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
Vvi18g1110 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1403 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1111 . . . . . . . . Cmo05g00309 . Cma01g01973 . Car01g01544 . Sed11g1087 . . Bhi04g00148 Tan02g2076 Cmetu03g0470 . Hepe10g0153 . Lcy13g1911 Cla08g01421 Cam08g1901 Cec08g1478 Cco08g1611 Clacu08g1592 . Cre08g1377 . . Cone17ag1404 Cone20ag0078 Lsi04g01747 Csa03g04282 Chy04g00415 Cme03g01880 . . Bda08g01219 . . Bpe05g00140 . Bma05g00165 Sed13g1568 Cmo01g02031 . . Cma05g00306 Car05g00254 . Cpe11g00255 Cpe02g00069 Bhi09g02085 Tan01g5020 Cmetu04g2273 . Hepe01g1612 Mch11g0114 . Cla05g01868 Cam05g1997 Cec05g2009 Cco05g2067 Clacu05g1989 Cmu05g1870 Cre05g1994 Lsi08g01317 Csa02g02134 Chy03g01385 Cme04g00466
Vvi18g1112 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1113 Blo01g01598 . Bda01g00484 . Bpe02g00348 . . . . . Cma01g01975 . . . . . . . . . . . . . . . . . . . . . . Cone17ag1406 Cone20ag0077 . Csa03g04284 Chy04g00413 . . . . . . . . . Sed01g2479 Cmo01g02033 . . . . . . Cpe02g00068 Bhi09g02083 Tan01g5022 Cmetu04g1253 . Hepe01g1611 Mch11g0113 . Cla05g01866 Cam05g1995 Cec05g2007 Cco05g2065 Clacu05g1987 Cmu05g1868 Cre05g1992 . . . Cme04g00464
Vvi18g1114 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1115 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1116 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1117 . . Bda01g00482 . Bpe02g00346 . Bma04g00249 . . . . . . . Sed08g2609 . Cpe07g00363 Bhi04g00145 Tan02g2079 Cmetu03g2170 . Hepe10g0157 . Lcy13g1909 Cla08g01419 Cam08g1899 Cec08g1475 Cco08g1608 Clacu08g1590 . Cre08g1374 . . . . . . . Cme03g01875 Blo17g00745 . . Bda01g01531 Bpe02g01727 . . . . . . Cma12g00406 . . . . . . . . . . . . . . . . . . . Lsi08g01314 . Chy03g01381 .
Vvi18g1118 Blo01g01599 . . . . . . Bma01g02369 Cmo05g00312 Cmo12g00357 . . . Car12g00384 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda08g01218 . . . Bma01g00727 . . . . . Cma05g00309 Car05g00257 . Cpe11g00258 . . . . . . . . . . . . . . . . Csa02g02138 . .
Vvi18g1119 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 31887075 31889029 + Bda002485.1 Bda01g00482 482
1 31893079 31895299 - Bda002487.1 Bda01g00484 484
1 51195512 51198337 - Bda003793.1 Bda01g01531 1531
8 50018721 50021191 + Bda030201.1 Bda08g01218 1218
8 50024893 50026592 - Bda030202.2 Bda08g01219 1219
4 3505584 3509904 + XM_039029242.1 Bhi04g00145 145
4 3616591 3619970 - XM_039028931.1 Bhi04g00148 148
9 59452994 59455712 - XM_039041216.1 Bhi09g02083 2083
9 59458670 59461870 - XM_039044144.1 Bhi09g02085 2085
1 55841924 55844340 + BLOR01598 Blo01g01598 1598
1 55850582 55852559 - BLOR01599 Blo01g01599 1599
17 23140449 23143112 + BLOR08291 Blo17g00745 745
1 6655160 6657991 + Bma000937.1 Bma01g00727 727
1 81353617 81355595 - Bma003240.2 Bma01g02369 2369
4 2124776 2127275 - Bma018701.1 Bma04g00249 249
5 4721887 4723690 + Bma020881.2 Bma05g00165 165
2 2281630 2283627 + Bpe008188.1 Bpe02g00346 346
2 2286282 2288461 - Bpe008190.1 Bpe02g00348 348
2 19721057 19723884 - Bpe009558.1 Bpe02g01727 1727
5 3281134 3282826 + Bpe017524.1 Bpe05g00140 140
5 28757295 28759614 - CaPI482276_05g019950.1 Cam05g1995 1995
5 28764244 28770689 - CaPI482276_05g019970.1 Cam05g1997 1997
8 24969632 24972972 + CaPI482276_08g018990.1 Cam08g1899 1899
8 24988037 24990586 - CaPI482276_08g019010.1 Cam08g1901 1901
1 12942907 12945535 + Carg17199-RA Car01g01544 1544
5 1418020 1421796 + Carg09404-RA Car05g00254 254
5 1429567 1430711 - Carg09402-RA Car05g00257 257
12 2452740 2454699 + Carg03991-RA Car12g00384 384
5 29691556 29694069 - CcPI632755_05g020650.1 Cco05g2065 2065
5 29698997 29700814 - CcPI632755_05g020670.1 Cco05g2067 2067
8 27635433 27638834 + CcPI632755_08g016080.1 Cco08g1608 1608
8 27653837 27656669 - CcPI632755_08g016110.1 Cco08g1611 1611
5 32056706 32059078 - CePI673135_05g020070.1 Cec05g2007 2007
5 32064272 32066089 - CePI673135_05g020090.1 Cec05g2009 2009
8 26498916 26502309 + CePI673135_08g014750.1 Cec08g1475 1475
8 26524580 26527405 - CePI673135_08g014780.1 Cec08g1478 1478
3 16629582 16632959 + Chy3G063610.1 Chy03g01381 1381
3 16644683 16646688 - Chy3G063650.1 Chy03g01385 1385
4 3686722 3689023 - Chy4G071310.1 Chy04g00413 413
4 3692335 3694291 - Chy4G071330.1 Chy04g00415 415
5 28958507 28960998 - ClG42_05g0198700.10 Clacu05g1987 1987
5 28966011 28967828 - ClG42_05g0198900.10 Clacu05g1989 1989
8 25715181 25718631 + ClG42_08g0159000.10 Clacu08g1590 1590
8 25738711 25741268 - ClG42_08g0159200.10 Clacu08g1592 1592
5 30539008 30541608 - ClCG05G018240.1 Cla05g01866 1866
5 30546621 30549161 - ClCG05G018260.2 Cla05g01868 1868
8 27071877 27075821 + ClCG08G014260.1 Cla08g01419 1419
8 27096830 27099662 - ClCG08G014280.1 Cla08g01421 1421
1 12714829 12719270 + CmaCh01G019730.1 Cma01g01973 1973
1 12720931 12723691 + CmaCh01G019750.1 Cma01g01975 1975
5 1327893 1331970 + CmaCh05G003060.1 Cma05g00306 306
5 1336705 1340028 - CmaCh05G003090.1 Cma05g00309 309
12 2106827 2110230 + CmaCh12G004060.1 Cma12g00406 406
3 26978404 26982315 + MELO3C011016.2.1 Cme03g01875 1875
3 26991826 26994023 - MELO3C011012.2.1 Cme03g01880 1880
4 3706037 3708756 - MELO3C003748.2.1 Cme04g00464 464
4 3711871 3714287 - MELO3C003750.2.1 Cme04g00466 466
3 2380173 2381959 + PI0013118.1 Cmetu03g0470 470
3 2394707 2398506 - PI0014550.1 Cmetu03g2170 2170
4 29660957 29663662 + PI0003186.1 Cmetu04g1253 1253
4 29648035 29651489 + PI0014687.3 Cmetu04g2273 2273
1 14251924 14254633 + CmoCh01G020310.1 Cmo01g02031 2031
1 14258749 14262286 + CmoCh01G020330.1 Cmo01g02033 2033
5 1369093 1373840 + CmoCh05G003090.1 Cmo05g00309 309
5 1379438 1382805 - CmoCh05G003120.1 Cmo05g00312 312
12 2218996 2222214 + CmoCh12G003570.1 Cmo12g00357 357
5 28684279 28686599 - CmPI595203_05g018680.1 Cmu05g1868 1868
5 28691767 28693584 - CmPI595203_05g018700.1 Cmu05g1870 1870
17 9666695 9668566 - Conep17aG0143900.1 Cone17ag1403 1403
17 9670132 9671851 + Conep17aG0144000.1 Cone17ag1404 1404
17 9673080 9674873 + Conep17aG0144200.1 Cone17ag1406 1406
20 366264 367826 - Conep20aG0008000.1 Cone20ag0077 77
20 369167 370960 - Conep20aG0008100.1 Cone20ag0078 78
2 358766 361538 - Cp4.1LG02g07900.1 Cpe02g00068 68
2 362176 365414 - Cp4.1LG02g07920.1 Cpe02g00069 69
7 2343891 2347626 + Cp4.1LG07g03620.1 Cpe07g00363 363
11 1384171 1387908 + Cp4.1LG11g02430.1 Cpe11g00255 255
11 1393631 1396727 - Cp4.1LG11g02730.1 Cpe11g00258 258
5 32000268 32002589 - CrPI670011_05g019920.1 Cre05g1992 1992
5 32006983 32008798 - CrPI670011_05g019940.1 Cre05g1994 1994
8 26775456 26778864 + CrPI670011_08g013740.1 Cre08g1374 1374
8 26794131 26796936 - CrPI670011_08g013770.1 Cre08g1377 1377
2 19339418 19342479 + CsaV3_2G029530.1 Csa02g02134 2134
2 19354765 19358611 - CsaV3_2G029570.1 Csa02g02138 2138
3 37503821 37507358 + CsaV3_3G045880.1 Csa03g04282 4282
3 37508898 37511729 + CsaV3_3G045900.1 Csa03g04284 4284
1 81379007 81381335 - Hsped.01g16110.1 Hepe01g1611 1611
1 81385061 81388049 - Hsped.01g16120.1 Hepe01g1612 1612
10 1575060 1577597 + Hsped.10g01530.1 Hepe10g0153 153
10 1607644 1608490 - Hsped.10g01570.1 Hepe10g0157 157
13 38048520 38052418 + Maker00033651 Lcy13g1909 1909
13 38072023 38075510 - Maker00033631 Lcy13g1911 1911
4 24753833 24764700 + Lsi04G017470.1 Lsi04g01747 1747
8 21511266 21515381 + Lsi08G013140.1 Lsi08g01314 1314
8 21529047 21532433 - Lsi08G013180.1 Lsi08g01317 1317
11 752471 755123 - MC11g0100 Mch11g0113 113
11 755770 759077 - MC11g0101 Mch11g0114 114
1 18543535 18547356 + Sed0006848.1 Sed01g2479 2479
8 38416771 38420201 + Sed0027140.1 Sed08g2609 2609
11 26474012 26475997 + Sed0011447.1 Sed11g1087 1087
13 20851685 20854591 - Sed0019370.1 Sed13g1568 1568
1 115875107 115877068 + Tan0019594.1 Tan01g5020 5020
1 115881906 115884557 + Tan0003705.1 Tan01g5022 5022
2 90239307 90241342 + Tan0017783.1 Tan02g2076 2076
2 90278083 90282059 - Tan0016895.1 Tan02g2079 2079
18 12292298 12294516 - Vvi18g1110 Vvi18g1110 1110
18 12299116 12301801 + Vvi18g1111 Vvi18g1111 1111
18 12302977 12305109 + Vvi18g1112 Vvi18g1112 1112
18 12306651 12309400 + Vvi18g1113 Vvi18g1113 1113
18 12310190 12311438 + Vvi18g1114 Vvi18g1114 1114
18 12314821 12316170 - Vvi18g1115 Vvi18g1115 1115
18 12335589 12336595 + Vvi18g1116 Vvi18g1116 1116
18 12336994 12339223 - Vvi18g1117 Vvi18g1117 1117
18 12339224 12341049 - Vvi18g1118 Vvi18g1118 1118
18 12341545 12342790 + Vvi18g1119 Vvi18g1119 1119
       

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