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
Vvi19g434 . . . Bda09g00385 . Bpe08g01139 . . . . Cma01g01150 . . . . . Cpe02g00751 Bhi09g01943 . . . Hepe01g1308 . . . . . . . . . Cone6ag0086 . . . Lsi04g01240 . . . . . . . . . Bma07g01313 . . Cmo01g01202 . . . . Car16g00562 . . . . . . . . . Cla05g01536 Cam05g1643 Cec05g1649 Cco05g1687 Clacu05g1637 Cmu05g1532 Cre05g1642 . . . .
Vvi19g435 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g436 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g437 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g438 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g439 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g440 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g441 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g442 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g443 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
9 4905904 4913010 - Bda030965.1 Bda09g00385 385
9 54078014 54113712 + XM_039041901.1 Bhi09g01943 1943
7 48685369 48692585 + Bma026589.1 Bma07g01313 1313
8 13258024 13265223 + Bpe023265.3 Bpe08g01139 1139
5 24137959 24166245 - CaPI482276_05g016430.1 Cam05g1643 1643
16 3552784 3564364 + Carg05647-RA Car16g00562 562
5 24664808 24679612 + CcPI632755_05g016870.1 Cco05g1687 1687
5 27027562 27057318 - CePI673135_05g016490.1 Cec05g1649 1649
5 24210133 24234866 - ClG42_05g0163700.10 Clacu05g1637 1637
5 25572477 25598768 - ClCG05G014770.2 Cla05g01536 1536
1 8405696 8416878 + CmaCh01G011500.1 Cma01g01150 1150
1 9735069 9739514 + CmoCh01G012020.1 Cmo01g01202 1202
5 23940814 23957166 - CmPI595203_05g015320.1 Cmu05g1532 1532
6 416828 423271 + Conep06aG0008600.1 Cone6ag0086 86
2 4775345 4788438 - Cp4.1LG02g01210.1 Cpe02g00751 751
5 27060554 27090200 - CrPI670011_05g016420.1 Cre05g1642 1642
1 78283070 78296360 + Hsped.01g13080.1 Hepe01g1308 1308
4 19289314 19319979 + Lsi04G012400.1 Lsi04g01240 1240
19 5563130 5626881 - Vvi19g434 Vvi19g434 434
19 5632104 5640466 + Vvi19g435 Vvi19g435 435
19 5676839 5712392 - Vvi19g436 Vvi19g436 436
19 5712425 5716609 - Vvi19g437 Vvi19g437 437
19 5716879 5720662 - Vvi19g438 Vvi19g438 438
19 5728069 5728504 - Vvi19g439 Vvi19g439 439
19 5735552 5737897 - Vvi19g440 Vvi19g440 440
19 5753820 5754800 - Vvi19g441 Vvi19g441 441
19 5754801 5755020 - Vvi19g442 Vvi19g442 442
19 5755025 5759869 - Vvi19g443 Vvi19g443 443
       

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