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
Vvi18g1180 . . Bda01g00652 . . . . . Cmo04g02531 Cmo15g00643 . . . . . . Cpe13g00656 Bhi04g01832 . . . Hepe02g2750 . . Cla08g00652 Cam08g1082 Cec08g0667 Cco08g0776 Clacu08g0785 . Cre08g0591 Cone4ag1446 Cone7ag1486 . . . . . Cme03g00427 . . . . . . . . . . . . . Car04g02329 Car15g00584 . . . . . . . . . . . . . . . . Lsi08g00511 . Chy03g00572 .
Vvi18g1181 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1182 . . . . . . . . . . Cma01g01016 . Car01g00897 . . . . Bhi04g02196 . . . . . . . . . . . . . . . Cone17ag0804 Cone20ag0409 . . . . . . . . . . . . . Cmo01g01058 . . . . . . Cpe02g00861 . . . . . . . . . . . . . . . . Chy03g00809 .
Vvi18g1183 . . . Bda03g00026 . . Bma04g00024 . . . Cma01g01015 . Car01g00896 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo01g01057 . . . . . . . . . . . . . . . . . . . . . . . Chy03g00810 .
Vvi18g1184 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1539 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1185 Blo01g01318 . Bda01g00686 . . . . Bma01g02103 . . . Cma09g01064 . . . Cpe06g00867 . Bhi04g02156 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo09g01073 . . . Car09g00967 . Cpe02g00865 . . . . . . . . . . . . . . Lsi08g00272 . Chy03g00836 .
Vvi18g1186 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1187 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1188 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1189 . Blo12g01112 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag1413 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 33517281 33521353 - Bda032910 Bda01g00652 652
1 34018412 34019401 - Bda002722.1 Bda01g00686 686
3 447265 448543 + Bda015959.1 Bda03g00026 26
4 45227193 45231886 + XM_039028157.1 Bhi04g01832 1832
4 58537081 58537920 + XM_039030035.1 Bhi04g02156 2156
4 60397890 60401884 + XM_039028407.1 Bhi04g02196 2196
1 50421234 50422247 - BLOR01318 Blo01g01318 1318
12 28789262 28790563 - BLOR05131 Blo12g01112 1112
1 77140411 77141400 - Bma002927.1 Bma01g02103 2103
4 306459 307752 + Bma018475.1 Bma04g00024 24
8 17163423 17164882 - CaPI482276_08g010820.1 Cam08g1082 1082
1 8465481 8467237 - Carg26861-RA Car01g00896 896
1 8469667 8474765 + Carg26862-RA Car01g00897 897
4 18764937 18769609 - Carg15763-RA Car04g02329 2329
9 6071542 6072456 + Carg26644-RA Car09g00967 967
15 3224526 3229324 + Carg01571-RA Car15g00584 584
8 19538892 19555728 - CcPI632755_08g007760.1 Cco08g0776 776
8 18379594 18381073 - CePI673135_08g006670.1 Cec08g0667 667
3 8152002 8156010 - Chy3G055520.1 Chy03g00572 572
3 11219991 11229451 - Chy3G057890.1 Chy03g00809 809
3 11247863 11249416 + Chy3G057900.1 Chy03g00810 810
3 11582426 11583442 - Chy3G058160.1 Chy03g00836 836
8 17882056 17883540 - ClG42_08g0078500.10 Clacu08g0785 785
8 18724501 18740351 - ClCG08G006310.2 Cla08g00652 652
1 7452552 7454233 - CmaCh01G010150.1 Cma01g01015 1015
1 7457018 7462001 + CmaCh01G010160.1 Cma01g01016 1016
9 5598124 5599164 + CmaCh09G010640.1 Cma09g01064 1064
3 5966702 5971364 + MELO3C008426.2.1 Cme03g00427 427
1 8495265 8496792 - CmoCh01G010570.1 Cmo01g01057 1057
1 8497567 8504693 + CmoCh01G010580.1 Cmo01g01058 1058
4 18596607 18601152 - CmoCh04G025310.1 Cmo04g02531 2531
9 5816960 5818000 + CmoCh09G010730.1 Cmo09g01073 1073
15 3121936 3126309 + CmoCh15G006430.1 Cmo15g00643 643
4 11479275 11481846 - Conep04aG0149800.1 Cone4ag1446 1446
4 11880067 11882733 - Conep04aG0159100.1 Cone4ag1539 1539
7 10091266 10093615 + Conep07aG0145500.1 Cone7ag1413 1413
7 10425499 10427383 + Conep07aG0152900.1 Cone7ag1486 1486
17 6359994 6361698 + Conep17aG0082200.1 Cone17ag0804 804
20 1985749 1987795 + Conep20aG0042300.1 Cone20ag0409 409
2 5757839 5762784 + Cp4.1LG02g00110.1 Cpe02g00861 861
2 5804442 5805311 - Cp4.1LG02g00050.1 Cpe02g00865 865
6 5657279 5658440 + Cp4.1LG06g07900.1 Cpe06g00867 867
13 6210136 6214760 - Cp4.1LG13g04270.1 Cpe13g00656 656
8 18826651 18828154 - CrPI670011_08g005910.1 Cre08g0591 591
2 76016297 76020540 - Hsped.02g27500.1 Hepe02g2750 2750
8 6816193 6817209 + Lsi08G002720.1 Lsi08g00272 272
8 13025417 13036371 - Lsi08G005110.1 Lsi08g00511 511
18 13073664 13087048 - Vvi18g1180 Vvi18g1180 1180
18 13112574 13112793 + Vvi18g1181 Vvi18g1181 1181
18 13133828 13157022 - Vvi18g1182 Vvi18g1182 1182
18 13176555 13178357 + Vvi18g1183 Vvi18g1183 1183
18 13191893 13196265 + Vvi18g1184 Vvi18g1184 1184
18 13199059 13200267 - Vvi18g1185 Vvi18g1185 1185
18 13208993 13210315 + Vvi18g1186 Vvi18g1186 1186
18 13231124 13232440 - Vvi18g1187 Vvi18g1187 1187
18 13277541 13280722 + Vvi18g1188 Vvi18g1188 1188
18 13303081 13304738 + Vvi18g1189 Vvi18g1189 1189
       

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