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
Vvi19g1124 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma03g00501 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1125 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1126 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1127 . . . . . . . . . . . . . . . . Cpe16g00712 . . . . . . . Cla02g01823 Cam02g1931 Cec02g1956 Cco02g1997 Clacu02g1912 Cmu02g1860 Cre02g2174 . . . . . . . . Blo15g00629 . . . . . . Bma12g00584 . . . . . . . . . Bhi10g00951 Tan05g0596 . . . . . . . . . . . . . Csa06g01157 Chy11g01034 .
Vvi19g1128 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1129 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1130 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1131 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1132 Blo04g00465 . . . Bpe07g00471 . . . . . . . . . Sed04g3516 . . Bhi05g01998 Tan02g0042 Cmetu01g1031 Lac12g0043 Hepe02g0016 . . . . . . . . . . . . . . . . . Blo15g00633 . . . . . Bma03g00497 . . . . . . . . . . . . . . . . . . . . . . . . . . Chy01g00859 .
Vvi19g1133 . . . . . . Bma08g00819 . . . . . . . . . Cpe16g00710 Bhi05g01997 . . . . . . . . . . . . . . . . . . . . . . . . . Bpe15g00916 . . Bma12g00579 . . . . . . . . Cpe05g01034 . . . . . . . . . . . . . . . Csa06g01152 . Cme01g01511
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 61514068 61517102 - XM_039032510.1 Bhi05g01997 1997
5 61521614 61524661 - XM_039032533.1 Bhi05g01998 1998
10 19343993 19347981 + XM_039046881.1 Bhi10g00951 951
4 3858254 3860684 - BLOR13377 Blo04g00465 465
15 16110614 16116431 - BLOR07023 Blo15g00629 629
15 16594365 16598857 - BLOR07027 Blo15g00633 633
3 3899461 3901953 - Bma016778.1 Bma03g00497 497
3 3922965 3926096 - Bma016782.1 Bma03g00501 501
8 45895131 45905417 + Bma028213.1 Bma08g00819 819
12 25156246 25158626 - Bma007741.1 Bma12g00579 579
12 25445708 25446895 + Bma007750.1 Bma12g00584 584
7 7570316 7940822 - Bpe021310.1 Bpe07g00471 471
15 18968521 18971041 + Bpe024591 Bpe15g00916 916
2 32412540 32419475 - CaPI482276_02g019310.1 Cam02g1931 1931
2 32927818 32932592 - CcPI632755_02g019970.1 Cco02g1997 1997
2 37428552 37433633 - CePI673135_02g019560.1 Cec02g1956 1956
1 7557415 7562376 - Chy1G008590.1 Chy01g00859 859
11 14773063 14792377 - Chy11G196140.1 Chy11g01034 1034
2 32671617 32678940 - ClG42_02g0191200.10 Clacu02g1912 1912
2 33373336 33378260 - ClCG02G018630.2 Cla02g01823 1823
1 19904572 19907870 - MELO3C012604.2.1 Cme01g01511 1511
1 7233922 7237261 - PI0002086.1 Cmetu01g1031 1031
2 32533916 32541228 - CmPI595203_02g018600.1 Cmu02g1860 1860
5 6779458 6783793 - Cp4.1LG05g10380.1 Cpe05g01034 1034
16 7260439 7263493 - Cp4.1LG16g07080.1 Cpe16g00710 710
16 7273988 7277076 + Cp4.1LG16g07050.1 Cpe16g00712 712
2 35374917 35382330 - CrPI670011_02g021740.1 Cre02g2174 2174
6 9603415 9606774 - CsaV3_6G013500.1 Csa06g01152 1152
6 9654187 9657880 + CsaV3_6G013550.1 Csa06g01157 1157
2 303027 305660 - Hsped.02g00160.1 Hepe02g0016 16
12 547634 551198 - Lag0014415.1 Lac12g0043 43
4 44635018 44638224 + Sed0000654.1 Sed04g3516 3516
2 641625 644670 - Tan0019432.1 Tan02g0042 42
5 4306281 4308817 + Tan0014507.3 Tan05g0596 596
19 22558793 22573951 + Vvi19g1124 Vvi19g1124 1124
19 22575605 22581761 + Vvi19g1125 Vvi19g1125 1125
19 22654524 22657736 + Vvi19g1126 Vvi19g1126 1126
19 22662520 22670040 - Vvi19g1127 Vvi19g1127 1127
19 22672339 22673080 - Vvi19g1128 Vvi19g1128 1128
19 22673123 22674794 + Vvi19g1129 Vvi19g1129 1129
19 22678797 22680489 + Vvi19g1130 Vvi19g1130 1130
19 22688698 22717134 + Vvi19g1131 Vvi19g1131 1131
19 22721759 22727850 - Vvi19g1132 Vvi19g1132 1132
19 22741009 22745951 - Vvi19g1133 Vvi19g1133 1133
       

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