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
Vvi18g870 Blo01g01548 Blo12g00917 . Bda03g00247 . . Bma04g00195 . . . . . Car01g01468 . . . . . . . . . . . . . . . . . . . . . Cone20ag0159 . Csa04g02345 Chy04g00541 . . . . . . . . . . Cmo01g01947 . . . . . . Cpe02g00147 . . . . . . . . . . . . . . . . Chy07g00077 Cme04g00631
Vvi18g871 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g872 Blo01g01549 . Bda01g00550 . Bpe02g00408 . . Bma01g02299 . . Cma01g01885 . Car01g01469 . . . . . . . . . . . . . . . . . . . Cone7ag1794 . . Lsi04g01634 Csa03g04178 Chy04g00540 . . . . . . . . . . Cmo01g01948 . . . . . . Cpe02g00146 . . . . . . . Cla05g01967 Cam05g2118 Cec05g2129 Cco05g2181 Clacu05g2106 Cmu05g1982 Cre05g2101 . . . Cme04g00630
Vvi18g873 Blo01g01550 . Bda01g00549 . Bpe02g00407 . . Bma01g02300 . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag1795 Cone17ag1315 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g874 . Blo12g00916 . Bda03g00248 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g875 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g876 . . . . . . . . . . . Cma09g00178 . . . Cpe06g00127 . . . . . . . . . . . . . . . . Cone7ag1796 . . . . . . . . . . . . . . . . Cmo09g00174 . . . Car09g00159 . . . . . . . . . . . . . . . . . . . .
Vvi18g877 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g878 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g879 . . . . . . . . Cmo05g00224 Cmo12g00443 . . . Car12g00468 . . Cpe07g00446 Bhi04g00285 . . . . . . Cla08g01521 Cam08g2012 Cec08g1588 Cco08g1723 Clacu08g1701 . Cre08g1483 Cone4ag1886 Cone7ag1797 Cone17ag1316 Cone20ag0158 . . . Cme03g01987 Blo17g00819 . Bda08g01302 . . Bpe05g00075 . Bma05g00105 . . . Cma12g00498 Cma05g00218 Car05g00178 . Cpe11g00180 . . . . . . . . . . . . . . . Lsi08g01424 Csa02g02018 Chy03g01493 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 32394869 32401128 + Bda002561.2 Bda01g00549 549
1 32416157 32417918 + Bda002562.1 Bda01g00550 550
3 2237331 2240002 - Bda016203.1 Bda03g00247 247
3 2242570 2244170 - Bda016204.1 Bda03g00248 248
8 52733587 52735495 - Bda030336.1 Bda08g01302 1302
4 6724062 6729244 - XM_039030021.1 Bhi04g00285 285
1 55148842 55163892 - BLOR01548 Blo01g01548 1548
1 55165282 55172873 - BLOR01549 Blo01g01549 1549
1 55182151 55184132 - BLOR01550 Blo01g01550 1550
12 27339185 27341791 + BLOR04935 Blo12g00916 916
12 27342804 27345450 + BLOR04936 Blo12g00917 917
17 26483341 26485838 - BLOR08365 Blo17g00819 819
1 80523334 80525125 - Bma003160.1 Bma01g02299 2299
1 80547855 80550082 - Bma003161.1 Bma01g02300 2300
4 1730702 1742769 - Bma018644.1 Bma04g00195 195
5 3318332 3320778 + Bma020801.1 Bma05g00105 105
2 2644526 2650679 + Bpe008248.2 Bpe02g00407 407
2 2652370 2654158 + Bpe008249.1 Bpe02g00408 408
5 1336953 1339491 + Bpe017464.1 Bpe05g00075 75
5 29649253 29651360 + CaPI482276_05g021180.1 Cam05g2118 2118
8 25841287 25844936 - CaPI482276_08g020120.1 Cam08g2012 2012
1 12570773 12574574 - Carg17123-RA Car01g01468 1468
1 12575054 12576922 - Carg17124-RA Car01g01469 1469
5 949704 953180 + Carg11825-RA Car05g00178 178
9 751444 753373 - Carg08743-RA Car09g00159 159
12 2948576 2954779 - Carg04076-RA Car12g00468 468
5 30615529 30617574 + CcPI632755_05g021810.1 Cco05g2181 2181
8 28530063 28539135 - CcPI632755_08g017230.1 Cco08g1723 1723
5 32987926 32990035 + CePI673135_05g021290.1 Cec05g2129 2129
8 27400995 27404647 - CePI673135_08g015880.1 Cec08g1588 1588
3 17326689 17330733 - Chy3G064730.1 Chy03g01493 1493
4 5431616 5433487 + Chy4G072580.1 Chy04g00540 540
4 5438974 5442225 + Chy4G072590.1 Chy04g00541 541
7 716837 721856 + Chy7G129070.1 Chy07g00077 77
5 29859855 29861964 + ClG42_05g0210600.10 Clacu05g2106 2106
8 26587777 26591425 - ClG42_08g0170100.10 Clacu08g1701 1701
5 31480075 31482429 + ClCG05G019240.1 Cla05g01967 1967
8 27977194 27982251 - ClCG08G015420.1 Cla08g01521 1521
1 12354740 12356679 - CmaCh01G018850.1 Cma01g01885 1885
5 921801 925589 + CmaCh05G002180.1 Cma05g00218 218
9 753541 756048 - CmaCh09G001780.1 Cma09g00178 178
12 2584714 2593348 - CmaCh12G004980.1 Cma12g00498 498
3 27671171 27676630 - MELO3C010913.2.1 Cme03g01987 1987
4 6123220 6125899 + MELO3C003890.2.1 Cme04g00630 630
4 6128661 6133677 + MELO3C003891.2.1 Cme04g00631 631
1 13868303 13872025 - CmoCh01G019470.1 Cmo01g01947 1947
1 13873519 13875330 - CmoCh01G019480.1 Cmo01g01948 1948
5 960048 964502 + CmoCh05G002240.1 Cmo05g00224 224
9 779483 783119 - CmoCh09G001740.1 Cmo09g00174 174
12 2722280 2728327 - CmoCh12G004430.1 Cmo12g00443 443
5 29587123 29589232 + CmPI595203_05g019820.1 Cmu05g1982 1982
4 13470594 13474661 + Conep04aG0194700.1 Cone4ag1886 1886
7 11761698 11762503 - Conep07aG0184800.1 Cone7ag1794 1794
7 11763816 11766337 - Conep07aG0184900.1 Cone7ag1795 1795
7 11767600 11769189 + Conep07aG0185000.1 Cone7ag1796 1796
7 11772289 11775657 + Conep07aG0185100.1 Cone7ag1797 1797
17 9323225 9325890 - Conep17aG0134700.1 Cone17ag1315 1315
17 9329308 9332589 + Conep17aG0134800.1 Cone17ag1316 1316
20 690007 693003 - Conep20aG0016600.1 Cone20ag0158 158
20 695537 698777 + Conep20aG0016700.1 Cone20ag0159 159
2 726560 731950 + Cp4.1LG02g07370.1 Cpe02g00146 146
2 732325 736080 + Cp4.1LG02g07400.1 Cpe02g00147 147
6 629953 632944 - Cp4.1LG06g01290.1 Cpe06g00127 127
7 2862267 2868511 - Cp4.1LG07g04650.1 Cpe07g00446 446
11 977738 981750 + Cp4.1LG11g01640.1 Cpe11g00180 180
5 32900204 32902321 + CrPI670011_05g021010.1 Cre05g2101 2101
8 27655277 27658918 - CrPI670011_08g014830.1 Cre08g1483 1483
2 18681338 18688764 + CsaV3_2G028370.1 Csa02g02018 2018
3 36659923 36662470 - CsaV3_3G044840.1 Csa03g04178 4178
4 23896902 23907136 + CsaV3_4G033710.1 Csa04g02345 2345
4 23826626 23833884 - Lsi04G016340.1 Lsi04g01634 1634
8 22473187 22478569 - Lsi08G014240.1 Lsi08g01424 1424
18 10015413 10021454 - Vvi18g870 Vvi18g870 870
18 10026698 10031929 - Vvi18g871 Vvi18g871 871
18 10033199 10037422 - Vvi18g872 Vvi18g872 872
18 10039445 10043834 - Vvi18g873 Vvi18g873 873
18 10047420 10049442 - Vvi18g874 Vvi18g874 874
18 10051705 10052113 - Vvi18g875 Vvi18g875 875
18 10062672 10065015 + Vvi18g876 Vvi18g876 876
18 10068355 10074521 - Vvi18g877 Vvi18g877 877
18 10074526 10075917 - Vvi18g878 Vvi18g878 878
18 10082484 10096930 + Vvi18g879 Vvi18g879 879
       

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