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
Vvi3g246 . . . . . . . . Cmo19g00801 . . . . . . . . Bhi05g01615 Tan02g0598 Cmetu01g0626 . . . . Cla02g00369 . . . Clacu02g0368 Cmu02g0365 Cre02g0699 . . . . . Csa07g00163 . Cme01g01172 . . . . . . . . . . . Cma11g01345 Cma19g00786 . . . . . . . . . . . . . . . . . . Lsi11g01265 . Chy01g00627 .
Vvi3g247 . . . . . . . . Cmo19g00802 . . . . . . . . Bhi05g01614 . . . . . . Cla02g00367 . . Cco02g0380 Clacu02g0367 Cmu02g0364 Cre02g0697 . . . . . Csa07g00164 . Cme01g01171 . . . . . . . . . . . . Cma19g00787 . . . . . . . . . . . . . . . . . . Lsi11g01267 . Chy01g00626 .
Vvi3g248 . . . . . . . . Cmo19g00803 . . . . . . . . Bhi05g01613 Tan02g0597 Cmetu01g0372 . . . . Cla02g00365 . . Cco02g0379 Clacu02g0365 Cmu02g0362 Cre02g0694 . . . . . Csa07g00165 . Cme01g01168 . . . . . . . . . . . . Cma19g00788 . . . . . . . . . . . . . . . . . . Lsi11g01268 . Chy01g00625 .
Vvi3g249 . . . . . . . . Cmo19g00804 . . . . . . . . Bhi05g01612 . . . . . . Cla02g00364 Cam02g0370 . . Clacu02g0364 Cmu02g0361 Cre02g0693 . . . . . Csa07g00167 . Cme01g01167 . . . . . . . . Sed01g0640 . . . Cma19g00789 . . . . Bhi10g01228 Tan05g1071 Cmetu11g0337 . Hepe08g0329 . . . . . . . . . Lsi11g01269 . Chy01g00623 .
Vvi3g250 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g251 . . . . . Bpe12g00140 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo04g00599 . . . Bpe15g00790 . . Bma08g00733 . . . . . . . . . Bhi10g01227 . . . . . . . . . . . . . . . . Cme11g01230
Vvi3g252 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed05g3478 . . . . . . . . Bhi10g01226 Tan05g1073 Cmetu11g1629 . Hepe08g0327 . . . . . . . . . . . . Cme11g01234
Vvi3g253 . . . . . . . . . Cmo11g01767 . . . . . . Cpe15g00628 . . . . . . . . . . . . . . Cone12ag1261 Cone8ag1316 Cone3ag1230 . . . . . Blo04g00598 . . . . . . Bma08g00575 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g254 . . . . . . . Bma12g00865 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed01g0645 . . . . . . . . Bhi10g01224 Tan05g1079 Cmetu11g1332 . Hepe08g0326 . . . . . . . . . . . . Cme11g01236
Vvi3g255 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 53064192 53066129 + XM_039033051.1 Bhi05g01612 1612
5 53077080 53077934 + XM_039031274.1 Bhi05g01613 1613
5 53088816 53089667 + XM_039031275.1 Bhi05g01614 1614
5 53096253 53097438 + XM_039032743.1 Bhi05g01615 1615
10 27089948 27097654 + XM_039045304.1 Bhi10g01224 1224
10 27127226 27129759 + XM_039046807.1 Bhi10g01226 1226
10 27373931 27375609 + XM_039046986.1 Bhi10g01227 1227
10 27405473 27406925 - XM_039046442.1 Bhi10g01228 1228
4 5134562 5141803 + BLOR13510 Blo04g00598 598
4 5162551 5163598 + BLOR13511 Blo04g00599 599
8 34100714 34102161 + Bma027846.1 Bma08g00575 575
8 43171573 43173049 - Bma028097.1 Bma08g00733 733
12 39604340 39611117 - Bma008185.1 Bma12g00865 865
12 1034624 1036121 + Bpe024874 Bpe12g00140 140
15 18153501 18154521 - Bpe001717.1 Bpe15g00790 790
2 4465129 4465756 + CaPI482276_02g003700.1 Cam02g0370 370
2 3462466 3462825 + CcPI632755_02g003790.1 Cco02g0379 379
2 3464574 3466876 + CcPI632755_02g003800.1 Cco02g0380 380
1 4388662 4389512 + Chy1G006230.1 Chy01g00623 623
1 4396442 4397293 + Chy1G006250.1 Chy01g00625 625
1 4403349 4404197 + Chy1G006260.1 Chy01g00626 626
1 4408121 4408969 + Chy1G006270.1 Chy01g00627 627
2 3337548 3338357 + ClG42_02g0036400.10 Clacu02g0364 364
2 3340250 3341107 + ClG42_02g0036500.10 Clacu02g0365 365
2 3348249 3350459 + ClG42_02g0036700.10 Clacu02g0367 367
2 3351230 3352081 + ClG42_02g0036800.10 Clacu02g0368 368
2 3550735 3551610 + ClCG02G003592.1 Cla02g00364 364
2 3553338 3554222 + ClCG02G003593.1 Cla02g00365 365
2 3557237 3559390 + ClCG02G003595.1 Cla02g00367 367
2 3564041 3566100 + ClCG02G003597.1 Cla02g00369 369
11 8918753 8919595 + CmaCh11G013450.1 Cma11g01345 1345
19 7643638 7644489 - CmaCh19G007860.1 Cma19g00786 786
19 7645697 7650925 - CmaCh19G007870.1 Cma19g00787 787
19 7652577 7655965 - CmaCh19G007880.1 Cma19g00788 788
19 7657871 7658695 - CmaCh19G007890.1 Cma19g00789 789
1 14925313 14926460 + MELO3C013274.2.1 Cme01g01167 1167
1 14930570 14931599 + MELO3C013275.2.1 Cme01g01168 1168
1 14938139 14939274 + MELO3C013273.2.1 Cme01g01171 1171
1 14938414 14939369 + MELO3C013277.2.1 Cme01g01172 1172
11 18785399 18787086 + MELO3C013641.2.1 Cme11g01230 1230
11 18847692 18850421 - MELO3C013644.2.1 Cme11g01234 1234
11 18871004 18878844 - MELO3C013645.2.1 Cme11g01236 1236
1 4674539 4675381 + PI0001314.1 Cmetu01g0372 372
1 4677990 4678836 + PI0013912.1 Cmetu01g0626 626
11 12249776 12251234 - PI0003935.1 Cmetu11g0337 337
11 12015359 12030660 + PI0024435.1 Cmetu11g1332 1332
11 12046351 12048992 + PI0016725.1 Cmetu11g1629 1629
11 12448437 12450787 + CmoCh11G017670.1 Cmo11g01767 1767
19 7971010 7971864 - CmoCh19G008010.1 Cmo19g00801 801
19 7978329 7979183 - CmoCh19G008020.1 Cmo19g00802 802
19 7985652 7986506 - CmoCh19G008030.1 Cmo19g00803 803
19 7990401 7991342 - CmoCh19G008040.1 Cmo19g00804 804
2 3331358 3332242 + CmPI595203_02g003610.1 Cmu02g0361 361
2 3334062 3334919 + CmPI595203_02g003620.1 Cmu02g0362 362
2 3342054 3344264 + CmPI595203_02g003640.1 Cmu02g0364 364
2 3345035 3345886 + CmPI595203_02g003650.1 Cmu02g0365 365
3 31083531 31084960 - Conep03aG0173700.1 Cone3ag1230 1230
8 10674331 10675490 + Conep08aG0135500.1 Cone8ag1316 1316
12 9682967 9684259 + Conep12aG0130200.1 Cone12ag1261 1261
15 6998806 7019842 + Cp4.1LG15g06260.1 Cpe15g00628 628
2 3899416 3900273 + CrPI670011_02g006930.1 Cre02g0693 693
2 3901913 3902770 + CrPI670011_02g006940.1 Cre02g0694 694
2 3910465 3911316 + CrPI670011_02g006970.1 Cre02g0697 697
2 3914978 3915832 + CrPI670011_02g006990.1 Cre02g0699 699
7 1377326 1395325 - CsaV3_7G001630.1 Csa07g00163 163
7 1380275 1381585 - CsaV3_7G001640.1 Csa07g00164 164
7 1388870 1390141 - CsaV3_7G001650.1 Csa07g00165 165
7 1396355 1397203 - CsaV3_7G001670.1 Csa07g00167 167
8 2916464 2924745 + Hsped.08g03260.1 Hepe08g0326 326
8 2929794 2931229 + Hsped.08g03270.1 Hepe08g0327 327
8 2950227 2951764 - Hsped.08g03290.1 Hepe08g0329 329
11 21260313 21261167 - Lsi11G012650.1 Lsi11g01265 1265
11 21275240 21276094 - Lsi11G012670.1 Lsi11g01267 1267
11 21282118 21282972 - Lsi11G012680.1 Lsi11g01268 1268
11 21285341 21286192 - Lsi11G012690.1 Lsi11g01269 1269
1 4674085 4676516 + Sed0020949.1 Sed01g0640 640
1 4699766 4709231 - Sed0019949.3 Sed01g0645 645
5 43586872 43588511 - Sed0004752.1 Sed05g3478 3478
2 5286991 5291801 + Tan0021378.1 Tan02g0597 597
2 5293671 5294546 + Tan0009202.1 Tan02g0598 598
5 9407271 9408495 + Tan0022542.1 Tan05g1071 1071
5 9470648 9474673 - Tan0014498.1 Tan05g1073 1073
5 9493660 9505071 - Tan0013114.1 Tan05g1079 1079
3 2442453 2443350 + Vvi3g246 Vvi3g246 246
3 2454188 2455085 + Vvi3g247 Vvi3g247 247
3 2456220 2457111 + Vvi3g248 Vvi3g248 248
3 2458652 2459552 + Vvi3g249 Vvi3g249 249
3 2462647 2464101 + Vvi3g250 Vvi3g250 250
3 2465509 2466922 - Vvi3g251 Vvi3g251 251
3 2475766 2477434 - Vvi3g252 Vvi3g252 252
3 2486947 2488738 - Vvi3g253 Vvi3g253 253
3 2491564 2500092 - Vvi3g254 Vvi3g254 254
3 2502520 2505976 + Vvi3g255 Vvi3g255 255
       

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