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
Vvi18g1760 Blo01g01690 Blo12g00809 . Bda03g00365 Bpe02g00252 . Bma04g00342 Bma01g02456 . . . Cma09g01244 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g00915 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1761 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1762 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1763 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1764 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1765 Blo01g01691 . . . Bpe02g00251 . . . . . Cma01g00882 . Car01g00806 . . . . . . . . . . . . . . . . . . . . . . . . . Cme09g00122 . . Bda11g00914 . . . . . . Cmo01g00925 . . . . . . . . . . . . . . . . . . . . . Lsi08g00179 . . .
Vvi18g1766 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1767 Blo01g01692 . . . Bpe02g00250 . . . . . Cma01g00885 . Car01g00808 . . . . . . . . . . . Cla08g00185 . Cec08g0060 Cco08g0256 . Cmu08g0174 Cre08g0162 . . . . . . . Cme09g00126 . . . . . . . . Sed10g1654 Cmo01g00930 . . . . . . Cpe02g00980 Bhi06g00106 Tan10g1831 Cmetu09g1351 . . . . . . . . . . . Lsi08g00182 . . .
Vvi18g1768 . Blo12g00808 . Bda03g00366 . Bpe04g00328 Bma04g00343 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1769 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 3075315 3076681 - Bda016328.1 Bda03g00365 365
3 3077521 3080252 + Bda016329.1 Bda03g00366 366
11 8946127 8948382 - Bda005669.1 Bda11g00914 914
11 8956790 8961314 + Bda005670.1 Bda11g00915 915
6 2899981 2911005 - XM_039034386.1 Bhi06g00106 106
1 56606697 56608192 - BLOR01690 Blo01g01690 1690
1 56620185 56622528 + BLOR01691 Blo01g01691 1691
1 56624825 56626675 + BLOR01692 Blo01g01692 1692
12 26455252 26457931 - BLOR04827 Blo12g00808 808
12 26460626 26462089 + BLOR04828 Blo12g00809 809
1 82154533 82156002 - Bma003326.1 Bma01g02456 2456
4 2786968 2788334 - Bma018801.2 Bma04g00342 342
4 2790408 2793122 + Bma018802.1 Bma04g00343 343
2 1704440 1705838 - Bpe008095.1 Bpe02g00250 250
2 1707686 1710057 - Bpe008096.1 Bpe02g00251 251
2 1716456 1717971 + Bpe008097.1 Bpe02g00252 252
4 2086171 2088878 + Bpe015024.1 Bpe04g00328 328
1 5367367 5370450 - Carg23029-RA Car01g00806 806
1 5415234 5417836 + Carg28136-RA Car01g00808 808
8 4642089 4648491 + CcPI632755_08g002560.1 Cco08g0256 256
8 950757 957312 - CePI673135_08g000600.1 Cec08g0060 60
8 3806219 3819957 + ClCG08G001850.2 Cla08g00185 185
1 5044061 5047534 - CmaCh01G008820.1 Cma01g00882 882
1 5097557 5100975 + CmaCh01G008850.1 Cma01g00885 885
9 8334540 8336895 + CmaCh09G012440.1 Cma09g01244 1244
9 912897 917212 - MELO3C022121.2.1 Cme09g00122 122
9 943746 946932 + MELO3C022118.2.1 Cme09g00126 126
9 20875678 20879672 - PI0019591.1 Cmetu09g1351 1351
1 5296922 5300035 - CmoCh01G009250.1 Cmo01g00925 925
1 5349033 5351309 + CmoCh01G009300.1 Cmo01g00930 930
8 3761363 3767487 + CmPI595203_08g001740.1 Cmu08g0174 174
2 8800277 8802497 - Cp4.1LG02g09800.1 Cpe02g00980 980
8 3729720 3736026 + CrPI670011_08g001620.1 Cre08g0162 162
8 3713964 3720951 - Lsi08G001790.1 Lsi08g00179 179
8 3932605 3939211 + Lsi08G001820.1 Lsi08g00182 182
10 33211423 33216372 + Sed0023430.1 Sed10g1654 1654
10 57161839 57168042 - Tan0015668.1 Tan10g1831 1831
18 28788083 28791193 - Vvi18g1760 Vvi18g1760 1760
18 28796897 28797942 - Vvi18g1761 Vvi18g1761 1761
18 28815585 28819171 - Vvi18g1762 Vvi18g1762 1762
18 28851986 28852224 - Vvi18g1763 Vvi18g1763 1763
18 28857271 28859085 - Vvi18g1764 Vvi18g1764 1764
18 28865683 28886369 - Vvi18g1765 Vvi18g1765 1765
18 28905443 28917298 + Vvi18g1766 Vvi18g1766 1766
18 28928370 28931148 + Vvi18g1767 Vvi18g1767 1767
18 28932157 28939425 + Vvi18g1768 Vvi18g1768 1768
18 28939532 28940614 - Vvi18g1769 Vvi18g1769 1769
       

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