1 Bma06g01400 1400
4 9973537 9974168 - Bpe015817.1 Bpe04g01136 1136
5 21288155 21299095 - Bpe018208.2 Bpe05g00795 795
13 14095909 14103765 - Bpe010451.1 Bpe13g00757 757
6 6307772 6324917 - CaPI482276_06g004190.1 Cam06g0419 419
6 6331461 6350346 + CaPI482276_06g004200.1 Cam06g0420 420
6 9274776 9275444 - Carg17336-RA Car06g01297 1297
8 7505970 7512282 + Carg18846-RA Car08g01105 1105
14 11617761 11620868 + Carg19601-RA Car14g01380 1380
14 11622439 11632040 + Carg19602-RA Car14g01381 1381
14 11632851 11634462 - Carg19603-RA Car14g01382 1382
17 2072407 2082999 + Carg05537-RA Car17g00331 331
6 4672054 4688696 - CcPI632755_06g004270.1 Cco06g0427 427
6 4697245 4714977 + CcPI632755_06g004280.1 Cco06g0428 428
6 4819282 4834154 - CePI673135_06g004270.1 Cec06g0427 427
6 4840206 4860340 + CePI673135_06g004280.1 Cec06g0428 428
11 22122448 22133251 + Chy11G201370.1 Chy11g01557 1557
6 4848336 4863216 - ClG42_06g0040600.10 Clacu06g0406 406
6 4869740 4888606 + ClG42_06g0040700.10 Clacu06g0407 407
6 4873161 4888760 - ClCG06G004270.1 Cla06g00398 398
6 4894948 4913414 + ClCG06G004280.1 Cla06g00399 399
8 7703562 7713606 + CmaCh08G012660.1 Cma08g01266 1266
14 11739365 11742162 + CmaCh14G015630.1 Cma14g01563 1563
14 11743952 11753790 + CmaCh14G015650.1 Cma14g01565 1565
14 11754473 11755917 - CmaCh14G015670.1 Cma14g01567 1567
17 1984908 1995194 + CmaCh17G003580.1 Cma17g00358 358
6 5628870 5630780 + MELO3C006744.2.1 Cme06g00822 822
6 5633061 5634018 + MELO3C031621.2.1 Cme06g00824 824
6 5636324 5638861 - MELO3C006746.2.1 Cme06g00825 825
11 28393905 28405038 + MELO3C021280.2.1 Cme11g02068 2068
6 5730872 5733386 + PI0027271.1 Cmetu06g0325 325
6 5727232 5728312 + PI0024662.1 Cmetu06g2035 2035
6 5733627 5736568 - PI0002340.1 Cmetu06g2692 2692
6 11096046 11097516 + CmoCh06G015780.1 Cmo06g01578 1578
8 7820141 7830106 + CmoCh08G012360.1 Cmo08g01236 1236
14 12664850 12667484 + CmoCh14G015990.1 Cmo14g01599 1599
14 12669516 12679349 + CmoCh14G016000.1 Cmo14g01600 1600
14 12680076 12681740 - CmoCh14G016020.1 Cmo14g01602 1602
17 2121689 2132160 + CmoCh17G003490.1 Cmo17g00349 349
6 4643385 4658423 - CmPI595203_06g004060.1 Cmu06g0406 406
6 4664963 4683822 + CmPI595203_06g004070.1 Cmu06g0407 407
14 3538708 3546163 + Conep14aG0070000.1 Cone14ag0685 685
14 3548900 3549756 - Conep14aG0070100.1 Cone14ag0686 686
15 3763965 3771264 + Conep15aG0071100.1 Cone15ag0697 697
15 3783097 3791239 - Conep15aG0071200.1 Cone15ag0698 698
3 10590729 10593777 + Cp4.1LG03g12000.1 Cpe03g01307 1307
3 10594682 10598585 + Cp4.1LG03g12020.1 Cpe03g01308 1308
3 10599106 10608887 + Cp4.1LG03g12030.1 Cpe03g01309 1309
3 10609571 10611405 - Cp4.1LG03g11970.1 Cpe03g01310 1310
8 753865 762147 - Cp4.1LG08g05580.1 Cpe08g00117 117
12 1860001 1876466 - Cp4.1LG12g02770.1 Cpe12g00279 279
12 2307256 2321990 - Cp4.1LG12g03480.1 Cpe12g00345 345
12 2329925 2342993 + Cp4.1LG12g03430.1 Cpe12g00346 346
6 5699010 5714417 - CrPI670011_06g011850.1 Cre06g1185 1185
6 5721313 5740233 + CrPI670011_06g011860.1 Cre06g1186 1186
5 61916755 61920465 + Hsped.05g13500.1 Hepe05g1350 1350
5 61935449 61938449 - Hsped.05g13520.1 Hepe05g1352 1352
11 36597132 36600107 + Maker00031549 Lcy11g1311 1311
12 12928557 12943503 + Maker00024711 Lcy12g0897 897
5 21792415 21796124 + Lsi05G013920.1 Lsi05g01392 1392
5 21799793 21802566 - Lsi05G013930.1 Lsi05g01393 1393
5 21806546 21808682 - Lsi05G013960.1 Lsi05g01396 1396
2 42220658 42225260 + Sed0003794.1 Sed02g0487 487
2 48375295 48378725 + Sed0020024.4 Sed02g1116 1116
12 4432754 4435981 - Sed0010906.1 Sed12g0749 749
10 10672090 10674244 + Tan0012508.1 Tan10g1105 1105
10 10692814 10696462 + Tan0020427.1 Tan10g1106 1106
10 10751751 10755085 - Tan0009439.1 Tan10g1110 1110
5 2451345 2459325 + Vvi5g239 Vvi5g239 239
5 2461818 2479636 - Vvi5g240 Vvi5g240 240
5 2482792 2484238 - Vvi5g241 Vvi5g241 241
5 2487509 2488654 + Vvi5g242 Vvi5g242 242
5 2489471 2490792 + Vvi5g243 Vvi5g243 243
5 2495247 2508560 + Vvi5g244 Vvi5g244 244
5 2509330 2521854 - Vvi5g245 Vvi5g245 245
5 2525136 2528540 - Vvi5g246 Vvi5g246 246
5 2539623 2542890 + Vvi5g247 Vvi5g247 247
5 2543550 2558096 + Vvi5g248 Vvi5g248 248
       

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