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
Vvi4g902 . . . . . . . . . . . Cma07g00747 . Car07g00734 . . . . . . . . . . . . . . . . . . . . . Lsi01g01044 . . . . . . . . . . . . . Cmo07g00768 . . . . . . . . . . . . . . . . . . . . . . Chy02g00964 .
Vvi4g903 . . Bda04g00316 . . . Bma09g00349 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1354 . . . . . . . . . . Bpe06g00244 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g904 . . . . . . . . . . . Cma07g00748 . Car07g00735 . . . . . . . . . . . . . . . . . . . Cone6ag1353 . Lsi01g01045 . . . . . . Bda14g01210 . . . . . . Cmo07g00769 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g905 . . Bda04g00317 . . . Bma09g00351 . . . . Cma07g00750 . Car07g00737 . . . . . . . . . . . . . . . . . . . Cone6ag1352 . Lsi01g01049 . . . . . . . . . . . . . Cmo07g00772 . . . . . . . . . . . . . . . . . . . . . . Chy02g00965 .
Vvi4g906 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1351 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g907 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda14g01209 . . Bma03g01076 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g908 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed05g3369 . . . . . . . . Bhi10g02233 Tan07g1028 Cmetu11g1847 . Hepe10g0828 . . . . . . . . . . . . .
Vvi4g909 . . Bda04g00318 . . . Bma09g00352 . . . . Cma07g00751 . Car07g00738 . . . . . . . . . . . . . . . . . . . . . Lsi01g01050 . . . . . . . . Bpe06g00246 . . . . Cmo07g00774 . . . . . . . . . . . . . . . . . . . . . . Chy02g00969 .
Vvi4g910 . . . Bda10g00322 . . . . . . . Cma07g00752 . Car07g00739 . . . . . . . . . . . . . . . . . . . . . Lsi01g01051 . . . . . . Bda14g01207 . . Bma03g01075 . . . Cmo07g00775 . . . . . . . . . . . . . . . . . . . . . . Chy02g00970 .
Vvi4g911 . . . . . . . . . . . Cma07g00753 . Car07g00740 . . . . . . . . . . . . . . . . . . . Cone6ag1348 . Lsi01g01052 . . . . . . . . . . . . . Cmo07g00776 . . . . . . . . . . . . . . . . . . . . . . Chy02g00972 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 46987682 46989592 + Bda019193.1 Bda04g00316 316
4 47007325 47008398 - Bda019194.1 Bda04g00317 317
4 47050670 47051521 - Bda019197.1 Bda04g00318 318
10 33200560 33201246 + Bda007105.1 Bda10g00322 322
14 12051870 12052301 + Bda028065.1 Bda14g01207 1207
14 12064480 12065052 + Bda028067.1 Bda14g01209 1209
14 12070710 12072170 - Bda028068.1 Bda14g01210 1210
10 57994256 58002445 - XM_039045840.1 Bhi10g02233 2233
3 13125784 13126491 + Bma017447.1 Bma03g01075 1075
3 13130026 13130598 + Bma017448.1 Bma03g01076 1076
9 30253413 30255356 + Bma029262.1 Bma09g00349 349
9 30326422 30328341 - Bma029264.1 Bma09g00351 351
9 30393472 30394326 - Bma029265.1 Bma09g00352 352
6 12860806 12862761 + Bpe019732.1 Bpe06g00244 244
6 12900598 12901449 - Bpe019736.1 Bpe06g00246 246
7 3791036 3797421 + Carg05255-RA Car07g00734 734
7 3795354 3797303 - Carg05256-RA Car07g00735 735
7 3806444 3808189 + Carg05259-RA Car07g00737 737
7 3808565 3809608 - Carg05260-RA Car07g00738 738
7 3812415 3813089 - Carg05261-RA Car07g00739 739
7 3816030 3816939 + Carg05262-RA Car07g00740 740
2 6421088 6424592 + Chy2G032310.1 Chy02g00964 964
2 6425884 6427797 - Chy2G032320.1 Chy02g00965 965
2 6443663 6444709 - Chy2G032360.1 Chy02g00969 969
2 6454953 6455642 - Chy2G032370.1 Chy02g00970 970
2 6476073 6477023 + Chy2G032390.1 Chy02g00972 972
7 3316436 3322784 + CmaCh07G007470.1 Cma07g00747 747
7 3322708 3324657 - CmaCh07G007480.1 Cma07g00748 748
7 3333507 3335252 + CmaCh07G007500.1 Cma07g00750 750
7 3335630 3336676 - CmaCh07G007510.1 Cma07g00751 751
7 3339684 3340358 - CmaCh07G007520.1 Cma07g00752 752
7 3342957 3344466 + CmaCh07G007530.1 Cma07g00753 753
11 29697100 29703730 - PI0020343.1 Cmetu11g1847 1847
7 3480473 3486018 + CmoCh07G007680.1 Cmo07g00768 768
7 3485955 3487904 - CmoCh07G007690.1 Cmo07g00769 769
7 3497486 3499231 + CmoCh07G007720.1 Cmo07g00772 772
7 3499573 3500616 - CmoCh07G007740.1 Cmo07g00774 774
7 3503464 3504138 - CmoCh07G007750.1 Cmo07g00775 775
7 3507080 3507988 + CmoCh07G007760.1 Cmo07g00776 776
6 10851017 10852745 - Conep06aG0140400.1 Cone6ag1348 1348
6 10871973 10872898 + Conep06aG0140700.1 Cone6ag1351 1351
6 10877275 10879708 + Conep06aG0140800.1 Cone6ag1352 1352
6 10880205 10882076 - Conep06aG0140900.1 Cone6ag1353 1353
6 10883670 10885643 - Conep06aG0141000.1 Cone6ag1354 1354
10 17199013 17205816 + Hsped.10g08280.1 Hepe10g0828 828
1 8655285 8660082 + Lsi01G010440.1 Lsi01g01044 1044
1 8661066 8662988 - Lsi01G010450.1 Lsi01g01045 1045
1 8683639 8685441 + Lsi01G010490.1 Lsi01g01049 1049
1 8685914 8686969 - Lsi01G010500.1 Lsi01g01050 1050
1 8701448 8702134 - Lsi01G010510.1 Lsi01g01051 1051
1 8715690 8716628 + Lsi01G010520.1 Lsi01g01052 1052
5 42898072 42909459 + Sed0007293.1 Sed05g3369 3369
7 26808964 26823561 + Tan0012680.2 Tan07g1028 1028
4 17456542 17465760 + Vvi4g902 Vvi4g902 902
4 17477773 17479756 + Vvi4g903 Vvi4g903 903
4 17481238 17483065 + Vvi4g904 Vvi4g904 904
4 17484663 17489709 - Vvi4g905 Vvi4g905 905
4 17490612 17491727 - Vvi4g906 Vvi4g906 906
4 17528925 17530608 - Vvi4g907 Vvi4g907 907
4 17548459 17551794 + Vvi4g908 Vvi4g908 908
4 17553880 17555447 - Vvi4g909 Vvi4g909 909
4 17564078 17565725 - Vvi4g910 Vvi4g910 910
4 17567650 17568947 + Vvi4g911 Vvi4g911 911
       

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