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
Vvi17g306 Blo04g00830 . . . . Bpe13g00355 Bma06g00047 . Cmo13g01061 Cmo18g00038 . . . . . Cpe20g00126 . . . . . . . . . . . . . . . . . Cone13ag0305 . Lsi02g00186 Csa01g00669 Chy12g01434 Cme12g01872 . . Bda11g01770 . . . Bma03g00896 . Sed08g2186 . . Cma13g01020 Cma18g00045 Car13g00854 Car18g00039 Cpe09g01135 . Bhi08g01239 Tan05g2262 Cmetu12g0605 Lac10g0242 Hepe07g2388 . . Cla04g01086 . . . . . . . . . .
Vvi17g307 . . . . . . . . . . . . . . . Cpe20g00125 . . . . . . . . . . . . . . . . . . . Lsi02g00185 Csa01g00668 . . . . . . . . . . . . . . . . . . . Bhi08g01238 . . . . . . . . . . . . . . . . .
Vvi17g308 Blo04g00828 . . . . . . . Cmo13g01062 . Cma10g00303 . Car10g00288 . . . . . . . . . . . Cla06g01460 Cam06g1612 Cec06g1674 Cco06g1668 Clacu06g1576 Cmu06g1528 Cre06g2339 . Cone16ag0570 . . . . Chy12g01435 Cme12g01873 . . . . . . . . . Cmo10g00324 . Cma13g01021 . . . . . Bhi08g01237 . . . . . . Cla04g01089 . . . . . . Lsi06g01323 Csa01g00394 Chy02g02355 Cme02g01732
Vvi17g309 . . . . . . . . Cmo13g01063 Cmo18g00037 Cma10g00302 . Car10g00287 Car11g00255 . Cpe20g00124 Cpe04g01398 . . . . . . . Cla06g01461 Cam06g1613 Cec06g1675 Cco06g1669 Clacu06g1577 Cmu06g1529 Cre06g2340 . Cone16ag0571 . . Lsi02g00184 Csa01g00667 Chy12g01436 Cme12g01874 . . . . . . . . Sed08g2185 Cmo10g00323 Cmo11g00284 . Cma18g00044 Car13g00856 Car18g00038 Cpe09g01136 . Bhi08g01235 Tan05g2265 Cmetu02g2026 Lac10g0240 Hepe07g2390 . . . . . . . . . Lsi06g01324 Csa01g00393 . Cme02g01733
Vvi17g310 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy02g02449 .
Vvi17g311 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g312 Blo04g00827 . . . . Bpe13g00353 Bma06g00046 . . . . Cma11g00280 . . . . . . . . . . . . Cla06g01462 . . . . . . . . . . Lsi02g00183 Csa01g00666 Chy12g01437 Cme12g01875 . . . . . Bpe15g00526 Bma03g00895 . . . Cmo11g00283 Cma13g01022 . . . . . Bhi08g01234 . . . . . . Cla04g01090 . . . . . . Lsi06g01325 Csa01g00392 Chy02g02356 Cme02g01734
Vvi17g313 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone2ag0635 Cone16ag0273 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g314 Blo04g00825 . Bda06g00808 Bda15g00661 Bpe12g00693 . . . Cmo13g01064 Cmo18g00036 Cma10g00230 Cma11g00279 Car10g00215 Car11g00253 . Cpe20g00122 Cpe04g01400 . . . . . . . Cla06g01463 Cam06g1615 Cec06g1678 Cco06g1671 Clacu06g1579 Cmu06g1531 Cre06g2342 . . Cone13ag0303 . Lsi02g00182 Csa01g00665 Chy12g01438 Cme12g01876 Blo13g00169 Blo15g00068 . . Bpe07g01037 Bpe15g00525 . Bma08g00060 Sed08g2182 Cmo10g00243 Cmo11g00282 Cma13g01023 Cma18g00043 Car13g00858 Car18g00037 Cpe09g01137 Cpe18g00762 Bhi08g01233 Tan05g2268 Cmetu12g1509 Lac10g0238 Hepe07g2392 . . Cla04g01092 Cam04g1143 Cec01g1653 Cco01g1702 Clacu04g1171 Cmu04g1152 Cre01g1447 Lsi06g01326 Csa01g00391 Chy02g02357 Cme02g01735
Vvi17g315 . . Bda06g00807 Bda15g00515 Bpe12g00692 . . Bma12g01232 . . Cma10g00231 Cma11g00277 Car10g00216 Car11g00252 . . Cpe04g01401 . . . . . . . Cla06g01464 Cam06g1617 Cec06g1679 Cco06g1672 Clacu06g1581 Cmu06g1532 Cre06g2344 . . . . . . . . Blo13g00167 Blo15g00069 . . Bpe07g01036 . . Bma08g00061 . . Cmo11g00281 . . . . . Cpe18g00761 . . . . . . . . . . . . . . Lsi06g01327 Csa01g00389 Chy02g02358 Cme02g01736
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 11311046 11316026 - Bda024136.1 Bda06g00807 807
6 11320119 11321458 - Bda024137.2 Bda06g00808 808
11 52548520 52553234 + Bda008690.1 Bda11g01770 1770
15 8228052 8232846 + Bda012345.1 Bda15g00515 515
15 10101812 10109051 - Bda012511.1 Bda15g00661 661
8 38241415 38243650 - XM_039039309.1 Bhi08g01233 1233
8 38257125 38258593 + XM_039038980.1 Bhi08g01234 1234
8 38266238 38268566 + XM_039037594.1 Bhi08g01235 1235
8 38269280 38279317 - XM_039038332.1 Bhi08g01237 1237
8 38269280 38279313 - XM_039038330.1 Bhi08g01238 1238
8 38315738 38325454 + XM_039038636.1 Bhi08g01239 1239
4 8695695 8701354 - BLOR13737 Blo04g00825 825
4 8734804 8735825 + BLOR13739 Blo04g00827 827
4 8736525 8740624 - BLOR13740 Blo04g00828 828
4 8751540 8766210 + BLOR13742 Blo04g00830 830
13 5942500 5947087 - BLOR05448 Blo13g00167 167
13 5996705 5997709 - BLOR05450 Blo13g00169 169
15 571507 580340 + BLOR06462 Blo15g00068 68
15 583900 588887 + BLOR06463 Blo15g00069 69
3 8850466 8851487 + Bma017219.1 Bma03g00895 895
3 8860622 8865484 + Bma017221.1 Bma03g00896 896
6 791934 792988 + Bma022656.1 Bma06g00046 46
6 801560 809762 + Bma022657.2 Bma06g00047 47
8 764530 765678 + Bma027057.1 Bma08g00060 60
8 769768 774566 + Bma027058.1 Bma08g00061 61
12 45248292 45259870 - Bma008596.2 Bma12g01232 1232
7 15874375 15885804 - Bpe021880.1 Bpe07g01036 1036
7 15889390 15890765 - Bpe021881.3 Bpe07g01037 1037
12 12499591 12505599 - Bpe005952.1 Bpe12g00692 692
12 12509573 12510781 - Bpe005953.1 Bpe12g00693 693
13 11329232 11330286 + Bpe006480.1 Bpe13g00353 353
13 11343248 11347950 + Bpe006482.1 Bpe13g00355 355
15 16408181 16409270 - Bpe001458.1 Bpe15g00525 525
15 16415326 16416344 + Bpe001459.1 Bpe15g00526 526
4 25502305 25503911 + CaPI482276_04g011430.1 Cam04g1143 1143
6 27591470 27594735 + CaPI482276_06g016120.1 Cam06g1612 1612
6 27595548 27596997 - CaPI482276_06g016130.1 Cam06g1613 1613
6 27616106 27617756 + CaPI482276_06g016150.1 Cam06g1615 1615
6 27627994 27631716 + CaPI482276_06g016170.1 Cam06g1617 1617
10 1031717 1033052 + Carg17928-RA Car10g00215 215
10 1036383 1040976 + Carg17927-RA Car10g00216 216
10 1382047 1384309 + Carg15154-RA Car10g00287 287
10 1384859 1387669 - Carg15155-RA Car10g00288 288
11 1400215 1401833 - Carg09137-RA Car11g00252 252
11 1404661 1406019 - Carg09136-RA Car11g00253 253
11 1411798 1413959 + Carg09134-RA Car11g00255 255
13 9114090 9120597 - Carg04818-RA Car13g00854 854
13 9123793 9126483 - Carg04816-RA Car13g00856 856
13 9133842 9135828 + Carg04814-RA Car13g00858 858
18 164214 165124 - Carg22749-RA Car18g00037 37
18 167333 169669 + Carg22748-RA Car18g00038 38
18 170209 176746 + Carg22747-RA Car18g00039 39
1 29741474 29743020 + CcPI632755_01g017020.1 Cco01g1702 1702
6 27262576 27265839 + CcPI632755_06g016680.1 Cco06g1668 1668
6 27266684 27268135 - CcPI632755_06g016690.1 Cco06g1669 1669
6 27293300 27294972 + CcPI632755_06g016710.1 Cco06g1671 1671
6 27305307 27309021 + CcPI632755_06g016720.1 Cco06g1672 1672
1 31186710 31188323 + CePI673135_01g016530.1 Cec01g1653 1653
6 30334718 30337447 + CePI673135_06g016740.1 Cec06g1674 1674
6 30338833 30340285 - CePI673135_06g016750.1 Cec06g1675 1675
6 30365947 30367626 + CePI673135_06g016780.1 Cec06g1678 1678
6 30378072 30381807 + CePI673135_06g016790.1 Cec06g1679 1679
2 27435385 27445813 + Chy2G046220.1 Chy02g02355 2355
2 27445914 27447018 - Chy2G046230.1 Chy02g02356 2356
2 27456766 27458322 + Chy2G046240.1 Chy02g02357 2357
2 27465992 27469533 + Chy2G046250.1 Chy02g02358 2358
2 28116829 28119368 - Chy2G047160.1 Chy02g02449 2449
12 18351428 18357606 - Chy12G220340.1 Chy12g01434 1434
12 18358815 18362738 + Chy12G220350.1 Chy12g01435 1435
12 18363361 18364956 - Chy12G220360.1 Chy12g01436 1436
12 18369691 18370741 - Chy12G220370.1 Chy12g01437 1437
12 18379377 18380842 + Chy12G220380.1 Chy12g01438 1438
4 25892325 25893944 + ClG42_04g0117100.10 Clacu04g1171 1171
6 26648182 26650911 + ClG42_06g0157600.10 Clacu06g1576 1576
6 26652254 26653706 - ClG42_06g0157700.10 Clacu06g1577 1577
6 26672764 26674426 + ClG42_06g0157900.10 Clacu06g1579 1579
6 26684819 26688539 + ClG42_06g0158100.10 Clacu06g1581 1581
4 26039448 26047756 - ClCG04G011040.2 Cla04g01086 1086
4 26060328 26062143 + ClCG04G011070.1 Cla04g01089 1089
4 26063644 26071815 - ClCG04G011080.2 Cla04g01090 1090
4 26099025 26100644 + ClCG04G011110.1 Cla04g01092 1092
6 28158474 28161978 + ClCG06G014710.2 Cla06g01460 1460
6 28162700 28164878 - ClCG06G014720.1 Cla06g01461 1461
6 28172841 28174635 - ClCG06G014730.1 Cla06g01462 1462
6 28183341 28186563 + ClCG06G014740.1 Cla06g01463 1463
6 28196041 28200823 + ClCG06G014750.2 Cla06g01464 1464
10 1021588 1023449 + CmaCh10G002300.1 Cma10g00230 230
10 1026601 1031391 + CmaCh10G002310.1 Cma10g00231 231
10 1367739 1370267 + CmaCh10G003020.1 Cma10g00302 302
10 1369255 1373526 - CmaCh10G003030.1 Cma10g00303 303
11 1383524 1387538 - CmaCh11G002770.1 Cma11g00277 277
11 1389994 1391498 - CmaCh11G002790.1 Cma11g00279 279
11 1393364 1398202 + CmaCh11G002800.1 Cma11g00280 280
13 7821116 7827973 - CmaCh13G010200.1 Cma13g01020 1020
13 7828480 7831285 + CmaCh13G010210.1 Cma13g01021 1021
13 7831487 7836093 - CmaCh13G010220.1 Cma13g01022 1022
13 7841204 7842988 + CmaCh13G010230.1 Cma13g01023 1023
18 174590 175573 - CmaCh18G000430.1 Cma18g00043 43
18 178614 180886 + CmaCh18G000440.1 Cma18g00044 44
18 181474 188328 + CmaCh18G000450.1 Cma18g00045 45
2 24324178 24327925 + MELO3C017317.2.1 Cme02g01732 1732
2 24327421 24329614 - MELO3C017316.2.1 Cme02g01733 1733
2 24335178 24336523 - MELO3C017315.2.1 Cme02g01734 1734
2 24345556 24347334 + MELO3C017314.2.1 Cme02g01735 1735
2 24354524 24359110 + MELO3C017313.2.1 Cme02g01736 1736
12 24919251 24926313 - MELO3C002093.2.1 Cme12g01872 1872
12 24926920 24931700 + MELO3C002092.2.1 Cme12g01873 1873
12 24931709 24934520 - MELO3C002091.2.1 Cme12g01874 1874
12 24937585 24939008 - MELO3C002090.2.1 Cme12g01875 1875
12 24949054 24950906 + MELO3C002089.2.1 Cme12g01876 1876
2 22701611 22703936 - PI0014521.2 Cmetu02g2026 2026
12 1295978 1302450 + PI0004917.1 Cmetu12g0605 605
12 1269889 1271567 - PI0000204.1 Cmetu12g1509 1509
10 1081086 1082595 + CmoCh10G002430.1 Cmo10g00243 243
10 1456361 1459412 + CmoCh10G003230.1 Cmo10g00323 323
10 1459859 1462905 - CmoCh10G003240.1 Cmo10g00324 324
11 1364309 1368164 - CmoCh11G002810.1 Cmo11g00281 281
11 1371030 1372415 - CmoCh11G002820.1 Cmo11g00282 282
11 1374418 1375700 + CmoCh11G002830.1 Cmo11g00283 283
11 1378361 1380710 + CmoCh11G002840.1 Cmo11g00284 284
13 8822188 8828936 - CmoCh13G010610.1 Cmo13g01061 1061
13 8829435 8832207 + CmoCh13G010620.1 Cmo13g01062 1062
13 8832448 8837139 - CmoCh13G010630.1 Cmo13g01063 1063
13 8842441 8844906 + CmoCh13G010640.1 Cmo13g01064 1064
18 213740 214908 - CmoCh18G000360.1 Cmo18g00036 36
18 217045 219288 + CmoCh18G000370.1 Cmo18g00037 37
18 219910 226451 + CmoCh18G000380.1 Cmo18g00038 38
4 26074358 26075977 + CmPI595203_04g011520.1 Cmu04g1152 1152
6 26551132 26554397 + CmPI595203_06g015280.1 Cmu06g1528 1528
6 26555205 26556657 - CmPI595203_06g015290.1 Cmu06g1529 1529
6 26575751 26577420 + CmPI595203_06g015310.1 Cmu06g1531 1531
6 26587803 26591523 + CmPI595203_06g015320.1 Cmu06g1532 1532
2 4119139 4122586 - Conep02aG0064900.1 Cone2ag0635 635
13 2373843 2375652 - Conep13aG0032100.1 Cone13ag0303 303
13 2383148 2387545 + Conep13aG0032300.1 Cone13ag0305 305
16 3106442 3109373 + Conep16aG0262200.1 Cone16ag0273 273
16 7564007 7566799 + Conep16aG0293100.1 Cone16ag0570 570
16 7569664 7571304 + Conep16aG0293200.1 Cone16ag0571 571
4 11292884 11295742 - Cp4.1LG04g14110.1 Cpe04g01398 1398
4 11301856 11303413 + Cp4.1LG04g13990.1 Cpe04g01400 1400
4 11306179 11310501 + Cp4.1LG04g13970.1 Cpe04g01401 1401
9 9721877 9728637 - Cp4.1LG09g11360.1 Cpe09g01135 1135
9 9729186 9731525 - Cp4.1LG09g11350.1 Cpe09g01136 1136
9 9735254 9736369 + Cp4.1LG09g11280.1 Cpe09g01137 1137
18 7295754 7307087 - Cp4.1LG18g07780.1 Cpe18g00761 761
18 7310238 7312070 - Cp4.1LG18g07730.1 Cpe18g00762 762
20 682246 684350 - Cp4.1LG20g01150.1 Cpe20g00122 122
20 691602 694102 + Cp4.1LG20g01240.1 Cpe20g00124 124
20 694365 697193 - Cp4.1LG20g01340.1 Cpe20g00125 125
20 697637 704403 + Cp4.1LG20g01290.1 Cpe20g00126 126
1 27718479 27720096 + CrPI670011_01g014470.1 Cre01g1447 1447
6 31338437 31341160 + CrPI670011_06g023390.1 Cre06g2339 2339
6 31342526 31343972 - CrPI670011_06g023400.1 Cre06g2340 2340
6 31363236 31364989 + CrPI670011_06g023420.1 Cre06g2342 2342
6 31375320 31381130 + CrPI670011_06g023440.1 Cre06g2344 2344
1 2412851 2416403 - CsaV3_1G003890.1 Csa01g00389 389
1 2423148 2424832 - CsaV3_1G003910.1 Csa01g00391 391
1 2431966 2433180 + CsaV3_1G003920.1 Csa01g00392 392
1 2437661 2439879 + CsaV3_1G003930.1 Csa01g00393 393
1 2439956 2443243 - CsaV3_1G003940.1 Csa01g00394 394
1 4277323 4279125 - CsaV3_1G006650.1 Csa01g00665 665
1 4287009 4288668 + CsaV3_1G006660.1 Csa01g00666 666
1 4292568 4295169 + CsaV3_1G006670.1 Csa01g00667 667
1 4295378 4299708 - CsaV3_1G006680.1 Csa01g00668 668
1 4298591 4307353 + CsaV3_1G006690.1 Csa01g00669 669
7 68216444 68222514 - Hsped.07g23880.1 Hepe07g2388 2388
7 68236367 68238909 - Hsped.07g23900.1 Hepe07g2390 2390
7 68266336 68267737 + Hsped.07g23920.1 Hepe07g2392 2392
10 1857593 1858897 - Lag0024283.1 Lac10g0238 238
10 1878559 1880678 + Lag0024285.1 Lac10g0240 240
10 1891995 1897834 + Lag0024287.1 Lac10g0242 242
2 1559712 1562055 - Lsi02G001820.1 Lsi02g00182 182
2 1571424 1572904 + Lsi02G001830.1 Lsi02g00183 183
2 1577360 1580031 + Lsi02G001840.1 Lsi02g00184 184
2 1581109 1589488 - Lsi02G001850.1 Lsi02g00185 185
2 1592575 1599618 + Lsi02G001860.1 Lsi02g00186 186
6 23817301 23821022 + Lsi06G013230.1 Lsi06g01323 1323
6 23821019 23823767 - Lsi06G013240.1 Lsi06g01324 1324
6 23833606 23835418 - Lsi06G013250.1 Lsi06g01325 1325
6 23847576 23850212 + Lsi06G013260.1 Lsi06g01326 1326
6 23860184 23864987 + Lsi06G013270.1 Lsi06g01327 1327
8 35745054 35746603 - Sed0003130.1 Sed08g2182 2182
8 35767028 35769435 + Sed0018729.2 Sed08g2185 2185
8 35770798 35779380 + Sed0021143.1 Sed08g2186 2186
5 73523215 73531199 - Tan0015665.1 Tan05g2262 2262
5 73548950 73551513 - Tan0020767.1 Tan05g2265 2265
5 73960172 73961777 + Tan0010040.2 Tan05g2268 2268
17 3361914 3388653 - Vvi17g306 Vvi17g306 306
17 3396900 3402903 + Vvi17g307 Vvi17g307 307
17 3407143 3414365 + Vvi17g308 Vvi17g308 308
17 3414628 3417929 - Vvi17g309 Vvi17g309 309
17 3419332 3425533 + Vvi17g310 Vvi17g310 310
17 3428365 3429668 - Vvi17g311 Vvi17g311 311
17 3453988 3455697 - Vvi17g312 Vvi17g312 312
17 3462739 3465475 - Vvi17g313 Vvi17g313 313
17 3477175 3478644 + Vvi17g314 Vvi17g314 314
17 3488429 3511867 + Vvi17g315 Vvi17g315 315
       

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