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
Vvi19g374 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g375 . . . . . . . . . . Cma01g01169 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g376 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g377 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g378 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g01264 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g379 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g380 . . . . . . . . . . . . . . . . . Bhi09g01973 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g381 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe11g00514 . . . . Cmo01g01225 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g382 . . . . Bpe09g00209 . Bma10g00522 Bma13g01002 Cmo16g00921 . . . . . . . . . . . . . . . . . . . . . . Cone3ag1371 Cone10ag1304 Cone8ag1470 Cone12ag1414 . . . Cme06g02311 Blo07g00932 Blo10g00788 Bda05g00750 Bda12g00873 . Bpe03g00815 . . . . . . Cma16g00813 . Car16g00864 Cpe14g00718 . . . . . . . . . . . . . . . . . . .
Vvi19g383 . . . . Bpe09g00207 . Bma10g00523 Bma13g00995 Cmo16g00922 . . . . . . . . . . . . . . . . . . . . . . Cone6ag0091 Cone9ag0120 Cone14ag1109 Cone15ag1123 . . . . Blo07g00931 Blo10g00789 Bda05g00749 Bda12g00874 . Bpe03g00814 . . . . . Cma04g00930 . Car04g00872 . . Cpe01g00845 . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 55968814 55970937 - Bda021898.1 Bda05g00749 749
5 55978123 55978485 - Bda021899.1 Bda05g00750 750
12 39432628 39432996 + Bda009403.1 Bda12g00873 873
12 39439736 39441457 + Bda009404.1 Bda12g00874 874
9 54932599 54937157 - XM_039041152.1 Bhi09g01973 1973
7 28487874 28489691 - BLOR18863 Blo07g00931 931
7 28524036 28524398 - BLOR18864 Blo07g00932 932
10 24665444 24665806 + BLOR02578 Blo10g00788 788
10 24669237 24679011 + BLOR02579 Blo10g00789 789
10 6046254 6046565 + Bma004212.1 Bma10g00522 522
10 6077022 6078545 + Bma004214.1 Bma10g00523 523
13 42101536 42103151 - Bma010113.1 Bma13g00995 995
13 42225725 42226087 + Bma010121.1 Bma13g01002 1002
3 28114596 28116121 - Bpe012724.1 Bpe03g00814 814
3 28124433 28124795 - Bpe012725.1 Bpe03g00815 815
9 1468532 1470208 - Bpe023873.1 Bpe09g00207 207
9 1485540 1485893 + Bpe023875.1 Bpe09g00209 209
11 3971230 3973701 + Bpe003882.1 Bpe11g00514 514
4 5019778 5020811 - Carg00047-RA Car04g00872 872
16 6389308 6389676 - Carg24830-RA Car16g00864 864
1 8503318 8504860 - CmaCh01G011690.1 Cma01g01169 1169
4 4798364 4800873 - CmaCh04G009300.1 Cma04g00930 930
16 4491823 4492179 - CmaCh16G008130.1 Cma16g00813 813
6 30476159 30476849 + MELO3C025433.2.1 Cme06g02311 2311
1 9840485 9843370 - CmoCh01G012250.1 Cmo01g01225 1225
16 5605780 5606148 - CmoCh16G009210.1 Cmo16g00921 921
16 5616846 5620190 + CmoCh16G009220.1 Cmo16g00922 922
3 32698383 32698792 - Conep03aG0188300.1 Cone3ag1371 1371
6 443963 444947 - Conep06aG0009100.1 Cone6ag0091 91
8 11261369 11262245 - Conep08aG0151200.1 Cone8ag1470 1470
9 526294 528120 - Conep09aG0012000.1 Cone9ag0120 120
10 10178309 10178674 - Conep10aG0134400.1 Cone10ag1304 1304
12 10329707 10330066 - Conep12aG0146000.1 Cone12ag1414 1414
14 9245987 9252616 + Conep14aG0113100.1 Cone14ag1109 1109
15 9155209 9156148 + Conep15aG0114900.1 Cone15ag1123 1123
1 5010154 5012594 - Cp4.1LG01g08320.1 Cpe01g00845 845
14 5022419 5024188 - Cp4.1LG14g07200.1 Cpe14g00718 718
4 19862104 19867778 - Lsi04G012640.1 Lsi04g01264 1264
19 4865992 4866144 + Vvi19g374 Vvi19g374 374
19 4866196 4867047 - Vvi19g375 Vvi19g375 375
19 4868315 4870178 - Vvi19g376 Vvi19g376 376
19 4899077 4903139 - Vvi19g377 Vvi19g377 377
19 4909145 4917818 - Vvi19g378 Vvi19g378 378
19 4918316 4925158 + Vvi19g379 Vvi19g379 379
19 4935374 4943417 - Vvi19g380 Vvi19g380 380
19 4943926 4947171 - Vvi19g381 Vvi19g381 381
19 4954906 4956200 + Vvi19g382 Vvi19g382 382
19 4962647 4967645 + Vvi19g383 Vvi19g383 383
       

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