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
Vvi1g1161 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag1125 . . . . . . . . Blo11g00982 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1162 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1163 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag1128 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1164 . . . . Bpe13g00521 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag1131 Cone19ag1110 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1165 . . . . . . Bma14g01881 . Cmo04g01912 . . . . . . . Cpe01g01601 . . . . . . . . . . . . . . . . . . Lsi04g00657 . . Cme10g00636 . Blo11g00981 . . . . . . . . . Cma04g01817 . Car04g01829 . . . . . . . . . . . . . . . . . . . . .
Vvi1g1166 . . . . . . . . . . . . . . . Cpe09g00571 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1167 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo06g00833 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1168 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00220 Cam06g0239 Cec06g0239 Cco06g0234 Clacu06g0233 Cmu06g0229 Cre06g1000 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1169 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0733 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1170 . . Bda01g01683 . . Bpe10g00788 . Bma15g00239 Cmo04g01917 . . . . . Sed06g1736 . Cpe01g01605 Bhi07g01894 Tan04g0086 Cmetu10g0989 Lac13g0075 Hepe10g1532 . . . . . . . . . . . Cone8ag0735 . Lsi04g00661 . . Cme10g00640 Blo06g00827 . . . . . . . . . . Cma04g01820 . Car04g01833 . . . . . . . . . . Cla11g01358 Cam11g1414 Cec11g1443 Cco11g1439 Clacu11g1573 Cmu11g1393 Cre11g1814 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 52889872 52893672 - Bda003958.1 Bda01g01683 1683
7 50876076 50881257 - XM_039036616.1 Bhi07g01894 1894
6 31516376 31520022 - BLOR17410 Blo06g00827 827
6 31566590 31572931 - BLOR17416 Blo06g00833 833
11 23772887 23779008 + BLOR03857 Blo11g00981 981
11 24005708 24012072 - BLOR03858 Blo11g00982 982
14 40287022 40287606 - Bma012666.1 Bma14g01881 1881
15 2394538 2398067 + Bma013225.1 Bma15g00239 239
10 14044295 14046841 - Bpe003093.1 Bpe10g00788 788
13 12515653 12518239 + Bpe010227.1 Bpe13g00521 521
6 4189233 4190288 + CaPI482276_06g002390.1 Cam06g0239 239
11 26824099 26855590 + CaPI482276_11g014140.1 Cam11g1414 1414
4 10597521 10598258 - Carg14276-RA Car04g01829 1829
4 10613661 10618217 - Carg14272-RA Car04g01833 1833
6 2499661 2500707 + CcPI632755_06g002340.1 Cco06g0234 234
11 27158920 27174436 + CcPI632755_11g014390.1 Cco11g1439 1439
6 2554739 2555797 + CePI673135_06g002390.1 Cec06g0239 239
11 28596697 28604002 + CePI673135_11g014430.1 Cec11g1443 1443
6 2713577 2714629 + ClG42_06g0023300.10 Clacu06g0233 233
11 26865679 26881124 + ClG42_11g0157300.10 Clacu11g1573 1573
6 2625118 2626191 + ClCG06G002370.2 Cla06g00220 220
11 27071174 27087123 + ClCG11G013855.1 Cla11g01358 1358
4 9156514 9157795 - CmaCh04G018170.1 Cma04g01817 1817
4 9173360 9178267 - CmaCh04G018200.1 Cma04g01820 1820
10 4048023 4048956 - MELO3C011890.2.1 Cme10g00636 636
10 4072903 4078129 - MELO3C011885.2.1 Cme10g00640 640
10 17864102 17868564 + PI0002487.1 Cmetu10g0989 989
4 9758309 9759058 - CmoCh04G019120.1 Cmo04g01912 1912
4 9774565 9779282 - CmoCh04G019170.1 Cmo04g01917 1917
6 2517799 2518851 + CmPI595203_06g002290.1 Cmu06g0229 229
11 26117749 26133194 + CmPI595203_11g013930.1 Cmu11g1393 1393
8 7361201 7367638 + Conep08aG0075700.1 Cone8ag0733 733
8 7373059 7377943 - Conep08aG0075900.1 Cone8ag0735 735
13 8969811 8971892 + Conep13aG0115700.1 Cone13ag1125 1125
13 8979250 8981331 + Conep13aG0116000.1 Cone13ag1128 1128
13 8987230 8987842 - Conep13aG0116300.1 Cone13ag1131 1131
19 8005163 8005962 - Conep19aG0114400.1 Cone19ag1110 1110
1 9780244 9780990 - Cp4.1LG01g16050.1 Cpe01g01601 1601
1 9795808 9800548 - Cp4.1LG01g16060.1 Cpe01g01605 1605
9 3944299 3949906 + Cp4.1LG09g06150.1 Cpe09g00571 571
6 3567285 3568337 + CrPI670011_06g010000.1 Cre06g1000 1000
11 29745967 29753312 + CrPI670011_11g018140.1 Cre11g1814 1814
10 52071613 52077059 + Hsped.10g15320.1 Hepe10g1532 1532
13 557721 562184 + Lag0039871.1 Lac13g0075 75
4 6001152 6001880 - Lsi04G006570.1 Lsi04g00657 657
4 6028536 6033930 - Lsi04G006610.1 Lsi04g00661 661
6 42014091 42019464 - Sed0015155.1 Sed06g1736 1736
4 623939 629348 + Tan0019643.1 Tan04g0086 86
1 19702806 19710688 - Vvi1g1161 Vvi1g1161 1161
1 19710736 19712696 - Vvi1g1162 Vvi1g1162 1162
1 19713107 19715139 - Vvi1g1163 Vvi1g1163 1163
1 19723130 19728782 + Vvi1g1164 Vvi1g1164 1164
1 19729450 19730764 + Vvi1g1165 Vvi1g1165 1165
1 19730784 19737152 - Vvi1g1166 Vvi1g1166 1166
1 19746048 19748206 + Vvi1g1167 Vvi1g1167 1167
1 19756000 19763729 - Vvi1g1168 Vvi1g1168 1168
1 19768991 19771314 + Vvi1g1169 Vvi1g1169 1169
1 19772665 19777638 - Vvi1g1170 Vvi1g1170 1170
       

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