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
Vvi19g4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0214 Cone9ag0245 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g6 . . . . Bpe09g00274 Bpe08g00996 Bma10g00467 . . Cmo04g00701 . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1012 . . . . . Blo07g01003 Blo10g00715 . . . Bpe03g00882 Bma07g01157 . . . . . . Car04g00605 Car16g00425 . Cpe01g00589 . . . . . . . Cla07g00994 Cam07g1069 Cec07g1141 Cco07g1119 Clacu07g1042 Cmu07g1034 Cre07g1410 . . . .
Vvi19g7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g8 . . . . . . . . . . Cma01g01278 . Car01g01093 . Sed04g2513 . Cpe02g00647 Bhi09g03588 Tan01g4237 Cmetu07g0669 . Hepe01g1479 Mch11g0969 . Cla11g01671 Cam11g1737 Cec11g1763 Cco11g1764 Clacu11g1896 Cmu11g1707 Cre11g2121 . . Cone14ag1013 . Lsi04g01965 Csa04g02244 . . . . . . Bpe11g00430 . . . . Cmo01g01331 Cmo09g00669 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g9 Blo03g00718 . . . . . . . . . . . . Car09g00605 Sed04g2511 Cpe06g00537 . Bhi09g03586 Tan01g4239 Cmetu07g1432 . Hepe01g1478 Mch11g0970 . Cla11g01672 Cam11g1738 Cec11g1764 Cco11g1765 Clacu11g1897 Cmu11g1708 Cre11g2122 . . . . Lsi04g01966 Csa04g02245 . . . . . Bda12g00751 Bpe11g00431 . . Bma14g00276 . . Cmo09g00667 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g10 . . . . . . . . . . . . . Car09g00604 . . . Bhi09g03584 . . . . Mch11g0971 . Cla11g01673 . . . . . . . . . . Lsi04g01967 Csa04g02246 . . . . . . . . . . . . Cmo09g00666 . . . . Cpe14g00338 . . . . . . . . . . . . . . . . . . .
Vvi19g11 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla07g00987 Cam07g1061 Cec07g1132 Cco07g1109 Clacu07g1033 Cmu07g1026 Cre07g1404 . . . .
Vvi19g12 . . . . Bpe09g00273 . . Bma13g00915 . . Cma01g01277 . Car01g01092 . . . Cpe02g00648 Bhi09g03581 Tan01g4242 . . . . . . . . . . . . . . . . Lsi04g01968 Csa04g02247 . . . Blo10g00716 . Bda12g00798 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g13 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
12 35451669 35452702 + Bda009234.1 Bda12g00751 751
12 36977730 36983997 + Bda009301.1 Bda12g00798 798
9 89675192 89682420 + XM_039042378.1 Bhi09g03581 3581
9 89684159 89686696 + XM_039042381.1 Bhi09g03584 3584
9 89686555 89689205 - XM_039042386.1 Bhi09g03586 3586
9 89703116 89704252 + XM_039043388.1 Bhi09g03588 3588
3 30383615 30385460 + BLOR11899 Blo03g00718 718
7 29611452 29621269 + BLOR18935 Blo07g01003 1003
10 22743438 22747158 - BLOR02505 Blo10g00715 715
10 22751686 22758549 - BLOR02506 Blo10g00716 716
7 45818739 45823484 - Bma026389.1 Bma07g01157 1157
10 5287820 5293976 + Bma004138.2 Bma10g00467 467
13 39553039 39558397 - Bma009992.1 Bma13g00915 915
14 3375597 3378353 - Bma010686.10 Bma14g00276 276
3 28584284 28587909 - Bpe012787.1 Bpe03g00882 882
8 12293073 12297968 - Bpe023121.1 Bpe08g00996 996
9 2027352 2033477 + Bpe023943.3 Bpe09g00273 273
9 2034941 2037559 + Bpe023944.1 Bpe09g00274 274
11 3281553 3281825 - Bpe003803.1 Bpe11g00430 430
11 3283567 3285610 + Bpe003804.1 Bpe11g00431 431
7 24967239 24975372 + CaPI482276_07g010610.1 Cam07g1061 1061
7 25029430 25032301 + CaPI482276_07g010690.1 Cam07g1069 1069
11 29972628 29977659 - CaPI482276_11g017370.1 Cam11g1737 1737
11 29980484 29982928 + CaPI482276_11g017380.1 Cam11g1738 1738
1 10221498 10227269 + Carg14757-RA Car01g01092 1092
1 10229290 10230145 + Carg14758-RA Car01g01093 1093
4 3471979 3476185 - Carg13100-RA Car04g00605 605
9 3429789 3432688 + Carg03087-RA Car09g00604 604
9 3431988 3434850 - Carg03088-RA Car09g00605 605
16 2656510 2658451 + Carg11392-RA Car16g00425 425
7 24655394 24655603 + CcPI632755_07g011090.1 Cco07g1109 1109
7 24727808 24730405 + CcPI632755_07g011190.1 Cco07g1119 1119
11 30377102 30382024 - CcPI632755_11g017640.1 Cco11g1764 1764
11 30384397 30386771 + CcPI632755_11g017650.1 Cco11g1765 1765
7 26559964 26570364 + CePI673135_07g011320.1 Cec07g1132 1132
7 26628683 26631386 + CePI673135_07g011410.1 Cec07g1141 1141
11 31839430 31844796 - CePI673135_11g017630.1 Cec11g1763 1763
11 31847629 31850077 + CePI673135_11g017640.1 Cec11g1764 1764
7 24761696 24767807 + ClG42_07g0103300.10 Clacu07g1033 1033
7 24824821 24826605 + ClG42_07g0104200.10 Clacu07g1042 1042
11 30005248 30005883 - ClG42_11g0189600.10 Clacu11g1896 1896
11 30008680 30011119 + ClG42_11g0189700.10 Clacu11g1897 1897
7 26083570 26097950 + ClCG07G010360.2 Cla07g00987 987
7 26153989 26155773 + ClCG07G010450.2 Cla07g00994 994
11 30341846 30342753 - ClCG11G017040.1 Cla11g01671 1671
11 30345458 30348635 + ClCG11G017050.1 Cla11g01672 1672
11 30348052 30359675 - ClCG11G017060.2 Cla11g01673 1673
1 9192302 9198519 + CmaCh01G012770.1 Cma01g01277 1277
1 9200080 9201280 + CmaCh01G012780.1 Cma01g01278 1278
7 21064862 21066219 - PI0020010.1 Cmetu07g0669 669
7 21069423 21071975 + PI0029184.1 Cmetu07g1432 1432
1 10568061 10578870 + CmoCh01G013310.1 Cmo01g01331 1331
4 3479202 3483094 - CmoCh04G007010.1 Cmo04g00701 701
9 3333911 3336640 + CmoCh09G006660.1 Cmo09g00666 666
9 3336382 3338100 - CmoCh09G006670.1 Cmo09g00667 667
9 3340757 3341386 + CmoCh09G006690.1 Cmo09g00669 669
7 25006223 25012334 + CmPI595203_07g010260.1 Cmu07g1026 1026
7 25069349 25071133 + CmPI595203_07g010340.1 Cmu07g1034 1034
11 29258263 29258898 - CmPI595203_11g017070.1 Cmu11g1707 1707
11 29261696 29264136 + CmPI595203_11g017080.1 Cmu11g1708 1708
6 1016608 1018525 - Conep06aG0021600.1 Cone6ag0214 214
9 1042654 1044496 - Conep09aG0024800.1 Cone9ag0245 245
14 8477347 8480330 - Conep14aG0103200.1 Cone14ag1012 1012
14 8484086 8484829 - Conep14aG0103300.1 Cone14ag1013 1013
1 3404293 3408670 - Cp4.1LG01g00590.1 Cpe01g00589 589
2 3982467 3985758 - Cp4.1LG02g02240.1 Cpe02g00647 647
2 3987382 3993600 - Cp4.1LG02g02220.1 Cpe02g00648 648
6 3205273 3208336 - Cp4.1LG06g05380.1 Cpe06g00537 537
14 2063042 2066188 + Cp4.1LG14g03730.1 Cpe14g00338 338
7 28939380 28949864 + CrPI670011_07g014040.1 Cre07g1404 1404
7 29005127 29007727 + CrPI670011_07g014100.1 Cre07g1410 1410
11 32926327 32926962 - CrPI670011_11g021210.1 Cre11g2121 2121
11 32929801 32932267 + CrPI670011_11g021220.1 Cre11g2122 2122
4 23093386 23094578 - CsaV3_4G032700.1 Csa04g02244 2244
4 23096244 23099611 + CsaV3_4G032710.1 Csa04g02245 2245
4 23097432 23101989 - CsaV3_4G032720.1 Csa04g02246 2246
4 23103461 23110644 - CsaV3_4G032730.1 Csa04g02247 2247
1 80078270 80081166 - Hsped.01g14780.1 Hepe01g1478 1478
1 80084014 80085044 + Hsped.01g14790.1 Hepe01g1479 1479
4 26722912 26723545 - Lsi04G019650.1 Lsi04g01965 1965
4 26726650 26731714 + Lsi04G019660.1 Lsi04g01966 1966
4 26728233 26730956 - Lsi04G019670.1 Lsi04g01967 1967
4 26730993 26740834 - Lsi04G019680.1 Lsi04g01968 1968
11 6646195 6647544 - MC11g_new0172 Mch11g0969 969
11 6649210 6651524 + MC11g0798 Mch11g0970 970
11 6651344 6654021 - MC11g_new0173 Mch11g0971 971
4 38070540 38073091 - Sed0027291.1 Sed04g2511 2511
4 38073953 38074885 + Sed0010429.2 Sed04g2513 2513
1 107186096 107187286 - Tan0010115.1 Tan01g4237 4237
1 107197839 107205200 + Tan0012079.1 Tan01g4239 4239
1 107209875 107215444 - Tan0017584.2 Tan01g4242 4242
19 38669 39146 + Vvi19g4 Vvi19g4 4
19 44336 45540 + Vvi19g5 Vvi19g5 5
19 48206 58620 - Vvi19g6 Vvi19g6 6
19 74011 75110 + Vvi19g7 Vvi19g7 7
19 75852 77852 - Vvi19g8 Vvi19g8 8
19 79523 84532 + Vvi19g9 Vvi19g9 9
19 85757 88311 - Vvi19g10 Vvi19g10 10
19 101179 112143 + Vvi19g11 Vvi19g11 11
19 114617 145720 + Vvi19g12 Vvi19g12 12
19 147059 149556 + Vvi19g13 Vvi19g13 13
       

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