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
Vvi2g262 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g263 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g264 . Blo03g00229 . . . . Bma07g01036 Bma14g00095 . . Cma02g00950 Cma15g01328 Car02g00699 Car15g01194 . Cpe14g00512 Cpe05g00764 . . . . . . . Cla07g00787 Cam07g0850 Cec07g0903 Cco07g0885 Clacu07g0825 Cmu07g0828 Cre07g1186 . . . . . Csa05g00152 Chy09g01344 Cme07g01642 Blo03g00796 Blo19g00133 Bda07g00157 Bda09g00631 Bpe08g00909 Bpe11g00376 . . . Cmo02g00958 . . Cma16g00603 . . . . Bhi12g00073 . . Lac11g1892 Hepe06g1425 . Lcy12g1503 Cla01g00135 Cam01g0137 Cec01g0137 Cco01g0139 Clacu01g0133 Cmu01g0135 Cre09g2370 Lsi09g00125 Csa04g00585 Chy07g01226 Cme09g01892
Vvi2g265 . . Bda06g00123 . . . Bma07g01037 Bma14g00094 . . Cma02g00951 . Car02g00700 Car15g01195 . . Cpe05g00763 . . . . . . . . . . . . . . Cone8ag0584 Cone12ag0568 . . . Csa05g00079 Chy09g01345 . . Blo19g00132 Bda07g00158 Bda09g00630 Bpe08g00910 Bpe11g00377 . . . Cmo02g00959 Cmo15g01392 . . . . . . Bhi12g00072 . . Lac11g1891 Hepe06g1424 . Lcy12g1502 Cla01g00134 Cam01g0136 Cec01g0136 Cco01g0138 Clacu01g0132 Cmu01g0134 Cre09g2371 Lsi09g00124 . . Cme09g01893
Vvi2g266 . . Bda06g01090 . . . . . . Cmo16g00650 . . Car02g00624 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g267 . . . . . . . . . Cmo16g00649 . . . . . Cpe14g00509 . . . . . . . . Cla07g00778 Cam07g0835 Cec07g0890 Cco07g0867 Clacu07g0813 Cmu07g0819 Cre07g1171 . . . . . . . Cme07g01634 . . . . . . Bma05g00545 . . . . . Cma16g00599 . . Cpe08g00602 . . . . . . . . . . . . . . . . Csa04g00590 . .
Vvi2g268 . . . . . . . . . . . Cma15g01332 . Car15g01197 . . . . . . . . . . . . . . . . . . . . . . Csa05g00149 Chy09g01346 . . . . . . . . . . . Cmo15g01394 . . . . . . Bhi12g00069 . . Lac11g1879 Hepe06g1420 . Lcy12g1498 Cla01g00132 Cam01g0134 Cec01g0135 Cco01g0136 Clacu01g0130 Cmu01g0132 Cre09g2373 Lsi09g00123 . . Cme09g01894
Vvi2g269 . . . . . . Bma07g01045 Bma14g00092 . . Cma02g00952 . Car02g00702 . . . Cpe05g00762 . . . . . . . . . . . . . . Cone8ag0583 Cone12ag0570 . . . . . . Blo03g00794 Blo19g00131 Bda07g00160 Bda09g00629 Bpe08g00911 Bpe11g00379 . . . Cmo02g00960 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g270 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone9ag0790 . . . . . . . . . . Bma05g00546 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g271 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 1924543 1927523 + Bda023318.1 Bda06g00123 123
6 38852391 38856535 + Bda022866.1 Bda06g01090 1090
7 1942676 1945789 - Bda025225.1 Bda07g00157 157
7 1948083 1951214 - Bda025226.2 Bda07g00158 158
7 1977281 1978486 + Bda025228.1 Bda07g00160 160
9 9255927 9257153 - Bda031259.1 Bda09g00629 629
9 9268441 9274452 + Bda031260.1 Bda09g00630 630
9 9278287 9280742 + Bda031261.1 Bda09g00631 631
12 1899077 1903074 - XM_039020386.1 Bhi12g00069 69
12 2008650 2020522 + XM_039019854.1 Bhi12g00072 72
12 2060491 2063659 + XM_039020235.1 Bhi12g00073 73
3 5099696 5103726 + BLOR11410 Blo03g00229 229
3 33037777 33039003 - BLOR11975 Blo03g00794 794
3 33087373 33096446 + BLOR11977 Blo03g00796 796
19 3799205 3800434 - BLOR09474 Blo19g00131 131
19 3859451 3866018 + BLOR09475 Blo19g00132 132
19 3869079 3871564 + BLOR09476 Blo19g00133 133
5 29815588 29818700 + Bma021512.1 Bma05g00545 545
5 29819752 29821554 - Bma021513.1 Bma05g00546 546
7 41824102 41826633 - Bma026230.1 Bma07g01036 1036
7 41838666 41842020 - Bma026231.1 Bma07g01037 1037
7 42110549 42111775 + Bma026240.1 Bma07g01045 1045
14 1310419 1311633 - Bma010498.2 Bma14g00092 92
14 1326163 1329265 + Bma010500.1 Bma14g00094 94
14 1331650 1334757 + Bma010501.1 Bma14g00095 95
8 11537853 11540424 - Bpe023032.1 Bpe08g00909 909
8 11544248 11550445 - Bpe023033.1 Bpe08g00910 910
8 11560085 11561314 + Bpe023034.1 Bpe08g00911 911
11 2851684 2854722 - Bpe003750.1 Bpe11g00376 376
11 2856463 2859608 - Bpe003751.2 Bpe11g00377 377
11 2873385 2874599 + Bpe003753.1 Bpe11g00379 379
1 1681625 1685331 - CaPI482276_01g001340.1 Cam01g0134 134
1 1695326 1701358 + CaPI482276_01g001360.1 Cam01g0136 136
1 1709312 1711634 + CaPI482276_01g001370.1 Cam01g0137 137
7 20903236 20907981 + CaPI482276_07g008350.1 Cam07g0835 835
7 21232485 21235079 + CaPI482276_07g008500.1 Cam07g0850 850
2 4706959 4711306 + Carg20247-RA Car02g00624 624
2 5179768 5182325 - Carg08524-RA Car02g00699 699
2 5185294 5189794 - Carg08523-RA Car02g00700 700
2 5198233 5199498 + Carg08521-RA Car02g00702 702
15 9296547 9299368 - Carg21318-RA Car15g01194 1194
15 9302618 9308249 - Carg21319-RA Car15g01195 1195
15 9312340 9315685 + Carg21321-RA Car15g01197 1197
1 1246073 1249788 - CcPI632755_01g001360.1 Cco01g0136 136
1 1259527 1265685 + CcPI632755_01g001380.1 Cco01g0138 138
1 1273701 1276026 + CcPI632755_01g001390.1 Cco01g0139 139
7 20116718 20123946 + CcPI632755_07g008670.1 Cco07g0867 867
7 20632984 20635582 + CcPI632755_07g008850.1 Cco07g0885 885
1 1271504 1275181 - CePI673135_01g001350.1 Cec01g0135 135
1 1276202 1290487 + CePI673135_01g001360.1 Cec01g0136 136
1 1298513 1300840 + CePI673135_01g001370.1 Cec01g0137 137
7 22037658 22048272 + CePI673135_07g008900.1 Cec07g0890 890
7 22429513 22432109 + CePI673135_07g009030.1 Cec07g0903 903
7 17050981 17053667 + Chy7G140560.1 Chy07g01226 1226
9 15291426 15293697 - Chy9G170600.1 Chy09g01344 1344
9 15298362 15303869 - Chy9G170610.1 Chy09g01345 1345
9 15308609 15312417 + Chy9G170620.1 Chy09g01346 1346
1 1293786 1297498 - ClG42_01g0013000.10 Clacu01g0130 130
1 1306968 1312659 + ClG42_01g0013200.10 Clacu01g0132 132
1 1320512 1322810 + ClG42_01g0013300.10 Clacu01g0133 133
7 20617322 20622258 + ClG42_07g0081300.10 Clacu07g0813 813
7 20914243 20916835 + ClG42_07g0082500.10 Clacu07g0825 825
1 1274549 1278500 - ClCG01G001360.1 Cla01g00132 132
1 1287669 1293995 + ClCG01G001380.2 Cla01g00134 134
1 1301378 1304621 + ClCG01G001390.1 Cla01g00135 135
7 21740772 21745928 + ClCG07G008160.1 Cla07g00778 778
7 22045770 22049126 + ClCG07G008250.1 Cla07g00787 787
2 5648207 5650915 - CmaCh02G009500.1 Cma02g00950 950
2 5653050 5657664 - CmaCh02G009510.1 Cma02g00951 951
2 5662435 5666104 + CmaCh02G009520.1 Cma02g00952 952
15 8339554 8342406 - CmaCh15G013280.1 Cma15g01328 1328
15 8354533 8357142 + CmaCh15G013320.1 Cma15g01332 1332
16 3092759 3098448 - CmaCh16G005990.1 Cma16g00599 599
16 3109923 3113382 + CmaCh16G006030.1 Cma16g00603 603
7 22094314 22102249 - MELO3C016358.2.1 Cme07g01634 1634
7 22146098 22151012 + MELO3C016366.2.1 Cme07g01642 1642
9 23045948 23049195 - MELO3C005798.2.1 Cme09g01892 1892
9 23052396 23058810 - MELO3C005799.2.1 Cme09g01893 1893
9 23062339 23065756 + MELO3C005800.2.1 Cme09g01894 1894
2 5872580 5875405 - CmoCh02G009580.1 Cmo02g00958 958
2 5878412 5882984 - CmoCh02G009590.1 Cmo02g00959 959
2 5891255 5894966 + CmoCh02G009600.1 Cmo02g00960 960
15 9470147 9476215 - CmoCh15G013920.1 Cmo15g01392 1392
15 9480233 9483583 + CmoCh15G013940.1 Cmo15g01394 1394
16 3197033 3202288 - CmoCh16G006490.1 Cmo16g00649 649
16 3205298 3210300 - CmoCh16G006500.1 Cmo16g00650 650
1 1238690 1242399 - CmPI595203_01g001320.1 Cmu01g0132 132
1 1252630 1258327 + CmPI595203_01g001340.1 Cmu01g0134 134
1 1266198 1268504 + CmPI595203_01g001350.1 Cmu01g0135 135
7 20831193 20836122 + CmPI595203_07g008190.1 Cmu07g0819 819
7 21128134 21130726 + CmPI595203_07g008280.1 Cmu07g0828 828
8 4840321 4844569 - Conep08aG0060400.1 Cone8ag0583 583
8 4853498 4857237 + Conep08aG0060500.1 Cone8ag0584 584
9 3792131 3794711 - Conep09aG0080800.1 Cone9ag0790 790
12 4159580 4163500 + Conep12aG0058900.1 Cone12ag0568 568
12 4186403 4187945 + Conep12aG0059100.1 Cone12ag0570 570
5 4714423 4718359 - Cp4.1LG05g07570.1 Cpe05g00762 762
5 4725677 4730281 + Cp4.1LG05g07710.1 Cpe05g00763 763
5 4732412 4735825 + Cp4.1LG05g07700.1 Cpe05g00764 764
8 3966708 3970595 - Cp4.1LG08g00740.1 Cpe08g00602 602
14 3221346 3226252 - Cp4.1LG14g02090.1 Cpe14g00509 509
14 3239644 3243371 + Cp4.1LG14g02150.1 Cpe14g00512 512
7 24146915 24151764 + CrPI670011_07g011710.1 Cre07g1171 1171
7 24727105 24729697 + CrPI670011_07g011860.1 Cre07g1186 1186
9 43022192 43024513 - CrPI670011_09g023700.1 Cre09g2370 2370
9 43032506 43038700 - CrPI670011_09g023710.1 Cre09g2371 2371
9 43048472 43052181 + CrPI670011_09g023730.1 Cre09g2373 2373
4 3850693 3854541 - CsaV3_4G005850.1 Csa04g00585 585
4 3888813 3895061 + CsaV3_4G005900.1 Csa04g00590 590
5 390326 394917 - CsaV3_5G000790.1 Csa05g00079 79
5 828219 833961 - CsaV3_5G001490.1 Csa05g00149 149
5 847228 850858 + CsaV3_5G001520.1 Csa05g00152 152
6 64622646 64626891 - Hsped.06g14200.1 Hepe06g1420 1420
6 64680808 64687392 + Hsped.06g14240.1 Hepe06g1424 1424
6 64696192 64699628 + Hsped.06g14250.1 Hepe06g1425 1425
11 33928849 33933284 - Lag0032517.1 Lac11g1879 1879
11 34048610 34054795 + Lag0032529.1 Lac11g1891 1891
11 34069384 34071775 + Lag0032530.1 Lac11g1892 1892
12 34445309 34447973 - Maker00029461 Lcy12g1498 1498
12 34522103 34530760 + Maker00029473 Lcy12g1502 1502
12 34544594 34548343 + Maker00029274 Lcy12g1503 1503
9 1184019 1189138 - Lsi09G001230.1 Lsi09g00123 123
9 1201273 1207550 + Lsi09G001240.1 Lsi09g00124 124
9 1214501 1218721 + Lsi09G001250.1 Lsi09g00125 125
2 2430221 2430832 + Vvi2g262 Vvi2g262 262
2 2433516 2434662 + Vvi2g263 Vvi2g263 263
2 2435452 2439133 - Vvi2g264 Vvi2g264 264
2 2441372 2448473 - Vvi2g265 Vvi2g265 265
2 2451945 2468894 + Vvi2g266 Vvi2g266 266
2 2469922 2473615 + Vvi2g267 Vvi2g267 267
2 2479857 2482925 + Vvi2g268 Vvi2g268 268
2 2485419 2489802 + Vvi2g269 Vvi2g269 269
2 2496155 2498001 - Vvi2g270 Vvi2g270 270
2 2501637 2512150 - Vvi2g271 Vvi2g271 271
       

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