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
Vvi17g846 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g847 . . Bda06g00619 . . . . Bma12g01057 Cmo13g00790 Cmo18g00158 . . . . . Cpe20g00344 . . . . . . . . . . . . . . . Cone2ag0936 Cone16ag0067 . . Lsi02g00423 Csa01g00891 Chy12g01232 Cme12g01656 . Blo15g00248 Bda11g01646 . Bpe07g00861 . . . Sed01g1616 . . Cma13g00760 Cma18g00196 Car13g00612 Car18g00190 Cpe09g00997 . Bhi08g01669 Tan05g1955 Cmetu12g1893 Lac10g0499 Hepe07g2193 . . Cla03g00292 Cam03g0310 Cec03g0305 Cco03g0318 Clacu03g0311 Cmu03g0921 Cre03g0612 . . . .
Vvi17g848 . . . Bda15g00537 Bpe12g00673 . . . Cmo13g00791 Cmo18g00159 . . . . . Cpe20g00343 . . . . . . . . . . . . . . . Cone2ag0937 Cone16ag0066 . . Lsi02g00424 Csa01g00892 . Cme12g01655 Blo13g00151 . . . Bpe07g00862 . . Bma08g00078 Sed08g2481 . . Cma13g00761 Cma18g00197 Car13g00613 Car18g00191 Cpe09g00996 . Bhi08g01670 Tan05g1953 Cmetu12g0311 Lac10g0500 Hepe07g2192 . . . . . . . . . . . . .
Vvi17g849 Blo04g00713 . . . . . . . Cmo13g00792 Cmo18g00160 . . . . . Cpe20g00342 . . . . . . . . . . . . . . . Cone2ag0938 Cone16ag0065 . . Lsi02g00425 Csa01g00893 Chy12g01231 Cme12g01654 . . . . . Bpe15g00658 . . Sed08g2480 . . Cma13g00762 Cma18g00198 Car13g00614 Car18g00192 Cpe09g00995 . Bhi08g01671 Tan05g1952 Cmetu03g2261 Lac10g0501 Hepe07g2191 . . Cla03g00293 . Cec03g0306 Cco03g0319 . Cmu03g0922 Cre03g0613 . . . .
Vvi17g850 . . Bda06g00620 Bda15g00536 Bpe12g00674 . . . . . . . . . . Cpe20g00341 . . . . . . . . . . . . . . . Cone2ag0939 Cone16ag0064 . . . Csa01g00904 . . . . . . . . . Bma08g00077 . . . . . Car13g00615 Car18g00195 Cpe09g00994 . . . . . . . . . . . . . . . . . . .
Vvi17g851 . . . Bda15g00535 . . . . Cmo13g00794 Cmo18g00165 . . . . . . . Bhi02g00597 . . . . . . Cla06g01705 . . . . . . . . . . Lsi02g00426 Csa01g00905 Chy12g01223 Cme12g01649 Blo13g00153 Blo15g00247 . . Bpe07g00863 . . . . Cmo10g00092 . Cma13g00766 . . . . . . . . . . . . Cla03g00297 . . . . . . . . Chy02g02614 .
Vvi17g852 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g853 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g854 . . . Bda15g00533 . . . . . Cmo18g00168 Cma10g00089 . . . . . Cpe04g01587 Bhi02g00596 . . . . . . . . . . . . . . . . . Lsi02g00427 Csa01g00906 Chy12g01222 Cme12g01648 . . . . . . . . . Cmo10g00091 . . Cma18g00201 . . . . Bhi08g01673 . . . . . . . . . . . . . . . . .
Vvi17g855 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 8469293 8470302 + Bda023890.1 Bda06g00619 619
6 8483640 8486852 - Bda023891.1 Bda06g00620 620
11 50499283 50500074 - Bda008537.1 Bda11g01646 1646
15 8378907 8380435 + Bda012365.1 Bda15g00533 533
15 8414481 8415902 + Bda012368.1 Bda15g00535 535
15 8417589 8420835 + Bda012369.2 Bda15g00536 536
15 8426015 8426833 + Bda012370.1 Bda15g00537 537
2 11273521 11274105 - XM_039024400.1 Bhi02g00596 596
2 11302544 11305340 - XM_039024314.1 Bhi02g00597 597
8 46957420 46958777 + XM_039038907.1 Bhi08g01669 1669
8 46962808 46966294 - XM_039037992.1 Bhi08g01670 1670
8 46970693 46976439 - XM_039038641.1 Bhi08g01671 1671
8 47004768 47006505 - XM_039039537.1 Bhi08g01673 1673
4 6579510 6583553 + BLOR13625 Blo04g00713 713
13 4767993 4768955 - BLOR05432 Blo13g00151 151
13 5117729 5120250 + BLOR05434 Blo13g00153 153
15 2578273 2579948 + BLOR06641 Blo15g00247 247
15 2588251 2589239 - BLOR06642 Blo15g00248 248
8 954251 957572 + Bma027076.1 Bma08g00077 77
8 960702 961664 + Bma027077.1 Bma08g00078 78
12 42646747 42647753 + Bma008406.1 Bma12g01057 1057
7 14738483 14739522 + Bpe021704.1 Bpe07g00861 861
7 14739644 14740604 - Bpe021705.1 Bpe07g00862 862
7 14741945 14743373 - Bpe021706.1 Bpe07g00863 863
12 12384988 12385950 - Bpe005932.1 Bpe12g00673 673
12 12388326 12391631 - Bpe005933.1 Bpe12g00674 674
15 17302430 17303740 - Bpe001591.1 Bpe15g00658 658
3 4340976 4342476 + CaPI482276_03g003100.1 Cam03g0310 310
13 7846979 7848165 + Carg07560-RA Car13g00612 612
13 7848577 7850964 - Carg07561-RA Car13g00613 613
13 7851990 7858980 - Carg07562-RA Car13g00614 614
13 7869463 7873159 - Carg07563-RA Car13g00615 615
18 1045202 1045904 + Carg06757-RA Car18g00190 190
18 1047066 1048073 - Carg06758-RA Car18g00191 191
18 1051246 1057478 - Carg06759-RA Car18g00192 192
18 1109202 1109715 - Carg06762-RA Car18g00195 195
3 3550093 3551585 + CcPI632755_03g003180.1 Cco03g0318 318
3 3552622 3562753 - CcPI632755_03g003190.1 Cco03g0319 319
3 3476281 3477046 + CePI673135_03g003050.1 Cec03g0305 305
3 3478821 3480281 - CePI673135_03g003060.1 Cec03g0306 306
2 29313281 29315050 - Chy2G048810.1 Chy02g02614 2614
12 16943230 16945650 + Chy12G218220.1 Chy12g01222 1222
12 16949768 16951562 + Chy12G218230.1 Chy12g01223 1223
12 17021797 17030370 + Chy12G218310.1 Chy12g01231 1231
12 17031406 17032162 - Chy12G218320.1 Chy12g01232 1232
3 3637277 3638783 + ClG42_03g0031100.10 Clacu03g0311 311
3 3579308 3580076 + ClCG03G003060.1 Cla03g00292 292
3 3581831 3591030 - ClCG03G003070.2 Cla03g00293 293
3 3652409 3656040 - ClCG03G003130.2 Cla03g00297 297
6 30628085 30630367 + ClCG06G017460.1 Cla06g01705 1705
10 365303 367138 - CmaCh10G000890.1 Cma10g00089 89
13 6608034 6609428 + CmaCh13G007600.1 Cma13g00760 760
13 6609931 6610953 - CmaCh13G007610.1 Cma13g00761 761
13 6614008 6619152 - CmaCh13G007620.1 Cma13g00762 762
13 6622562 6632459 - CmaCh13G007660.1 Cma13g00766 766
18 1027339 1028685 + CmaCh18G001960.1 Cma18g00196 196
18 1030468 1031475 - CmaCh18G001970.1 Cma18g00197 197
18 1035052 1041991 - CmaCh18G001980.1 Cma18g00198 198
18 1084997 1088972 - CmaCh18G002010.1 Cma18g00201 201
12 23574628 23580076 + MELO3C002311.2.1 Cme12g01648 1648
12 23585241 23587647 + MELO3C002310.2.1 Cme12g01649 1649
12 23611151 23616657 + MELO3C002307.2.1 Cme12g01654 1654
12 23617767 23621021 + MELO3C002306.2.1 Cme12g01655 1655
12 23621452 23622862 - MELO3C002305.2.1 Cme12g01656 1656
3 261305 262476 - PI0013704.1 Cmetu03g2261 2261
12 2688415 2692313 - PI0003613.1 Cmetu12g0311 311
12 2686607 2687893 + PI0001304.1 Cmetu12g1893 1893
10 399381 401653 - CmoCh10G000910.1 Cmo10g00091 91
10 402352 403938 - CmoCh10G000920.1 Cmo10g00092 92
13 7530119 7531250 + CmoCh13G007900.1 Cmo13g00790 790
13 7531989 7533011 - CmoCh13G007910.1 Cmo13g00791 791
13 7535561 7542478 - CmoCh13G007920.1 Cmo13g00792 792
13 7543201 7544953 - CmoCh13G007940.1 Cmo13g00794 794
18 1098992 1100177 + CmoCh18G001580.1 Cmo18g00158 158
18 1101044 1104148 - CmoCh18G001590.1 Cmo18g00159 159
18 1105084 1109088 - CmoCh18G001600.1 Cmo18g00160 160
18 1158785 1160761 - CmoCh18G001650.1 Cmo18g00165 165
18 1168228 1169685 - CmoCh18G001680.1 Cmo18g00168 168
3 3879363 3880131 + CmPI595203_03g009210.1 Cmu03g0921 921
3 3881890 3883350 - CmPI595203_03g009220.1 Cmu03g0922 922
2 35093322 35094399 + Conep02aG0197000.1 Cone2ag0936 936
2 35094570 35096293 - Conep02aG0197100.1 Cone2ag0937 937
2 35096959 35100532 - Conep02aG0197200.1 Cone2ag0938 938
2 35101796 35105237 - Conep02aG0197300.1 Cone2ag0939 939
16 329697 332656 + Conep16aG0006500.1 Cone16ag0064 64
16 334344 337889 + Conep16aG0006600.1 Cone16ag0065 65
16 338609 340652 + Conep16aG0006700.1 Cone16ag0066 66
16 341205 342030 - Conep16aG0006800.1 Cone16ag0067 67
4 12371286 12375150 + Cp4.1LG04g15950.1 Cpe04g01587 1587
9 8807089 8810701 + Cp4.1LG09g09920.1 Cpe09g00994 994
9 8847691 8855370 + Cp4.1LG09g10030.1 Cpe09g00995 995
9 8856249 8858884 + Cp4.1LG09g10010.1 Cpe09g00996 996
9 8859628 8860814 - Cp4.1LG09g10080.1 Cpe09g00997 997
20 1931784 1935501 + Cp4.1LG20g03420.1 Cpe20g00341 341
20 1946811 1953317 + Cp4.1LG20g03380.1 Cpe20g00342 342
20 1954778 1957607 + Cp4.1LG20g03390.1 Cpe20g00343 343
20 1957893 1959234 - Cp4.1LG20g03470.1 Cpe20g00344 344
3 5047659 5049205 + CrPI670011_03g006120.1 Cre03g0612 612
3 5050254 5060198 - CrPI670011_03g006130.1 Cre03g0613 613
1 5541607 5542854 + CsaV3_1G008910.1 Csa01g00891 891
1 5543366 5546924 - CsaV3_1G008920.1 Csa01g00892 892
1 5547302 5553208 - CsaV3_1G008930.1 Csa01g00893 893
1 5630767 5634746 - CsaV3_1G009040.1 Csa01g00904 904
1 5635608 5637524 + CsaV3_1G009050.1 Csa01g00905 905
1 5639661 5641504 + CsaV3_1G009060.1 Csa01g00906 906
7 66312966 66318729 + Hsped.07g21910.1 Hepe07g2191 2191
7 66320229 66322877 + Hsped.07g21920.1 Hepe07g2192 2192
7 66327895 66329538 - Hsped.07g21930.1 Hepe07g2193 2193
10 3829821 3830586 + Lag0024544.1 Lac10g0499 499
10 3834748 3838531 - Lag0024545.1 Lac10g0500 500
10 3844058 3850636 - Lag0024546.1 Lac10g0501 501
2 3499324 3500852 + Lsi02G004230.1 Lsi02g00423 423
2 3502020 3503329 - Lsi02G004240.1 Lsi02g00424 424
2 3507075 3515757 - Lsi02G004250.1 Lsi02g00425 425
2 3517047 3522579 - Lsi02G004260.1 Lsi02g00426 426
2 3522958 3526699 - Lsi02G004270.1 Lsi02g00427 427
1 11762776 11764214 - Sed0015834.1 Sed01g1616 1616
8 37717813 37723674 + Sed0007484.1 Sed08g2480 2480
8 37726400 37727390 + Sed0024178.1 Sed08g2481 2481
5 69049380 69055314 + Tan0005565.1 Tan05g1952 1952
5 69060536 69064289 + Tan0016697.1 Tan05g1953 1953
5 69156502 69157652 - Tan0016877.1 Tan05g1955 1955
17 11125690 11128290 + Vvi17g846 Vvi17g846 846
17 11135752 11137581 + Vvi17g847 Vvi17g847 847
17 11137853 11141274 - Vvi17g848 Vvi17g848 848
17 11153635 11159809 - Vvi17g849 Vvi17g849 849
17 11172237 11176735 - Vvi17g850 Vvi17g850 850
17 11179543 11181431 - Vvi17g851 Vvi17g851 851
17 11181906 11182219 + Vvi17g852 Vvi17g852 852
17 11182220 11182762 + Vvi17g853 Vvi17g853 853
17 11202227 11204433 + Vvi17g854 Vvi17g854 854
17 11213164 11213993 + Vvi17g855 Vvi17g855 855
       

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