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
Vvi5g159 . . . . . Bpe14g01121 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g160 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g161 . . . . . . . . . . . Cma14g01612 . Car14g01431 . . Cpe03g01354 . . . . . . . . . . . . . . Cone14ag0751 Cone15ag0758 . . . . . . . Blo07g00169 Bda11g00520 . . Bpe13g00670 . Bma06g01495 . . Cmo14g01650 . . . . . . . . . . . . . Cla05g00667 Cam05g0731 Cec05g0739 Cco05g0738 Clacu05g0724 Cmu05g0689 Cre05g0763 . Csa03g01484 Chy06g00721 .
Vvi5g162 . . . . . Bpe14g01122 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag0134 Cone4ag0139 . . . . Blo02g00498 . . Bda13g00194 . . Bma02g00906 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g163 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g164 . Blo12g00385 . . . Bpe14g01123 . . . . Cma06g01515 . . . . Cpe08g00173 . . . . . . . . . . . . . . . . . Cone7ag0135 Cone4ag0140 . . . . . . . Bda13g00193 . . . . . . . . . . . . . . . . . . . . Cla05g00666 Cam05g0730 Cec05g0737 Cco05g0737 Clacu05g0723 Cmu05g0688 Cre05g0762 . Csa03g01483 Chy06g00720 .
Vvi5g165 . . . . . . . . Cmo08g01211 Cmo17g00327 . . . . . . . . . . . . . . Cla06g00466 Cam06g0500 Cec06g0502 Cco06g0501 Clacu06g0484 Cmu06g0485 Cre06g1259 . Cone15ag0759 Cone7ag0136 . Lsi05g01410 Csa06g01793 Chy11g01525 . Blo02g00499 . . . . . . . Sed09g0251 . . Cma08g01236 Cma17g00338 . Car17g00311 Cpe12g00288 Cpe17g00034 Bhi12g02039 Tan06g2694 Cmetu11g2071 Lac11g0854 Hepe03g0090 . Lcy12g0748 . . . . . . . Lsi09g01447 . . Cme11g02028
Vvi5g166 Blo01g00066 . . Bda08g00297 . . . . Cmo08g01209 . . . . . . Cpe08g00174 . . . . . . . . Cla06g00468 Cam06g0502 Cec06g0504 Cco06g0505 Clacu06g0486 Cmu06g0488 Cre06g1260 . . Cone7ag0137 Cone4ag0141 . . . . . . . . Bpe05g00828 . . . Sed09g0250 . . Cma08g01234 . . . . . Bhi12g02040 Tan06g2693 Cmetu11g0533 Lac11g0851 Hepe03g0091 . Lcy12g0744 Cla05g00665 Cam05g0729 Cec05g0736 Cco05g0736 Clacu05g0722 Cmu05g0687 Cre05g0761 Lsi09g01443 Csa03g01482 Chy06g00719 .
Vvi5g167 . . . . . . . . . . . Cma14g01614 . Car14g01433 . Cpe08g00175 Cpe03g01355 . . . . . . . Cla06g00469 Cam06g0503 Cec06g0505 Cco06g0506 Clacu06g0487 Cmu06g0489 Cre06g1261 Cone14ag0752 Cone15ag0760 Cone7ag0138 Cone4ag0142 . Csa06g01796 Chy11g01522 . . . . Bda13g00192 . . Bma02g00905 . Sed02g1173 . Cmo14g01651 Cma08g01233 Cma17g00336 . Car17g00309 Cpe12g00285 Cpe17g00032 Bhi12g02041 Tan06g2692 Cmetu06g1266 . . . Lcy12g0743 . . . . . . . Lsi09g01442 Csa03g01481 . Cme11g02023
Vvi5g168 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone15ag0761 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 3115889 3116496 - Bda024731.1 Bda08g00297 297
11 5500978 5503191 - Bda033042 Bda11g00520 520
13 2395944 2398927 + Bda032840 Bda13g00192 192
13 2415399 2419951 + Bda001061.1 Bda13g00193 193
13 2424611 2426661 + Bda001062.1 Bda13g00194 194
12 63621289 63623418 + XM_039019996.1 Bhi12g02039 2039
12 63643910 63644896 + XM_039019731.1 Bhi12g02040 2040
12 63651499 63653890 - XM_039050854.1 Bhi12g02041 2041
1 822627 823261 + BLOR00066 Blo01g00066 66
2 7733401 7744319 - BLOR10228 Blo02g00498 498
2 7774068 7775480 + BLOR10229 Blo02g00499 499
7 2159461 2163772 - BLOR18101 Blo07g00169 169
12 20428918 20429223 - BLOR04404 Blo12g00385 385
2 47961168 47964418 + Bma015682.1 Bma02g00905 905
2 47992282 47997494 + Bma015685.1 Bma02g00906 906
6 51459029 51461232 - Bma024607.1 Bma06g01495 1495
5 21544195 21544791 + Bpe018241.1 Bpe05g00828 828
13 13453730 13455957 + Bpe010371.1 Bpe13g00670 670
14 8350922 8352098 + Bpe014496.1 Bpe14g01121 1121
14 8352990 8357893 - Bpe014497.1 Bpe14g01122 1122
14 8359963 8378488 - Bpe014498.3 Bpe14g01123 1123
5 6337096 6341391 - CaPI482276_05g007290.1 Cam05g0729 729
5 6363224 6366591 + CaPI482276_05g007300.1 Cam05g0730 730
5 6369036 6371498 + CaPI482276_05g007310.1 Cam05g0731 731
6 7097360 7099031 + CaPI482276_06g005000.1 Cam06g0500 500
6 7117638 7118171 + CaPI482276_06g005020.1 Cam06g0502 502
6 7121297 7123291 - CaPI482276_06g005030.1 Cam06g0503 503
14 11981421 11984853 - Carg19653-RA Car14g01431 1431
14 11987061 11989573 - Carg19655-RA Car14g01433 1433
17 1925118 1927608 + Carg05515-RA Car17g00309 309
17 1932399 1934085 - Carg05517-RA Car17g00311 311
5 6047806 6052061 - CcPI632755_05g007360.1 Cco05g0736 736
5 6058652 6062012 + CcPI632755_05g007370.1 Cco05g0737 737
5 6065136 6067608 + CcPI632755_05g007380.1 Cco05g0738 738
6 5491517 5493187 + CcPI632755_06g005010.1 Cco06g0501 501
6 5528270 5528783 + CcPI632755_06g005050.1 Cco06g0505 505
6 5532009 5534007 - CcPI632755_06g005060.1 Cco06g0506 506
5 6068202 6068730 - CePI673135_05g007360.1 Cec05g0736 736
5 6084787 6088152 + CePI673135_05g007370.1 Cec05g0737 737
5 6090965 6093431 + CePI673135_05g007390.1 Cec05g0739 739
6 5625927 5627598 + CePI673135_06g005020.1 Cec06g0502 502
6 5650055 5650574 + CePI673135_06g005040.1 Cec06g0504 504
6 5653766 5655761 - CePI673135_06g005050.1 Cec06g0505 505
6 4898604 4899100 - Chy6G112470.1 Chy06g00719 719
6 4908138 4911248 + Chy6G112480.1 Chy06g00720 720
6 4913503 4916067 + Chy6G112490.1 Chy06g00721 721
11 21837972 21840016 + Chy11G201020.1 Chy11g01522 1522
11 21852963 21854603 - Chy11G201050.1 Chy11g01525 1525
5 6072476 6073036 - ClG42_05g0072200.10 Clacu05g0722 722
5 6083993 6087358 + ClG42_05g0072300.10 Clacu05g0723 723
5 6090022 6092489 + ClG42_05g0072400.10 Clacu05g0724 724
6 5632639 5634310 + ClG42_06g0048400.10 Clacu06g0484 484
6 5658783 5659312 + ClG42_06g0048600.10 Clacu06g0486 486
6 5662536 5664526 - ClG42_06g0048700.10 Clacu06g0487 487
5 6178104 6179172 - ClCG05G006210.2 Cla05g00665 665
5 6189721 6195077 + ClCG05G006220.1 Cla05g00666 666
5 6197616 6201170 + ClCG05G006230.2 Cla05g00667 667
6 5680081 5687440 + ClCG06G004990.2 Cla06g00466 466
6 5708349 5708881 + ClCG06G005010.1 Cla06g00468 468
6 5711885 5714326 - ClCG06G005020.1 Cla06g00469 469
6 9580529 9583824 + CmaCh06G015150.1 Cma06g01515 1515
8 7567217 7569835 + CmaCh08G012330.1 Cma08g01233 1233
8 7571639 7572360 - CmaCh08G012340.1 Cma08g01234 1234
8 7578482 7580613 - CmaCh08G012360.1 Cma08g01236 1236
14 12110352 12114720 - CmaCh14G016120.1 Cma14g01612 1612
14 12116188 12120377 - CmaCh14G016140.1 Cma14g01614 1614
17 1836590 1839989 + CmaCh17G003360.1 Cma17g00336 336
17 1843990 1846209 - CmaCh17G003380.1 Cma17g00338 338
11 28082677 28085445 + MELO3C021317.2.1 Cme11g02023 2023
11 28098688 28101363 - MELO3C021314.2.1 Cme11g02028 2028
6 5128344 5131394 + PI0013706.1 Cmetu06g1266 1266
11 4112074 4112870 + PI0022567.1 Cmetu11g0533 533
11 4099750 4102858 + PI0007025.1 Cmetu11g2071 2071
8 7677738 7678594 - CmoCh08G012090.1 Cmo08g01209 1209
8 7683983 7686199 - CmoCh08G012110.1 Cmo08g01211 1211
14 13046710 13050181 - CmoCh14G016500.1 Cmo14g01650 1650
14 13053597 13056443 - CmoCh14G016510.1 Cmo14g01651 1651
17 1973466 1975240 - CmoCh17G003270.1 Cmo17g00327 327
5 5915786 5916342 - CmPI595203_05g006870.1 Cmu05g0687 687
5 5927293 5930658 + CmPI595203_05g006880.1 Cmu05g0688 688
5 5933305 5935772 + CmPI595203_05g006890.1 Cmu05g0689 689
6 5434574 5436245 + CmPI595203_06g004850.1 Cmu06g0485 485
6 5460732 5461273 + CmPI595203_06g004880.1 Cmu06g0488 488
6 5464508 5466498 - CmPI595203_06g004890.1 Cmu06g0489 489
4 634165 638720 - Conep04aG0014400.1 Cone4ag0139 139
4 639276 641829 - Conep04aG0014500.1 Cone4ag0140 140
4 643968 644554 - Conep04aG0014600.1 Cone4ag0141 141
4 648480 650865 - Conep04aG0014800.1 Cone4ag0142 142
7 563215 563892 - Conep07aG0013500.1 Cone7ag0134 134
7 564406 566096 - Conep07aG0013600.1 Cone7ag0135 135
7 568213 569851 + Conep07aG0013700.1 Cone7ag0136 136
7 571400 572430 - Conep07aG0013800.1 Cone7ag0137 137
7 574287 576696 - Conep07aG0013900.1 Cone7ag0138 138
14 4203754 4206640 - Conep14aG0076800.1 Cone14ag0751 751
14 4210509 4213378 - Conep14aG0076900.1 Cone14ag0752 752
15 4475536 4478248 - Conep15aG0077300.1 Cone15ag0758 758
15 4486968 4488464 + Conep15aG0077400.1 Cone15ag0759 759
15 4489850 4492657 - Conep15aG0077500.1 Cone15ag0760 760
15 4497108 4503796 - Conep15aG0077600.1 Cone15ag0761 761
3 10966402 10969806 - Cp4.1LG03g11590.1 Cpe03g01354 1354
3 10972384 10975108 - Cp4.1LG03g11550.1 Cpe03g01355 1355
8 1208996 1212429 - Cp4.1LG08g04930.1 Cpe08g00173 173
8 1215040 1216935 + Cp4.1LG08g04960.1 Cpe08g00174 174
8 1217340 1220106 - Cp4.1LG08g04890.1 Cpe08g00175 175
12 1908143 1911205 + Cp4.1LG12g02830.1 Cpe12g00285 285
12 1915799 1918269 - Cp4.1LG12g02940.1 Cpe12g00288 288
17 215990 218615 + Cp4.1LG17g00700.1 Cpe17g00032 32
17 226961 228466 - Cp4.1LG17g00600.1 Cpe17g00034 34
5 6716293 6720629 - CrPI670011_05g007610.1 Cre05g0761 761
5 6727125 6730492 + CrPI670011_05g007620.1 Cre05g0762 762
5 6733244 6735709 + CrPI670011_05g007630.1 Cre05g0763 763
6 6502311 6503982 + CrPI670011_06g012590.1 Cre06g1259 1259
6 6522766 6523254 + CrPI670011_06g012600.1 Cre06g1260 1260
6 6526488 6528482 - CrPI670011_06g012610.1 Cre06g1261 1261
3 10994408 10997947 + CsaV3_3G014810.1 Csa03g01481 1481
3 11000943 11002209 - CsaV3_3G014820.1 Csa03g01482 1482
3 11009987 11013719 + CsaV3_3G014830.1 Csa03g01483 1483
3 11015505 11018983 + CsaV3_3G014840.1 Csa03g01484 1484
6 15851473 15857716 + CsaV3_6G023870.1 Csa06g01793 1793
6 15868950 15872055 - CsaV3_6G023900.1 Csa06g01796 1796
3 1115714 1117383 + Hsped.03g00900.1 Hepe03g0090 90
3 1136911 1137744 + Hsped.03g00910.1 Hepe03g0091 91
11 9145730 9146219 - Lag0031489.1 Lac11g0851 851
11 9170266 9171952 - Lag0031492.1 Lac11g0854 854
12 9444916 9446725 + Maker00025084 Lcy12g0743 743
12 9450124 9451237 - Maker00024834 Lcy12g0744 744
12 9529636 9531132 - Maker00024857 Lcy12g0748 748
5 22033559 22040079 - Lsi05G014100.1 Lsi05g01410 1410
9 22410598 22413107 + Lsi09G014420.1 Lsi09g01442 1442
9 22418761 22419281 - Lsi09G014430.1 Lsi09g01443 1443
9 22438702 22440828 - Lsi09G014470.1 Lsi09g01447 1447
2 48785054 48787647 - Sed0020505.1 Sed02g1173 1173
9 1972055 1974000 - Sed0005161.1 Sed09g0250 250
9 1997171 1999132 - Sed0028174.1 Sed09g0251 251
6 79344179 79347302 + Tan0000635.1 Tan06g2692 2692
6 79349872 79350861 - Tan0008212.1 Tan06g2693 2693
6 79371999 79374363 - Tan0004824.1 Tan06g2694 2694
5 1571670 1574165 + Vvi5g159 Vvi5g159 159
5 1574358 1575136 + Vvi5g160 Vvi5g160 160
5 1575484 1580625 - Vvi5g161 Vvi5g161 161
5 1581334 1592577 - Vvi5g162 Vvi5g162 162
5 1593980 1599561 - Vvi5g163 Vvi5g163 163
5 1602117 1614345 - Vvi5g164 Vvi5g164 164
5 1620964 1622613 + Vvi5g165 Vvi5g165 165
5 1646054 1646805 + Vvi5g166 Vvi5g166 166
5 1650302 1654995 - Vvi5g167 Vvi5g167 167
5 1655451 1664828 - Vvi5g168 Vvi5g168 168
       

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