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
Vvi1g1381 . . . Bda11g00359 Bpe13g00846 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo02g00225 . . Bda11g00359 Bpe14g00835 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1382 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1383 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1384 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1385 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo02g00226 . . . Bpe14g00836 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1386 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1387 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00150 Cam06g0064 Cec06g0166 Cco06g0160 Clacu06g0161 Cmu06g0158 Cre06g0932 . . . . . . Chy11g01840 Cme11g02376 . . . . . . . . Sed09g0351 . . . . . . Cpe17g00949 . Bhi12g02379 Tan06g1430 Cmetu11g0377 . Hepe03g1179 . . . . . . . . . Lsi09g01778 . . .
Vvi1g1388 . . . Bda11g00358 Bpe13g00847 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g00358 . . . Bma06g01311 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1389 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone15ag0644 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1390 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 3976742 3981508 + Bda005092.1 Bda11g00358 358
11 3987323 3988145 - Bda005094.1 Bda11g00359 359
12 75117571 75120255 - XM_039019694.1 Bhi12g02379 2379
2 2111681 2114604 + BLOR09955 Blo02g00225 225
2 2115620 2127191 - BLOR09956 Blo02g00226 226
6 50111352 50116085 + Bma024421.1 Bma06g01311 1311
13 14662614 14663776 + Bpe010536.1 Bpe13g00846 846
13 14664553 14669418 - Bpe010537.1 Bpe13g00847 847
14 6275748 6277096 + Bpe014212.1 Bpe14g00835 835
14 6277951 6280163 - Bpe014213.1 Bpe14g00836 836
6 2495667 2497337 + CaPI482276_06g000640.1 Cam06g0064 64
6 1666885 1669453 - CcPI632755_06g001600.1 Cco06g0160 160
6 1695080 1697689 - CePI673135_06g001660.1 Cec06g0166 166
11 24721439 24723274 + Chy11G204200.1 Chy11g01840 1840
6 1837627 1840194 - ClG42_06g0016100.10 Clacu06g0161 161
6 1704924 1718007 - ClCG06G001660.1 Cla06g00150 150
11 30715606 30716293 + MELO3C022365.2.1 Cme11g02376 2376
11 1334012 1334849 - PI0025141.1 Cmetu11g0377 377
6 1644080 1645762 - CmPI595203_06g001580.1 Cmu06g0158 158
15 3376714 3378273 + Conep15aG0065700.1 Cone15ag0644 644
17 7278335 7279738 + Cp4.1LG17g09520.1 Cpe17g00949 949
6 2725403 2735751 - CrPI670011_06g009320.1 Cre06g0932 932
3 65591220 65591999 + Hsped.03g11790.1 Hepe03g1179 1179
9 26524696 26543723 + Lsi09G017780.1 Lsi09g01778 1778
9 3200253 3203857 + Sed0013590.1 Sed09g0351 351
6 18879274 18881490 - Tan0000819.1 Tan06g1430 1430
1 22826372 22828816 + Vvi1g1381 Vvi1g1381 1381
1 22842548 22844572 + Vvi1g1382 Vvi1g1382 1382
1 22844921 22845044 + Vvi1g1383 Vvi1g1383 1383
1 22845051 22853689 - Vvi1g1384 Vvi1g1384 1384
1 22854789 22859753 - Vvi1g1385 Vvi1g1385 1385
1 22861921 22863800 + Vvi1g1386 Vvi1g1386 1386
1 22865692 22867173 + Vvi1g1387 Vvi1g1387 1387
1 22867506 22871451 - Vvi1g1388 Vvi1g1388 1388
1 22873386 22877304 - Vvi1g1389 Vvi1g1389 1389
1 22886258 22887162 - Vvi1g1390 Vvi1g1390 1390
       

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