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
Vvi2g132 . Blo03g00248 Bda06g00146 Bda08g00465 . Bpe07g00072 . . . Cmo16g00597 . . . . . Cpe14g00462 . . . . . . . . Cla07g01426 Cam07g1528 Cec07g1624 Cco07g1584 Clacu07g1515 Cmu07g1486 Cre07g1863 . Cone12ag0251 Cone6ag0851 Cone9ag0852 . . . . . Blo19g00367 . . Bpe08g01520 . . Bma12g00607 . . . . Cma16g00545 . . . . . . . . . . . . . . . . . . . Csa04g00657 Chy07g01154 .
Vvi2g133 Blo02g01150 . Bda06g00147 . Bpe05g00694 Bpe07g00071 . . Cmo06g01042 Cmo16g00596 . . . . . Cpe14g00461 . . . . . . . . . . . . . . . Cone8ag0244 . . . . . . . . . . . . . . Bma12g00608 . . . . Cma16g00544 Car06g00858 . . . . . . . . . . . . . . . . . . Csa04g00658 Chy07g01153 .
Vvi2g134 . . . . . . Bma07g01685 . . . Cma02g00914 Cma15g01281 Car02g00665 Car15g01155 . . Cpe05g00796 . . . . . . . . . . . . . . . Cone12ag0248 . . . Csa05g00199 Chy09g01298 . . Blo19g00368 . Bda09g00014 . . . . . Cmo02g00921 Cmo15g01350 . . . . . Cpe13g00108 Bhi12g00138 . . Lac11g1984 Hepe06g1474 . Lcy12g1566 Cla01g00182 Cam01g0186 Cec01g0183 Cco01g0186 Clacu01g0183 Cmu01g0179 Cre09g2326 Lsi09g00170 . . Cme09g01844
Vvi2g135 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g136 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g137 Blo02g01151 . . Bda08g00464 Bpe05g00695 . . . . . . . . . . . . . . . . . . . Cla07g01099 Cam07g1399 Cec07g1261 Cco07g1241 Clacu07g1162 Cmu07g1142 Cre07g1523 . . Cone6ag0853 Cone9ag0854 . . . . . . . . . . Bma05g00877 . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00661 Chy07g01150 .
Vvi2g138 . . . . . . Bma07g01686 . . . . . . . . . Cpe05g00604 . . . . . . . . . . . . . . Cone8ag0242 Cone12ag0246 . Cone9ag0855 . . . . . Blo19g00369 Bda07g01930 Bda09g00013 Bpe08g01521 . . . . Cmo02g01141 Cmo15g01093 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g139 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g140 . . . . . . . . . . . . . . . . . . . . . . . . Cla07g01098 Cam07g1400 Cec07g1260 Cco07g1240 Clacu07g1161 Cmu07g1141 Cre07g1521 . . Cone6ag0854 Cone9ag0856 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00662 Chy07g01149 .
Vvi2g141 . . . . . . . . . Cmo16g00594 . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0855 Cone9ag0857 . . . . . . . . . . . . . . . . Cma16g00542 . . . . . . . . . . . . . . . . . . . Csa04g00664 Chy07g01148 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 2168869 2173107 - Bda023347.1 Bda06g00146 146
6 2176696 2178640 - Bda023348.1 Bda06g00147 147
7 36802986 36808767 + Bda028910.1 Bda07g01930 1930
8 4837131 4837857 + Bda024915.1 Bda08g00464 464
8 4855970 4869346 + Bda024917.1 Bda08g00465 465
9 277939 279217 - Bda030531.3 Bda09g00013 13
9 280717 283964 - Bda030532.1 Bda09g00014 14
12 4138104 4141292 + XM_039020329.1 Bhi12g00138 138
2 43096774 43099220 - BLOR10880 Blo02g01150 1150
2 43134951 43135673 - BLOR10881 Blo02g01151 1151
3 5320773 5324666 - BLOR11429 Blo03g00248 248
19 23432031 23439469 - BLOR09710 Blo19g00367 367
19 23439867 23443715 + BLOR09711 Blo19g00368 368
19 23464772 23466194 + BLOR09712 Blo19g00369 369
5 46487356 46488078 - Bma022000.1 Bma05g00877 877
7 52424777 52428056 + Bma026982.1 Bma07g01685 1685
7 52429428 52430706 + Bma026983.2 Bma07g01686 1686
12 27407015 27409827 - Bma007784.1 Bma12g00607 607
12 27411199 27412801 - Bma007785.1 Bma12g00608 608
5 20561452 20570086 - Bpe018107.1 Bpe05g00694 694
5 20576217 20576939 - Bpe018108.1 Bpe05g00695 695
7 533142 534941 + Bpe020883.1 Bpe07g00071 71
7 535918 539420 + Bpe020884.1 Bpe07g00072 72
8 15849590 15859747 - Bpe023631.1 Bpe08g01520 1520
8 15865054 15866491 + Bpe023633.1 Bpe08g01521 1521
1 2202696 2205095 + CaPI482276_01g001860.1 Cam01g0186 186
7 28515990 28516694 - CaPI482276_07g013990.1 Cam07g1399 1399
7 28523662 28534226 + CaPI482276_07g014000.1 Cam07g1400 1400
7 29911863 29915710 - CaPI482276_07g015280.1 Cam07g1528 1528
2 4974201 4978060 - Carg08558-RA Car02g00665 665
6 6703989 6706348 + Carg20892-RA Car06g00858 858
15 9078119 9080934 - Carg21279-RA Car15g01155 1155
1 1792695 1795102 + CcPI632755_01g001860.1 Cco01g0186 186
7 26263667 26274339 - CcPI632755_07g012400.1 Cco07g1240 1240
7 26281367 26282068 + CcPI632755_07g012410.1 Cco07g1241 1241
7 29864992 29868764 - CcPI632755_07g015840.1 Cco07g1584 1584
1 1784476 1786858 + CePI673135_01g001830.1 Cec01g0183 183
7 28107699 28126898 - CePI673135_07g012600.1 Cec07g1260 1260
7 28133912 28134622 + CePI673135_07g012610.1 Cec07g1261 1261
7 31773142 31777036 - CePI673135_07g016240.1 Cec07g1624 1624
7 16379828 16388189 - Chy7G139780.1 Chy07g01148 1148
7 16388715 16393804 - Chy7G139790.1 Chy07g01149 1149
7 16398818 16399540 + Chy7G139800.1 Chy07g01150 1150
7 16428613 16431809 + Chy7G139830.1 Chy07g01153 1153
7 16434693 16440270 + Chy7G139840.1 Chy07g01154 1154
9 14944637 14947087 - Chy9G170140.1 Chy09g01298 1298
1 1824067 1826463 + ClG42_01g0018300.10 Clacu01g0183 183
7 26280193 26294793 - ClG42_07g0116100.10 Clacu07g1161 1161
7 26301479 26302183 + ClG42_07g0116200.10 Clacu07g1162 1162
7 29760181 29773443 - ClG42_07g0151500.10 Clacu07g1515 1515
1 1825592 1828761 + ClCG01G001840.2 Cla01g00182 182
7 27669565 27681637 - ClCG07G011580.2 Cla07g01098 1098
7 27690380 27691084 + ClCG07G011600.1 Cla07g01099 1099
7 31467728 31481747 - ClCG07G015030.2 Cla07g01426 1426
2 5449313 5452550 - CmaCh02G009140.1 Cma02g00914 914
15 8118914 8122409 - CmaCh15G012810.1 Cma15g01281 1281
16 2783837 2787670 - CmaCh16G005420.1 Cma16g00542 542
16 2796001 2799029 + CmaCh16G005440.1 Cma16g00544 544
16 2799600 2804576 + CmaCh16G005450.1 Cma16g00545 545
9 22679854 22682970 - MELO3C005754.2.1 Cme09g01844 1844
2 5665099 5668232 - CmoCh02G009210.1 Cmo02g00921 921
2 6909454 6920010 + CmoCh02G011410.1 Cmo02g01141 1141
6 8109911 8111764 + CmoCh06G010420.1 Cmo06g01042 1042
15 7300075 7312311 - CmoCh15G010930.1 Cmo15g01093 1093
15 9240332 9243138 - CmoCh15G013500.1 Cmo15g01350 1350
16 2885224 2889487 - CmoCh16G005940.1 Cmo16g00594 594
16 2899336 2902792 + CmoCh16G005960.1 Cmo16g00596 596
16 2903364 2908360 + CmoCh16G005970.1 Cmo16g00597 597
1 1777171 1779567 + CmPI595203_01g001790.1 Cmu01g0179 179
7 26525999 26537681 - CmPI595203_07g011410.1 Cmu07g1141 1141
7 26544688 26545392 + CmPI595203_07g011420.1 Cmu07g1142 1142
7 30021457 30025233 - CmPI595203_07g014860.1 Cmu07g1486 1486
6 4349333 4353503 - Conep06aG0087700.1 Cone6ag0851 851
6 4358711 4359430 - Conep06aG0087900.1 Cone6ag0853 853
6 4363167 4365612 + Conep06aG0088000.1 Cone6ag0854 854
6 4366271 4369593 + Conep06aG0088100.1 Cone6ag0855 855
8 1385679 1387276 - Conep08aG0025200.1 Cone8ag0242 242
8 1399617 1401689 + Conep08aG0025400.1 Cone8ag0244 244
9 4163170 4167487 - Conep09aG0087200.1 Cone9ag0852 852
9 4170497 4171849 - Conep09aG0087400.1 Cone9ag0854 854
9 4178504 4180100 + Conep09aG0087500.1 Cone9ag0855 855
9 4180810 4182995 + Conep09aG0087600.1 Cone9ag0856 856
9 4184311 4187827 + Conep09aG0087700.1 Cone9ag0857 857
12 1314949 1316953 - Conep12aG0025100.1 Cone12ag0246 246
12 1328428 1331789 - Conep12aG0025300.1 Cone12ag0248 248
12 1337171 1340117 + Conep12aG0025600.1 Cone12ag0251 251
5 3669556 3679843 - Cp4.1LG05g06090.1 Cpe05g00604 604
5 4934059 4937293 + Cp4.1LG05g07960.1 Cpe05g00796 796
13 771517 786522 + Cp4.1LG13g01130.1 Cpe13g00108 108
14 2904452 2906674 + Cp4.1LG14g02530.1 Cpe14g00461 461
14 2907118 2913459 + Cp4.1LG14g02570.1 Cpe14g00462 462
7 30481525 30501010 - CrPI670011_07g015210.1 Cre07g1521 1521
7 30507693 30508394 + CrPI670011_07g015230.1 Cre07g1523 1523
7 34022566 34026361 - CrPI670011_07g018630.1 Cre07g1863 1863
9 42532785 42535226 - CrPI670011_09g023260.1 Cre09g2326 2326
4 4407865 4415301 - CsaV3_4G006570.1 Csa04g00657 657
4 4416124 4419240 - CsaV3_4G006580.1 Csa04g00658 658
4 4447748 4449118 - CsaV3_4G006610.1 Csa04g00661 661
4 4453115 4457126 + CsaV3_4G006620.1 Csa04g00662 662
4 4462029 4465283 + CsaV3_4G006640.1 Csa04g00664 664
5 1187513 1190758 + CsaV3_5G001990.1 Csa05g00199 199
6 65307237 65310597 + Hsped.06g14740.1 Hepe06g1474 1474
11 35363350 35366119 + Lag0032622.1 Lac11g1984 1984
12 35647973 35651228 + Maker00029215 Lcy12g1566 1566
9 1766909 1782575 + Lsi09G001700.1 Lsi09g00170 170
2 1370271 1378550 - Vvi2g132 Vvi2g132 132
2 1379252 1382859 - Vvi2g133 Vvi2g133 133
2 1390395 1397380 + Vvi2g134 Vvi2g134 134
2 1403543 1404804 + Vvi2g135 Vvi2g135 135
2 1420762 1423272 + Vvi2g136 Vvi2g136 136
2 1423489 1424381 - Vvi2g137 Vvi2g137 137
2 1427738 1444597 + Vvi2g138 Vvi2g138 138
2 1445715 1451555 + Vvi2g139 Vvi2g139 139
2 1453846 1458053 + Vvi2g140 Vvi2g140 140
2 1459282 1461484 + Vvi2g141 Vvi2g141 141
       

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