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
Vvi3g856 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g857 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g858 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g859 . . . . . Bpe12g00720 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa07g00645 . Cme01g00158 . Blo13g00205 Bda15g00481 . . . . Bma08g00030 . . . . Cma19g00491 . . . . . . . . . . . Cla09g01620 Cam09g1529 Cec09g1785 Cco09g1868 . . Cre01g0776 . . Chy01g00166 .
Vvi3g860 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g861 . Blo03g00041 Bda06g01135 . . . . Bma12g00326 . . . . . . . . . . . . . . . . Cla10g00940 Cam10g0960 Cec10g0997 Cco10g0956 Clacu10g0985 Cmu10g1768 Cre10g1143 . Cone8ag1034 . . . . . . . . . . . . . . . . Cmo16g00302 . . . . Cpe14g00236 . . . . . . . . . . . . . . . . . . .
Vvi3g862 Blo02g00897 . . . . . . . . . . . . . . . . . . . . . . . Cla10g00937 Cam10g0958 Cec10g0996 Cco10g0955 Clacu10g0982 Cmu10g1767 Cre10g1141 Cone12ag1008 . Cone3ag1072 Cone10ag1085 . . . . . . . . . . . . . Cmo04g00443 . . . . . . Cpe01g00372 . . . . . . . . . . . . . . . . . .
Vvi3g863 Blo02g00878 . . . Bpe07g00342 . . . . . . . . . . . . . . . . . . . Cla10g00936 Cam10g0957 Cec10g0995 Cco10g0954 . . Cre10g1140 . . . . . . . . . . . . . . . . Sed07g1161 . . . . . . . . Bhi11g01071 Tan01g0574 Cmetu07g2119 . . Mch10g0385 . . . . . . . . . . . .
Vvi3g864 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g865 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 40272900 40277454 - Bda022931.1 Bda06g01135 1135
15 7986106 7989206 + Bda012310.1 Bda15g00481 481
11 31636505 31640399 + XM_039049081.1 Bhi11g01071 1071
2 33941578 33944872 + BLOR10608 Blo02g00878 878
2 34652310 34671251 + BLOR10627 Blo02g00897 897
3 1708961 1713172 - BLOR11222 Blo03g00041 41
13 8451146 8455228 + BLOR05486 Blo13g00205 205
8 480401 483499 + Bma027023.1 Bma08g00030 30
12 5174807 5178539 + Bma007243.1 Bma12g00326 326
7 2690408 2693573 - Bpe021152.2 Bpe07g00342 342
12 12737475 12738992 - Bpe005981.1 Bpe12g00720 720
9 25671835 25676258 - CaPI482276_09g015290.1 Cam09g1529 1529
10 21562687 21566092 - CaPI482276_10g009570.1 Cam10g0957 957
10 21574564 21578298 - CaPI482276_10g009580.1 Cam10g0958 958
10 21632937 21641650 + CaPI482276_10g009600.1 Cam10g0960 960
9 31898275 31902694 + CcPI632755_09g018680.1 Cco09g1868 1868
10 20739044 20742457 - CcPI632755_10g009540.1 Cco10g0954 954
10 20745503 20748775 - CcPI632755_10g009550.1 Cco10g0955 955
10 20811291 20820021 + CcPI632755_10g009560.1 Cco10g0956 956
9 33553224 33557647 + CePI673135_09g017850.1 Cec09g1785 1785
10 22448473 22451882 - CePI673135_10g009950.1 Cec10g0995 995
10 22454872 22458536 - CePI673135_10g009960.1 Cec10g0996 996
10 22509998 22523362 + CePI673135_10g009970.1 Cec10g0997 997
1 1143317 1147175 - Chy1G001660.1 Chy01g00166 166
10 21172914 21182935 - ClG42_10g0098200.10 Clacu10g0982 982
10 21229151 21245133 + ClG42_10g0098500.10 Clacu10g0985 985
9 32397675 32402494 + ClCG09G016500.1 Cla09g01620 1620
10 22132516 22136450 - ClCG10G009780.1 Cla10g00936 936
10 22139219 22143113 - ClCG10G009790.1 Cla10g00937 937
10 22196325 22205290 + ClCG10G009810.1 Cla10g00940 940
19 5832576 5838352 - CmaCh19G004910.1 Cma19g00491 491
1 1121796 1125310 - MELO3C018558.2.1 Cme01g00158 158
7 118437 121832 + PI0024769.1 Cmetu07g2119 2119
4 2194771 2198125 + CmoCh04G004430.1 Cmo04g00443 443
16 1387655 1394389 - CmoCh16G003020.1 Cmo16g00302 302
10 21780823 21790846 - CmPI595203_10g017670.1 Cmu10g1767 1767
10 21844396 21853086 + CmPI595203_10g017680.1 Cmu10g1768 1768
3 29374131 29374697 - Conep03aG0157500.1 Cone3ag1072 1072
8 9563588 9567433 - Conep08aG0106200.1 Cone8ag1034 1034
10 7529978 7530762 - Conep10aG0111200.1 Cone10ag1085 1085
12 8529566 8532501 + Conep12aG0103600.1 Cone12ag1008 1008
1 2140189 2144026 + Cp4.1LG01g02950.1 Cpe01g00372 372
14 1371709 1377180 - Cp4.1LG14g04720.1 Cpe14g00236 236
1 8373674 8377690 - CrPI670011_01g007760.1 Cre01g0776 776
10 23486000 23489413 - CrPI670011_10g011400.1 Cre10g1140 1140
10 23492456 23496172 - CrPI670011_10g011410.1 Cre10g1141 1141
10 23550848 23559573 + CrPI670011_10g011430.1 Cre10g1143 1143
7 4638790 4642663 + CsaV3_7G007440.1 Csa07g00645 645
10 2560285 2568062 + MC10g0316 Mch10g0385 385
7 8695297 8701007 - Sed0014122.1 Sed07g1161 1161
1 5346630 5350289 + Tan0016797.1 Tan01g0574 574
3 10688975 10693463 - Vvi3g856 Vvi3g856 856
3 10700917 10703632 + Vvi3g857 Vvi3g857 857
3 10713058 10717173 - Vvi3g858 Vvi3g858 858
3 10777678 10805376 + Vvi3g859 Vvi3g859 859
3 10807576 10824893 + Vvi3g860 Vvi3g860 860
3 10825482 10834289 - Vvi3g861 Vvi3g861 861
3 10861542 10868308 + Vvi3g862 Vvi3g862 862
3 10899747 10904643 + Vvi3g863 Vvi3g863 863
3 10904729 10904951 + Vvi3g864 Vvi3g864 864
3 10909099 10909219 - Vvi3g865 Vvi3g865 865
       

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