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
Vvi4g342 Blo01g01710 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy04g00273 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme04g00305
Vvi4g343 . . . . Bpe02g01197 . . . Cmo05g00632 . . Cma05g00730 . . . . . Bhi04g00821 . . . . . . . . . . . . . . . Cone17ag1106 . . . . Cme03g01725 . Blo18g00068 . . . . Bma01g01331 . . . . . . . Car05g00549 Cpe11g00651 . . . . . . . . Cla08g01238 Cam08g1696 Cec08g1275 Cco08g1396 Clacu08g1393 . Cre08g1178 Lsi08g01101 . Chy03g01230 .
Vvi4g344 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g345 . . . . . . . Bma01g02488 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g04428 . . . . . . . . . . . . . Cma09g00548 . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g346 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g347 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g348 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g349 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g350 . . . . . Bpe02g00233 . . Cmo05g00420 . . . Car09g00480 . . . Cpe06g00415 . . . . . . . . . . . . . . . . . . Lsi04g02218 . . . . . . . . . . . . . Cmo09g00538 . . . Car05g00343 . . . . . . . . . . . . . . . . . . . .
Vvi4g351 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 20607815 20644023 + XM_039029775.1 Bhi04g00821 821
1 56856213 56866877 + BLOR01710 Blo01g01710 1710
18 495677 509629 + BLOR08556 Blo18g00068 68
1 18242597 18263426 + Bma001650.1 Bma01g01331 1331
1 82630936 82631529 + Bma003366.1 Bma01g02488 2488
2 1596299 1600882 - Bpe008077.1 Bpe02g00233 233
2 15662450 15689280 - Bpe009058.1 Bpe02g01197 1197
8 23271066 23288267 - CaPI482276_08g016960.1 Cam08g1696 1696
5 1972553 1976257 - Carg09316-RA Car05g00343 343
5 3216285 3231737 - Carg08292-RA Car05g00549 549
9 2675409 2677639 - Carg02962-RA Car09g00480 480
8 25903688 25919400 - CcPI632755_08g013960.1 Cco08g1396 1396
8 24752676 24768381 - CePI673135_08g012750.1 Cec08g1275 1275
3 15368567 15383381 + Chy3G062100.1 Chy03g01230 1230
4 2401665 2416073 + Chy4G069910.1 Chy04g00273 273
8 24023174 24038927 - ClG42_08g0139300.10 Clacu08g1393 1393
8 25315605 25334609 - ClCG08G012400.1 Cla08g01238 1238
5 4105532 4119713 + CmaCh05G007300.1 Cma05g00730 730
9 2476458 2486797 - CmaCh09G005480.1 Cma09g00548 548
3 25811670 25828456 + MELO3C011159.2.1 Cme03g01725 1725
4 2378504 2380623 + MELO3C003592.2.1 Cme04g00305 305
5 1934255 1937888 - CmoCh05G004200.1 Cmo05g00420 420
5 3185501 3202454 - CmoCh05G006320.1 Cmo05g00632 632
9 2557715 2559546 - CmoCh09G005380.1 Cmo09g00538 538
17 8192832 8203834 + Conep17aG0113400.1 Cone17ag1106 1106
6 2370147 2372058 - Cp4.1LG06g04490.1 Cpe06g00415 415
11 4305212 4319768 + Cp4.1LG11g06730.1 Cpe11g00651 651
8 25063528 25079054 - CrPI670011_08g011780.1 Cre08g1178 1178
3 38649239 38666353 - CsaV3_3G047340.1 Csa03g04428 4428
4 29238561 29241649 - Lsi04G022180.1 Lsi04g02218 2218
8 19660913 19682732 - Lsi08G011010.1 Lsi08g01101 1101
4 3287093 3289106 + Vvi4g342 Vvi4g342 342
4 3297142 3326185 - Vvi4g343 Vvi4g343 343
4 3333417 3333701 + Vvi4g344 Vvi4g344 344
4 3333795 3334424 + Vvi4g345 Vvi4g345 345
4 3337922 3339472 + Vvi4g346 Vvi4g346 346
4 3339975 3350798 + Vvi4g347 Vvi4g347 347
4 3367196 3369092 + Vvi4g348 Vvi4g348 348
4 3375987 3377199 + Vvi4g349 Vvi4g349 349
4 3380179 3381794 + Vvi4g350 Vvi4g350 350
4 3391702 3393275 + Vvi4g351 Vvi4g351 351
       

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