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
Vvi3g476 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi11g01035 . . .
Vvi3g477 . . . . . . . . Cmo19g00644 . . . . . . . Cpe15g00508 Bhi05g01158 . . . Hepe06g0397 . . . . . . . . . . . . . . Csa07g00790 . . . . . Bda14g00528 . . . . . . . Cma11g01775 Cma19g00626 . Car19g00478 . . . . . . . . . . . . . . . . Lsi11g01036 . . .
Vvi3g478 . . . . . . . . . . . . . . Sed10g2056 . . Bhi05g01159 Tan02g0871 Cmetu01g1249 . Hepe02g0559 . . . . . . . . . . Cone8ag1160 . . Lsi10g00318 . . . . . . . . . . . . . . . . . . . Cpe05g01229 . . . . . . . . . . . . . . . . . .
Vvi3g479 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag1118 . . . . Csa07g00791 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g480 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g481 . . . . . . . . Cmo19g00645 . . . . . . . Cpe15g00509 Bhi05g01160 . . . . . . . . . . . . . . . . . . . . . . . . Bda14g00529 . . . . . . . . Cma19g00627 . . . . . . . . . . . . . . . . . . . . . .
Vvi3g482 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa07g00792 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g483 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g484 . . . . . . . . . . . . . . . . . . . . . . . . Cla02g00573 Cam02g0604 Cec02g0604 Cco02g0617 Clacu02g0599 Cmu02g0597 Cre02g0927 . Cone8ag1161 . . . Csa07g00793 Chy11g00429 Cme01g00021 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy01g00026 .
Vvi3g485 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme01g00020 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy01g00025 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
14 3816920 3818895 - Bda027274.1 Bda14g00528 528
14 3819848 3821008 - Bda027275.1 Bda14g00529 529
5 41495630 41501174 - XM_039031467.1 Bhi05g01158 1158
5 41530043 41532531 - XM_039031470.1 Bhi05g01159 1159
5 41575011 41577252 - XM_039032942.1 Bhi05g01160 1160
2 6869817 6873185 + CaPI482276_02g006040.1 Cam02g0604 604
19 6421691 6427188 - Carg22046-RA Car19g00478 478
2 6049634 6051313 + CcPI632755_02g006170.1 Cco02g0617 617
2 5931741 5933466 + CePI673135_02g006040.1 Cec02g0604 604
1 180415 183046 + Chy1G000250.1 Chy01g00025 25
1 183695 184629 + Chy1G000260.1 Chy01g00026 26
11 4134944 4137503 + Chy11G190090.1 Chy11g00429 429
2 5861172 5862400 + ClG42_02g0059900.10 Clacu02g0599 599
2 6137759 6138987 + ClCG02G005640.1 Cla02g00573 573
11 11868700 11871080 - CmaCh11G017750.1 Cma11g01775 1775
19 6758376 6759836 - CmaCh19G006260.1 Cma19g00626 626
19 6761115 6764981 - CmaCh19G006270.1 Cma19g00627 627
1 178121 179996 + MELO3C028576.2.1 Cme01g00020 20
1 180323 181663 + MELO3C018425.2.1 Cme01g00021 21
1 208942 210799 + PI0012282.1 Cmetu01g1249 1249
19 6965152 6966899 - CmoCh19G006440.1 Cmo19g00644 644
19 6976833 6979634 - CmoCh19G006450.1 Cmo19g00645 645
2 5767927 5769155 + CmPI595203_02g005970.1 Cmu02g0597 597
8 10067253 10068397 - Conep08aG0119200.1 Cone8ag1160 1160
8 10069417 10070583 - Conep08aG0119300.1 Cone8ag1161 1161
12 9038465 9040140 - Conep12aG0115400.1 Cone12ag1118 1118
5 8620489 8622950 - Cp4.1LG05g12340.1 Cpe05g01229 1229
15 6018436 6019998 - Cp4.1LG15g05120.1 Cpe15g00508 508
15 6021892 6026835 - Cp4.1LG15g05140.1 Cpe15g00509 509
2 6363724 6365464 + CrPI670011_02g009270.1 Cre02g0927 927
7 5542035 5543455 - CsaV3_7G008890.1 Csa07g00790 790
7 5545224 5547466 - CsaV3_7G008900.1 Csa07g00791 791
7 5548437 5551140 - CsaV3_7G008910.1 Csa07g00792 792
7 5551757 5553380 - CsaV3_7G008920.1 Csa07g00793 793
2 5656540 5658570 + Hsped.02g05590.1 Hepe02g0559 559
6 14796022 14800475 + Hsped.06g03970.1 Hepe06g0397 397
10 5124845 5134269 - Lsi10G003180.1 Lsi10g00318 318
11 17834632 17838610 - Lsi11G010350.1 Lsi11g01035 1035
11 17852243 17853129 - Lsi11G010360.1 Lsi11g01036 1036
10 37095066 37097864 - Sed0021702.1 Sed10g2056 2056
2 9699877 9702206 + Tan0012012.1 Tan02g0871 871
3 4642800 4644279 - Vvi3g476 Vvi3g476 476
3 4651537 4653024 - Vvi3g477 Vvi3g477 477
3 4667873 4668867 - Vvi3g478 Vvi3g478 478
3 4670023 4676294 - Vvi3g479 Vvi3g479 479
3 4676349 4690973 + Vvi3g480 Vvi3g480 480
3 4691609 4693091 - Vvi3g481 Vvi3g481 481
3 4701571 4707486 - Vvi3g482 Vvi3g482 482
3 4708035 4709541 + Vvi3g483 Vvi3g483 483
3 4709978 4710972 - Vvi3g484 Vvi3g484 484
3 4712113 4722039 - Vvi3g485 Vvi3g485 485
       

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