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
Vvi1g1171 . . . . . Bpe10g00784 . . Cmo04g01918 Cmo18g00700 . Cma18g00712 . Car18g00657 Sed06g0143 Cpe09g00577 Cpe01g01606 Bhi07g01896 Tan04g0084 Cmetu10g0294 Lac13g0072 . . . . . . . . . . . . . . Lsi04g00663 . . Cme10g00641 Blo06g00828 . . . . . . . . . . Cma04g01821 . Car04g01834 . . . . . . . . . . Cla11g01357 . Cec11g1442 Cco11g1438 Clacu11g1572 Cmu11g1392 Cre11g1813 . . . .
Vvi1g1172 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1173 Blo01g00369 . Bda01g02187 . Bpe13g00524 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma01g00021 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1174 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1175 Blo01g00367 . Bda01g02185 . Bpe13g00526 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0738 . . . . . . . . . . . Bma01g00019 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1176 . . . . . . . . . Cmo18g00699 . Cma18g00711 . Car18g00656 . Cpe09g00578 . Bhi07g01897 . . . Hepe10g1531 . . . . . . . . . . . Cone8ag0739 . Lsi04g00664 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla11g01356 . Cec11g1440 . Clacu11g1571 Cmu11g1391 Cre11g1812 . . . .
Vvi1g1177 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1178 . . . . . . . . Cmo04g01919 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1179 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1180 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g00665 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57831342 57835400 - Bda004527.1 Bda01g02185 2185
1 57839586 57845959 + Bda032995 Bda01g02187 2187
7 50886033 50894329 - XM_039036138.1 Bhi07g01896 1896
7 50925546 50929962 - XM_039035897.1 Bhi07g01897 1897
1 4291730 4295970 - BLOR00367 Blo01g00367 367
1 4301240 4309081 + BLOR00369 Blo01g00369 369
6 31522169 31530025 - BLOR17411 Blo06g00828 828
1 316526 320576 - Bma000190.3 Bma01g00019 19
1 325305 343660 + Bma030161 Bma01g00021 21
10 14005456 14012345 - Bpe003090.1 Bpe10g00784 784
13 12532976 12539439 - Bpe025223 Bpe13g00524 524
13 12543580 12547602 + Bpe010231.1 Bpe13g00526 526
4 10620210 10628837 - Carg14271-RA Car04g01834 1834
18 7823182 7826244 + Carg21239-RA Car18g00656 656
18 7827208 7836330 + Carg21240-RA Car18g00657 657
11 27134531 27154658 + CcPI632755_11g014380.1 Cco11g1438 1438
11 28561759 28568016 + CePI673135_11g014400.1 Cec11g1440 1440
11 28585401 28596504 + CePI673135_11g014420.1 Cec11g1442 1442
11 26840256 26843126 + ClG42_11g0157100.10 Clacu11g1571 1571
11 26849384 26861717 + ClG42_11g0157200.10 Clacu11g1572 1572
11 27043311 27046578 + ClCG11G013840.1 Cla11g01356 1356
11 27054853 27064001 + ClCG11G013850.2 Cla11g01357 1357
4 9179924 9188352 - CmaCh04G018210.1 Cma04g01821 1821
18 6466272 6469715 + CmaCh18G007110.1 Cma18g00711 711
18 6470561 6474466 + CmaCh18G007120.1 Cma18g00712 712
10 4079847 4089053 - MELO3C011884.2.1 Cme10g00641 641
10 17850938 17861821 + PI0019769.1 Cmetu10g0294 294
4 9781512 9789924 - CmoCh04G019180.1 Cmo04g01918 1918
4 9791425 9794768 + CmoCh04G019190.1 Cmo04g01919 1919
18 8852746 8856605 + CmoCh18G006990.1 Cmo18g00699 699
18 8857779 8867261 + CmoCh18G007000.1 Cmo18g00700 700
11 26092354 26095229 + CmPI595203_11g013910.1 Cmu11g1391 1391
11 26101467 26112852 + CmPI595203_11g013920.1 Cmu11g1392 1392
8 7446774 7451567 + Conep08aG0076200.1 Cone8ag0738 738
8 7451642 7452553 - Conep08aG0076300.1 Cone8ag0739 739
1 9802155 9810601 - Cp4.1LG01g16080.1 Cpe01g01606 1606
9 3984607 3994306 - Cp4.1LG09g06100.1 Cpe09g00577 577
9 3995260 3999256 - Cp4.1LG09g06000.1 Cpe09g00578 578
11 29711394 29715745 + CrPI670011_11g018120.1 Cre11g1812 1812
11 29720372 29745784 + CrPI670011_11g018130.1 Cre11g1813 1813
10 52051005 52067371 + Hsped.10g15310.1 Hepe10g1531 1531
13 528278 530048 + Lag0039868.1 Lac13g0072 72
4 6051159 6059630 - Lsi04G006630.1 Lsi04g00663 663
4 6067578 6071856 - Lsi04G006640.1 Lsi04g00664 664
4 6071816 6076351 + Lsi04G006650.1 Lsi04g00665 665
6 1000931 1009428 - Sed0016931.2 Sed06g0143 143
4 610147 619834 + Tan0017683.2 Tan04g0084 84
1 19784550 19799430 - Vvi1g1171 Vvi1g1171 1171
1 19802032 19816465 - Vvi1g1172 Vvi1g1172 1172
1 19816504 19833346 - Vvi1g1173 Vvi1g1173 1173
1 19834918 19840992 - Vvi1g1174 Vvi1g1174 1174
1 19850529 19856793 + Vvi1g1175 Vvi1g1175 1175
1 19857099 19861937 - Vvi1g1176 Vvi1g1176 1176
1 19868495 19868696 + Vvi1g1177 Vvi1g1177 1177
1 19877397 19881935 + Vvi1g1178 Vvi1g1178 1178
1 19882931 19887719 + Vvi1g1179 Vvi1g1179 1179
1 19888621 19890374 + Vvi1g1180 Vvi1g1180 1180
       

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