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
Vvi17g626 . . . . . . . . . . Cma10g00227 . Car10g00212 . . . . . . . . . . . Cla06g01552 Cam06g1713 Cec06g1774 Cco06g1775 Clacu06g1681 Cmu06g1626 Cre06g2439 . . Cone2ag0525 Cone16ag0488 . . . . . . . . . . . . . Cmo10g00238 . . . . . . Cpe18g00766 . . . . . . . . . . . . . . Lsi06g01426 Csa01g00279 Chy02g02454 Cme02g01842
Vvi17g627 . Blo16g00174 . . . Bpe13g00306 Bma06g00158 . Cmo13g01133 . . . . . . Cpe20g00065 . . . . . . . . . . . . . . . Cone2ag0819 . Cone13ag0042 Cone19ag0048 Lsi02g00107 . Chy12g01511 Cme12g01956 . . Bda11g01716 . . . . . Sed08g2107 . . . . Car13g00921 . . . Bhi08g01105 Tan05g2378 Cmetu12g0499 . Hepe07g2476 . . Cla04g01166 Cam04g1225 Cec01g1736 Cco01g1782 Clacu04g1252 Cmu04g1231 Cre01g1526 . . . .
Vvi17g628 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g629 . Blo16g00172 . . . Bpe13g00308 Bma06g00156 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g630 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g631 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g632 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g633 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g634 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g635 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 51585375 51591138 - Bda008613.1 Bda11g01716 1716
8 35515467 35522357 + XM_039037868.1 Bhi08g01105 1105
16 3888732 3892917 - BLOR07420 Blo16g00172 172
16 3909329 3914902 + BLOR07422 Blo16g00174 174
6 2032494 2036582 - Bma022775.1 Bma06g00156 156
6 2049929 2055590 + Bma031270 Bma06g00158 158
13 10887267 10892957 - Bpe006432.1 Bpe13g00306 306
13 10908919 10912901 + Bpe006434.1 Bpe13g00308 308
4 26280304 26286737 + CaPI482276_04g012250.1 Cam04g1225 1225
6 28481007 28482449 - CaPI482276_06g017130.1 Cam06g1713 1713
10 1020277 1021719 - Carg17931-RA Car10g00212 212
13 9493185 9500107 + Carg04750-RA Car13g00921 921
1 30538320 30543772 + CcPI632755_01g017820.1 Cco01g1782 1782
6 28190144 28191586 - CcPI632755_06g017750.1 Cco06g1775 1775
1 31960917 31968569 + CePI673135_01g017360.1 Cec01g1736 1736
6 31253501 31254943 - CePI673135_06g017740.1 Cec06g1774 1774
2 28158010 28159452 - Chy2G047210.1 Chy02g02454 2454
12 18917618 18923735 + Chy12G221110.1 Chy12g01511 1511
4 26635600 26641711 + ClG42_04g0125200.10 Clacu04g1252 1252
6 27539600 27542844 - ClG42_06g0168100.10 Clacu06g1681 1681
4 26871888 26881058 + ClCG04G011910.1 Cla04g01166 1166
6 29091601 29103318 - ClCG06G015760.1 Cla06g01552 1552
10 1010513 1011955 - CmaCh10G002270.1 Cma10g00227 227
2 25117659 25121019 - MELO3C017213.2.1 Cme02g01842 1842
12 25457623 25462729 + MELO3C002017.2.1 Cme12g01956 1956
12 672109 679503 - PI0008852.1 Cmetu12g0499 499
10 1069558 1071000 - CmoCh10G002380.1 Cmo10g00238 238
13 9207336 9214770 + CmoCh13G011330.1 Cmo13g01133 1133
4 26817517 26824831 + CmPI595203_04g012310.1 Cmu04g1231 1231
6 27448293 27449735 - CmPI595203_06g016260.1 Cmu06g1626 1626
2 2895873 2897315 + Conep02aG0053800.1 Cone2ag0525 525
2 34206611 34218141 + Conep02aG0184700.1 Cone2ag0819 819
13 253807 258701 + Conep13aG0004500.1 Cone13ag0042 42
16 6994146 6997100 - Conep16aG0284600.1 Cone16ag0488 488
19 315111 318546 + Conep19aG0005200.1 Cone19ag0048 48
18 7320315 7323542 + Cp4.1LG18g07640.1 Cpe18g00766 766
20 314864 321809 - Cp4.1LG20g00680.1 Cpe20g00065 65
1 28483281 28488862 + CrPI670011_01g015260.1 Cre01g1526 1526
6 32252983 32255283 - CrPI670011_06g024390.1 Cre06g2439 2439
1 1752379 1754759 + CsaV3_1G002790.1 Csa01g00279 279
7 69085603 69092827 + Hsped.07g24760.1 Hepe07g2476 2476
2 870509 877383 - Lsi02G001070.1 Lsi02g00107 107
6 24814094 24817255 - Lsi06G014260.1 Lsi06g01426 1426
8 35124806 35136256 - Sed0024530.4 Sed08g2107 2107
5 75149934 75158290 + Tan0011872.2 Tan05g2378 2378
17 7659525 7662326 - Vvi17g626 Vvi17g626 626
17 7668204 7676883 - Vvi17g627 Vvi17g627 627
17 7682412 7685594 - Vvi17g628 Vvi17g628 628
17 7701815 7708142 - Vvi17g629 Vvi17g629 629
17 7713433 7715371 - Vvi17g630 Vvi17g630 630
17 7725750 7727693 - Vvi17g631 Vvi17g631 631
17 7756997 7761593 - Vvi17g632 Vvi17g632 632
17 7764657 7767737 - Vvi17g633 Vvi17g633 633
17 7777017 7784744 - Vvi17g634 Vvi17g634 634
17 7802415 7816859 - Vvi17g635 Vvi17g635 635
       

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