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
Vvi17g966 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g967 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g968 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g969 . . . . . . . . Cmo13g01001 Cmo18g00070 . . . . . Cpe20g00174 . . . . . . . . . . . . . . . . . . . Lsi02g00263 Csa01g00743 Chy12g01370 Cme12g01802 . . . . . . . . Sed08g2788 . . Cma13g00966 Cma18g00093 Car13g00800 Car18g00083 Cpe09g01097 . Bhi08g01335 Tan05g2152 Cmetu12g1789 Lac10g0317 Hepe07g2326 . . Cla01g01468 Cam01g1537 Cec01g1576 Cco01g1624 Clacu01g1561 Cmu01g1451 Cre01g1373 . . . .
Vvi17g970 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g971 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g972 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g973 . . . . Bpe12g00630 . . Bma12g01259 . . . . . . . Cpe20g00050 . . . . . . . . . . . . . . . . . . . Lsi02g00032 Csa01g00508 Chy12g01576 Cme12g02034 . . . . Bpe07g01066 . . . . . . Cma13g01102 . Car13g00936 . . . . . . . . . . . . . . . . . . . . .
Vvi17g974 . . Bda06g00834 . . . . . . . . . . . . Cpe20g00047 . . . . . . . . . . . . . . . . . . . Lsi02g00035 Csa01g00512 Chy12g01573 Cme12g02031 . Blo15g00049 . . Bpe07g01060 . . . . . . Cma13g01106 . Car13g00939 . . . . . . . . . . . . . . . . . . . . .
Vvi17g975 . . Bda06g00835 . . . . . . . . . . . . Cpe20g00046 . . . . . . . . . . . . . . . . . . . Lsi02g00036 . Chy12g01572 Cme12g02030 . Blo15g00048 . . . . . . . . . Cma13g01107 . Car13g00940 . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 11581808 11582797 + Bda024167.1 Bda06g00834 834
6 11584710 11586837 - Bda024168.1 Bda06g00835 835
8 40545467 40550512 - XM_039038045.1 Bhi08g01335 1335
15 363652 366122 + BLOR06442 Blo15g00048 48
15 367779 379532 - BLOR06443 Blo15g00049 49
12 45640733 45641966 + Bma008624.1 Bma12g01259 1259
7 16057879 16058868 + Bpe021903.1 Bpe07g01060 1060
7 16080707 16081928 + Bpe021909.1 Bpe07g01066 1066
12 11952975 11954272 + Bpe005890.1 Bpe12g00630 630
1 28929231 28935499 + CaPI482276_01g015370.1 Cam01g1537 1537
13 8831146 8833546 + Carg04872-RA Car13g00800 800
13 9584128 9585399 - Carg04735-RA Car13g00936 936
13 9594048 9598182 + Carg04732-RA Car13g00939 939
13 9598784 9602026 - Carg04731-RA Car13g00940 940
18 441192 450866 - Carg06648-RA Car18g00083 83
1 28927970 28934240 + CcPI632755_01g016240.1 Cco01g1624 1624
1 30345307 30351631 + CePI673135_01g015760.1 Cec01g1576 1576
12 17900373 17904954 + Chy12G219700.1 Chy12g01370 1370
12 19261979 19264992 + Chy12G221720.1 Chy12g01572 1572
12 19268024 19270424 - Chy12G221730.1 Chy12g01573 1573
12 19283284 19284431 + Chy12G221760.1 Chy12g01576 1576
1 27717900 27722083 + ClG42_01g0156100.10 Clacu01g1561 1561
1 29223170 29228487 + ClCG01G014890.2 Cla01g01468 1468
13 7538834 7543850 + CmaCh13G009660.1 Cma13g00966 966
13 8279051 8280303 - CmaCh13G011020.1 Cma13g01102 1102
13 8290909 8293744 + CmaCh13G011060.1 Cma13g01106 1106
13 8297458 8299746 - CmaCh13G011070.1 Cma13g01107 1107
18 430763 436686 - CmaCh18G000930.1 Cma18g00093 93
12 24490685 24495794 + MELO3C002160.2.1 Cme12g01802 1802
12 25815568 25818506 + MELO3C001950.2.1 Cme12g02030 2030
12 25821374 25825782 - MELO3C001949.2.1 Cme12g02031 2031
12 25836771 25838732 + MELO3C001946.2.1 Cme12g02034 2034
12 1766710 1772056 - PI0015517.1 Cmetu12g1789 1789
13 8525059 8530039 + CmoCh13G010010.1 Cmo13g01001 1001
18 476172 481659 - CmoCh18G000700.1 Cmo18g00070 70
1 28061299 28067653 + CmPI595203_01g014510.1 Cmu01g1451 1451
9 9472194 9478545 + Cp4.1LG09g10950.1 Cpe09g01097 1097
20 206824 212066 + Cp4.1LG20g00490.1 Cpe20g00046 46
20 210402 214799 - Cp4.1LG20g00530.1 Cpe20g00047 47
20 224669 228246 + Cp4.1LG20g00450.1 Cpe20g00050 50
20 992807 998080 - Cp4.1LG20g01800.1 Cpe20g00174 174
1 26915925 26922307 + CrPI670011_01g013730.1 Cre01g1373 1373
1 3392877 3394527 - CsaV3_1G005080.1 Csa01g00508 508
1 3405378 3409861 + CsaV3_1G005110.1 Csa01g00512 512
1 4728771 4734337 - CsaV3_1G007430.1 Csa01g00743 743
7 67591010 67597964 + Hsped.07g23260.1 Hepe07g2326 2326
10 2469204 2474356 - Lag0024362.1 Lac10g0317 317
2 359526 363317 - Lsi02G000320.1 Lsi02g00032 32
2 378206 380630 + Lsi02G000350.1 Lsi02g00035 35
2 379730 386414 - Lsi02G000360.1 Lsi02g00036 36
2 2249148 2258516 - Lsi02G002630.1 Lsi02g00263 263
8 39402581 39408871 - Sed0000369.1 Sed08g2788 2788
5 72251874 72257268 + Tan0001960.2 Tan05g2152 2152
17 14981192 14986226 - Vvi17g966 Vvi17g966 966
17 15022817 15030555 + Vvi17g967 Vvi17g967 967
17 15096384 15096735 + Vvi17g968 Vvi17g968 968
17 15114054 15127169 + Vvi17g969 Vvi17g969 969
17 15154114 15154728 - Vvi17g970 Vvi17g970 970
17 15172308 15173997 + Vvi17g971 Vvi17g971 971
17 15412930 15415693 - Vvi17g972 Vvi17g972 972
17 15501811 15504523 - Vvi17g973 Vvi17g973 973
17 15569451 15578036 + Vvi17g974 Vvi17g974 974
17 15591163 15596491 - Vvi17g975 Vvi17g975 975
       

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