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
Vvi17g276 . . . . . . . . . Cmo18g00044 . . . . . . . . . . . . . . . . . . . . . . . . . . Csa01g00696 . Cme12g01851 . . . . . . . . Sed01g1748 . . . Cma18g00054 . Car18g00048 . . Bhi08g01264 Tan05g2226 Cmetu12g1408 Lac10g0267 Hepe07g2370 . . Cla04g01068 Cam04g1112 Cec01g1626 Cco01g1672 Clacu04g1138 Cmu04g1120 Cre01g1421 . . . .
Vvi17g277 . Blo16g00128 . . . Bpe13g00365 . . . Cmo18g00043 . . . . . . . . . . . . . . . . . . . . . Cone2ag0742 . . . Lsi02g00213 Csa01g00695 Chy12g01416 Cme12g01852 . . . . . . . . Sed08g2743 . . . Cma18g00053 . Car18g00047 Cpe09g01127 . Bhi08g01263 Tan05g2228 Cmetu09g1201 Lac10g0266 Hepe07g2371 . . Cla04g01069 Cam04g1113 Cec01g1627 Cco01g1673 Clacu04g1139 Cmu04g1121 Cre01g1422 . . . .
Vvi17g278 . . . . Bpe12g00707 Bpe13g00364 Bma06g00053 . Cmo13g01045 Cmo18g00042 . . . . . Cpe20g00137 . . . . . . . . . . . . . . . . . Cone13ag0314 . Lsi02g00212 Csa01g00694 Chy12g01417 Cme12g01853 Blo13g00184 . Bda11g01777 . . . . Bma08g00004 . . . Cma13g01007 Cma18g00052 Car13g00842 Car18g00045 Cpe09g01128 . Bhi08g01262 . . Lac10g0265 . . . Cla04g01070 Cam04g1114 Cec01g1628 Cco01g1674 Clacu04g1140 Cmu04g1122 Cre01g1423 . . . .
Vvi17g279 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g280 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda14g00970 . Bpe15g00477 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g281 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g282 . . . Bda15g00498 Bpe12g00708 . . . . . Cma10g00309 Cma11g00290 Car10g00294 Car11g00265 . . Cpe04g01390 . . . . . . . Cla06g01448 Cam06g1601 Cec06g1663 Cco06g1657 Clacu06g1566 Cmu06g1519 Cre06g2330 Cone2ag0741 . Cone13ag0313 . . . . . Blo13g00185 . . . . . . Bma08g00003 . Cmo10g00332 Cmo11g00295 . . . . . . . . . . . . . . . . . . . . Lsi06g01314 Csa01g00402 Chy02g02347 Cme02g01724
Vvi17g283 . . . . . . . . . Cmo18g00041 . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00209 Csa01g00691 Chy12g01420 Cme12g01856 . . . . . . . . Sed01g1743 . . . Cma18g00051 . Car18g00044 Cpe09g01130 . Bhi08g01258 Tan05g2233 Cmetu10g1289 Lac10g0263 Hepe07g2374 . . Cla04g01073 Cam04g1117 Cec01g1631 Cco01g1677 Clacu04g1143 Cmu04g1124 Cre01g1425 . . . .
Vvi17g284 . . . . . . . . . . . Cma11g00289 . Car11g00263 . . Cpe04g01391 . . . . . . . Cla06g01449 Cam06g1602 Cec06g1664 Cco06g1658 Clacu06g1567 Cmu06g1520 Cre06g2331 . . . . . . . . . . . . . . . . . . Cmo11g00292 . . . . . . . . . . . . . . . . . . . . Lsi06g01315 Csa01g00401 Chy02g02348 Cme02g01725
Vvi17g285 Blo04g00833 Blo16g00131 . . . Bpe13g00360 Bma06g00050 . Cmo13g01049 Cmo18g00040 . . . . . Cpe20g00132 . . . . . . . . . . . . . . . . . . . Lsi02g00207 Csa01g00689 Chy12g01421 Cme12g01857 . . Bda11g01773 . . Bpe15g00531 Bma03g00900 . . . . Cma13g01010 Cma18g00049 Car13g00845 Car18g00043 Cpe09g01132 . Bhi08g01257 . . . . . . Cla04g01075 Cam04g1119 Cec01g1632 Cco01g1678 Clacu04g1145 Cmu04g1126 Cre01g1427 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 52582826 52603139 + Bda008694.1 Bda11g01773 1773
11 52613344 52616192 + Bda008698.2 Bda11g01777 1777
14 7807671 7813554 - Bda027761.1 Bda14g00970 970
15 8078753 8081450 - Bda012326.1 Bda15g00498 498
8 38676240 38681870 + XM_039039559.1 Bhi08g01257 1257
8 38707434 38710619 + XM_039039191.1 Bhi08g01258 1258
8 38945911 38948812 + XM_039038526.1 Bhi08g01262 1262
8 38948956 38953119 - XM_039038524.1 Bhi08g01263 1263
8 38954670 38958561 - XM_039037810.1 Bhi08g01264 1264
4 8863056 8870247 + BLOR13745 Blo04g00833 833
13 7340468 7342444 - BLOR05465 Blo13g00184 184
13 7356230 7357574 + BLOR05466 Blo13g00185 185
16 2941915 2942577 + BLOR07376 Blo16g00128 128
16 2970456 2981678 - BLOR07379 Blo16g00131 131
3 8943399 8947008 + Bma017225.1 Bma03g00900 900
6 839137 847767 + Bma022661.1 Bma06g00050 50
6 856216 858728 + Bma022664.1 Bma06g00053 53
8 90440 93130 - Bma026993.1 Bma08g00003 3
8 94838 97206 + Bma026994.1 Bma08g00004 4
12 12634981 12638022 - Bpe005968.1 Bpe12g00707 707
12 12639057 12641672 + Bpe005969.1 Bpe12g00708 708
13 11369978 11380102 + Bpe006487.1 Bpe13g00360 360
13 11388861 11391821 + Bpe024937 Bpe13g00364 364
13 11392354 11396979 - Bpe006491.2 Bpe13g00365 365
15 16097025 16102973 + Bpe001411.4 Bpe15g00477 477
15 16465499 16469602 + Bpe001466.1 Bpe15g00531 531
4 25244521 25251078 + CaPI482276_04g011120.1 Cam04g1112 1112
4 25253615 25257057 + CaPI482276_04g011130.1 Cam04g1113 1113
4 25257638 25259966 - CaPI482276_04g011140.1 Cam04g1114 1114
4 25284355 25287530 - CaPI482276_04g011170.1 Cam04g1117 1117
4 25294441 25298925 - CaPI482276_04g011190.1 Cam04g1119 1119
6 27498845 27504179 - CaPI482276_06g016010.1 Cam06g1601 1601
6 27505996 27509555 + CaPI482276_06g016020.1 Cam06g1602 1602
10 1418486 1421247 + Carg15161-RA Car10g00294 294
11 1451323 1454289 - Carg09126-RA Car11g00263 263
11 1455128 1457916 + Carg09124-RA Car11g00265 265
13 9058900 9060851 - Carg04830-RA Car13g00842 842
13 9071156 9076079 - Carg04827-RA Car13g00845 845
18 189065 193920 + Carg22743-RA Car18g00043 43
18 198492 200364 + Carg22742-RA Car18g00044 44
18 205912 208381 + Carg22741-RA Car18g00045 45
18 209758 211830 - Carg22739-RA Car18g00047 47
18 212496 215997 - Carg22738-RA Car18g00048 48
1 29460300 29468598 + CcPI632755_01g016720.1 Cco01g1672 1672
1 29471126 29474613 + CcPI632755_01g016730.1 Cco01g1673 1673
1 29475003 29477526 - CcPI632755_01g016740.1 Cco01g1674 1674
1 29504691 29507959 - CcPI632755_01g016770.1 Cco01g1677 1677
1 29514785 29518912 - CcPI632755_01g016780.1 Cco01g1678 1678
6 27169573 27174831 - CcPI632755_06g016570.1 Cco06g1657 1657
6 27176646 27180202 + CcPI632755_06g016580.1 Cco06g1658 1658
1 30898385 30904896 + CePI673135_01g016260.1 Cec01g1626 1626
1 30909028 30912460 + CePI673135_01g016270.1 Cec01g1627 1627
1 30913048 30915374 - CePI673135_01g016280.1 Cec01g1628 1628
1 30942960 30946300 - CePI673135_01g016310.1 Cec01g1631 1631
1 30951995 30957389 - CePI673135_01g016320.1 Cec01g1632 1632
6 30242110 30247451 - CePI673135_06g016630.1 Cec06g1663 1663
6 30249273 30252832 + CePI673135_06g016640.1 Cec06g1664 1664
2 27365327 27369340 - Chy2G046140.1 Chy02g02347 2347
2 27372205 27375456 + Chy2G046150.1 Chy02g02348 2348
12 18246100 18248927 + Chy12G220160.1 Chy12g01416 1416
12 18249762 18251784 - Chy12G220170.1 Chy12g01417 1417
12 18264352 18265996 - Chy12G220200.1 Chy12g01420 1420
12 18269722 18274674 - Chy12G220210.1 Chy12g01421 1421
4 25618774 25626584 + ClG42_04g0113800.10 Clacu04g1138 1138
4 25629133 25632600 + ClG42_04g0113900.10 Clacu04g1139 1139
4 25633185 25635516 - ClG42_04g0114000.10 Clacu04g1140 1140
4 25659984 25663254 - ClG42_04g0114300.10 Clacu04g1143 1143
4 25670143 25674604 - ClG42_04g0114500.10 Clacu04g1145 1145
6 26556429 26561759 - ClG42_06g0156600.10 Clacu06g1566 1566
6 26563208 26566762 + ClG42_06g0156700.10 Clacu06g1567 1567
4 25842773 25852256 + ClCG04G010860.2 Cla04g01068 1068
4 25854411 25858845 + ClCG04G010880.1 Cla04g01069 1069
4 25858914 25861494 - ClCG04G010890.1 Cla04g01070 1070
4 25886104 25889569 - ClCG04G010930.1 Cla04g01073 1073
4 25897161 25901705 - ClCG04G010950.2 Cla04g01075 1075
6 28061951 28067731 - ClCG06G014600.1 Cla06g01448 1448
6 28068986 28072962 + ClCG06G014610.2 Cla06g01449 1449
10 1399203 1406830 + CmaCh10G003090.1 Cma10g00309 309
11 1435374 1443888 - CmaCh11G002890.1 Cma11g00289 289
11 1438460 1439179 + CmaCh11G002900.1 Cma11g00290 290
13 7766129 7769909 - CmaCh13G010070.1 Cma13g01007 1007
13 7779614 7784739 - CmaCh13G010100.1 Cma13g01010 1010
18 199485 204418 + CmaCh18G000490.1 Cma18g00049 49
18 210563 212767 + CmaCh18G000510.1 Cma18g00051 51
18 217902 221289 + CmaCh18G000520.1 Cma18g00052 52
18 220973 224133 - CmaCh18G000530.1 Cma18g00053 53
18 224573 228427 - CmaCh18G000540.1 Cma18g00054 54
2 24253570 24258322 - MELO3C017325.2.1 Cme02g01724 1724
2 24258879 24264273 + MELO3C017324.2.1 Cme02g01725 1725
12 24814709 24818364 + MELO3C002112.2.1 Cme12g01851 1851
12 24818953 24822420 + MELO3C002111.2.1 Cme12g01852 1852
12 24822621 24825236 - MELO3C002110.2.1 Cme12g01853 1853
12 24836824 24838582 - MELO3C002107.2.1 Cme12g01856 1856
12 24843747 24847922 - MELO3C002106.2.1 Cme12g01857 1857
9 4775636 4783155 - PI0028536.1 Cmetu09g1201 1201
10 20577660 20579269 + PI0015893.1 Cmetu10g1289 1289
12 1411631 1416315 - PI0024761.1 Cmetu12g1408 1408
10 1494009 1497567 + CmoCh10G003320.1 Cmo10g00332 332
11 1418338 1420416 - CmoCh11G002920.1 Cmo11g00292 292
11 1421292 1422316 + CmoCh11G002950.1 Cmo11g00295 295
13 8758588 8761712 - CmoCh13G010450.1 Cmo13g01045 1045
13 8771988 8777077 - CmoCh13G010490.1 Cmo13g01049 1049
18 240276 245260 + CmoCh18G000400.1 Cmo18g00040 40
18 249306 251438 + CmoCh18G000410.1 Cmo18g00041 41
18 256295 259643 + CmoCh18G000420.1 Cmo18g00042 42
18 259392 262506 - CmoCh18G000430.1 Cmo18g00043 43
18 263137 276750 - CmoCh18G000440.1 Cmo18g00044 44
4 25798566 25807683 + CmPI595203_04g011200.1 Cmu04g1120 1120
4 25810231 25813697 + CmPI595203_04g011210.1 Cmu04g1121 1121
4 25813721 25816603 - CmPI595203_04g011220.1 Cmu04g1122 1122
4 25841043 25844316 - CmPI595203_04g011240.1 Cmu04g1124 1124
4 25851202 25855316 - CmPI595203_04g011260.1 Cmu04g1126 1126
6 26459649 26464978 - CmPI595203_06g015190.1 Cmu06g1519 1519
6 26466796 26470354 + CmPI595203_06g015200.1 Cmu06g1520 1520
2 33162938 33164299 - Conep02aG0175400.1 Cone2ag0741 741
2 33167464 33171074 - Conep02aG0175500.1 Cone2ag0742 742
13 2505423 2509753 - Conep13aG0033200.1 Cone13ag0313 313
13 2519642 2523146 + Conep13aG0033300.1 Cone13ag0314 314
4 11250098 11254133 - Cp4.1LG04g13880.1 Cpe04g01390 1390
4 11250508 11257606 + Cp4.1LG04g13810.1 Cpe04g01391 1391
9 9683239 9691468 + Cp4.1LG09g11270.1 Cpe09g01127 1127
9 9689616 9693762 - Cp4.1LG09g11340.1 Cpe09g01128 1128
9 9698914 9700893 - Cp4.1LG09g11370.1 Cpe09g01130 1130
9 9704624 9712799 - Cp4.1LG09g11380.1 Cpe09g01132 1132
20 743439 748054 + Cp4.1LG20g01270.1 Cpe20g00132 132
20 762209 765074 + Cp4.1LG20g01260.1 Cpe20g00137 137
1 27450068 27458394 + CrPI670011_01g014210.1 Cre01g1421 1421
1 27460950 27464417 + CrPI670011_01g014220.1 Cre01g1422 1422
1 27464678 27467336 - CrPI670011_01g014230.1 Cre01g1423 1423
1 27496250 27499570 - CrPI670011_01g014250.1 Cre01g1425 1425
1 27506515 27510646 - CrPI670011_01g014270.1 Cre01g1427 1427
6 31247168 31252450 - CrPI670011_06g023300.1 Cre06g2330 2330
6 31254288 31257825 + CrPI670011_06g023310.1 Cre06g2331 2331
1 2501029 2504944 - CsaV3_1G004010.1 Csa01g00401 401
1 2506396 2511082 + CsaV3_1G004020.1 Csa01g00402 402
1 4380893 4384939 + CsaV3_1G006890.1 Csa01g00689 689
1 4388895 4390997 + CsaV3_1G006910.1 Csa01g00691 691
1 4402194 4409190 + CsaV3_1G006940.1 Csa01g00694 694
1 4405839 4408921 - CsaV3_1G006950.1 Csa01g00695 695
1 4409657 4413266 - CsaV3_1G006960.1 Csa01g00696 696
7 68078771 68081934 + Hsped.07g23700.1 Hepe07g2370 2370
7 68084111 68087888 + Hsped.07g23710.1 Hepe07g2371 2371
7 68114846 68117565 - Hsped.07g23740.1 Hepe07g2374 2374
10 2006727 2008428 + Lag0024308.1 Lac10g0263 263
10 2027803 2030261 + Lag0024310.1 Lac10g0265 265
10 2031065 2033617 - Lag0024311.1 Lac10g0266 266
10 2034958 2038242 - Lag0024312.1 Lac10g0267 267
2 1725699 1734657 + Lsi02G002070.1 Lsi02g00207 207
2 1735448 1738101 + Lsi02G002090.1 Lsi02g00209 209
2 1751250 1762307 + Lsi02G002120.1 Lsi02g00212 212
2 1762569 1766615 - Lsi02G002130.1 Lsi02g00213 213
6 23715570 23722973 - Lsi06G013140.1 Lsi06g01314 1314
6 23725086 23731069 + Lsi06G013150.1 Lsi06g01315 1315
1 12657388 12660188 + Sed0027643.1 Sed01g1743 1743
1 12696657 12706337 - Sed0017039.1 Sed01g1748 1748
8 39144439 39147830 - Sed0014158.9 Sed08g2743 2743
5 73212721 73215297 + Tan0015660.2 Tan05g2226 2226
5 73228552 73231803 + Tan0013513.1 Tan05g2228 2228
5 73279695 73282342 - Tan0003785.1 Tan05g2233 2233
17 3076360 3086257 + Vvi17g276 Vvi17g276 276
17 3086514 3092680 + Vvi17g277 Vvi17g277 277
17 3094095 3100458 - Vvi17g278 Vvi17g278 278
17 3106994 3109413 - Vvi17g279 Vvi17g279 279
17 3110881 3118753 - Vvi17g280 Vvi17g280 280
17 3128738 3129930 + Vvi17g281 Vvi17g281 281
17 3130838 3135923 + Vvi17g282 Vvi17g282 282
17 3141357 3143615 - Vvi17g283 Vvi17g283 283
17 3148655 3153072 + Vvi17g284 Vvi17g284 284
17 3160576 3167175 - Vvi17g285 Vvi17g285 285
       

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