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
Vvi18g360 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g361 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g362 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy04g00282 . . . . . . . . . . . . . . . . . Cpe02g00391 . . . . . . . . . . . . . . Lsi08g00357 . . .
Vvi18g363 . . . Bda03g00506 . Bpe04g00461 . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1355 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g364 . Blo12g00695 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g365 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g366 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme04g00291
Vvi18g367 . . . . . . . . . Cmo15g00749 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g368 . . . . Bpe02g00092 . . Bma01g02626 . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1354 Cone7ag1274 . . . . . . . . . . . . . . . . . . . . Car15g00671 . . . . . . . . . . . . . . . . . . . .
Vvi18g369 . . . Bda03g00504 . Bpe04g00460 Bma04g00464 Bma01g02625 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 4272633 4275591 - Bda016473.1 Bda03g00504 504
3 4282278 4282878 - Bda016475.1 Bda03g00506 506
12 25205369 25215772 + BLOR04714 Blo12g00695 695
1 83812419 83815429 - Bma003510.3 Bma01g02625 2625
1 83823968 83827057 - Bma003511.1 Bma01g02626 2626
4 3905809 3911513 - Bma018931.1 Bma04g00464 464
2 692098 695186 + Bpe007943.1 Bpe02g00092 92
4 2933503 2936449 - Bpe015147.1 Bpe04g00460 460
4 2941960 2942549 - Bpe015148.1 Bpe04g00461 461
15 3743521 3748891 - Carg01484-RA Car15g00671 671
4 2505358 2507754 - Chy4G070000.1 Chy04g00282 282
4 2288605 2296869 - MELO3C003578.2.1 Cme04g00291 291
15 3671504 3673099 + CmoCh15G007490.1 Cmo15g00749 749
4 11038032 11040909 - Conep04aG0140200.1 Cone4ag1354 1354
4 11048599 11049544 - Conep04aG0140300.1 Cone4ag1355 1355
7 9450042 9455030 - Conep07aG0131200.1 Cone7ag1274 1274
2 2170403 2173724 - Cp4.1LG02g04760.1 Cpe02g00391 391
8 9774356 9781723 - Lsi08G003570.1 Lsi08g00357 357
18 3979748 3980165 - Vvi18g360 Vvi18g360 360
18 3980568 3988108 - Vvi18g361 Vvi18g361 361
18 3994149 4000643 + Vvi18g362 Vvi18g362 362
18 4003410 4004435 + Vvi18g363 Vvi18g363 363
18 4014839 4015257 + Vvi18g364 Vvi18g364 364
18 4033184 4034494 - Vvi18g365 Vvi18g365 365
18 4035263 4040612 + Vvi18g366 Vvi18g366 366
18 4042007 4046846 - Vvi18g367 Vvi18g367 367
18 4048719 4052933 - Vvi18g368 Vvi18g368 368
18 4062209 4068891 + Vvi18g369 Vvi18g369 369
       

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