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
Vvi18g130 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo18g00751 . Bda01g01555 Bpe02g01750 . Bma01g00707 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g131 . . . . . . . . Cmo05g01012 Cmo12g00605 . . . Car12g00647 Sed08g1824 . Cpe07g00581 Bhi04g01553 Tan02g1543 Cmetu03g1408 . Hepe08g1476 . Lcy13g2246 Cla08g00965 Cam08g1414 Cec08g0993 Cco08g1116 Clacu08g1117 . Cre08g0901 . . . . . . . Cme03g01359 Blo17g00718 Blo18g00752 Bda08g01178 Bda01g01554 Bpe02g01749 Bpe05g00170 Bma01g00708 . . . . Cma12g00666 Cma05g00994 Car05g00876 . . . . . . . . . . . . . . . . . Lsi08g00805 . . .
Vvi18g132 . . Bda01g00717 . . . . . Cmo05g01014 . . . . . . . . Bhi04g01549 . . . Hepe08g1468 . Lcy13g2242 Cla08g00967 Cam08g1416 Cec08g0995 Cco08g1118 Clacu08g1119 . Cre08g0903 . . . Cone20ag0044 . . . Cme03g01363 . Blo18g00754 . Bda01g01551 Bpe02g01747 . Bma01g00710 . . . . . Cma05g00996 Car05g00878 . Cpe11g00805 . . . . . . . . . . . . . . . Lsi08g00809 . Chy03g00636 .
Vvi18g133 Blo01g01352 . . . . . . . Cmo05g01015 . . . . . . . . Bhi04g01548 Tan02g1549 . . Hepe08g1467 . . . . . . . . . . . . Cone20ag0045 . . . Cme03g01364 . . . . . . . . . . . . Cma05g00997 Car05g00879 . Cpe11g00806 . . . . . . . . . . . . . . . Lsi08g00811 . . .
Vvi18g134 . . . . . . . . Cmo05g01018 . . . . . . . . Bhi04g01547 Tan02g1550 . . Hepe08g1466 . . . . . . . . . . . . . . . . Cme03g01365 Blo17g00721 . Bda08g01180 . . . . . . . . . Cma05g00998 Car05g00880 . Cpe11g00807 . . . . . . . . . . . . . . . Lsi08g00814 . . .
Vvi18g135 . . . . Bpe02g00324 . . Bma01g02099 . . . . . . . . . Bhi04g00091 . . . . . . Cla08g01387 Cam08g1860 Cec08g1439 Cco08g1571 Clacu08g1554 . Cre08g1338 . . . . . . . Cme03g01549 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi08g01277 . Chy03g00560 .
Vvi18g136 . . . . . Bpe04g00016 Bma04g00023 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car09g00061 . Cpe02g00877 . . . . . . . . . . . . . . . . . .
Vvi18g137 Blo01g01619 . . . Bpe02g00325 . . Bma01g02394 Cmo05g00336 . Cma01g01997 Cma09g00072 Car01g01569 . . . . Bhi04g00090 . . . Hepe10g0675 . . Cla08g01388 Cam08g1861 Cec08g1440 Cco08g1572 Clacu08g1555 . Cre08g1339 . Cone7ag1919 Cone17ag1436 Cone20ag0046 Lsi04g01790 Csa04g02681 . Cme03g01548 Blo17g00723 Blo18g00757 Bda08g01183 . . Bpe05g00167 Bma01g00712 . Sed03g1664 Cmo01g02058 Cmo09g00073 . Cma05g00335 Car05g00279 . . . Bhi09g02935 Tan01g5072 . . Hepe01g2318 Mch11g0074 . Cla05g01582 Cam05g1690 Cec05g1693 Cco05g1740 Clacu05g1679 Cmu05g1570 Cre05g1687 Lsi08g01278 . Chy07g00372 Cme07g00076
Vvi18g138 Blo01g01618 . . . Bpe02g00326 . . Bma01g02393 . . Cma01g01996 . Car01g01568 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g00955 . . . . . . Cmo01g02057 . . . . . . Cpe02g00049 . . . . . . . . . . . . . . . . . .
Vvi18g139 . . . . . . . . Cmo05g00335 . . . . . Sed11g1117 . . Bhi04g00089 Tan02g2797 Cmetu03g2098 . Hepe10g0193 . Lcy13g1873 Cla08g01389 Cam08g1862 Cec08g1441 Cco08g1573 Clacu08g1556 . Cre08g1340 . . . Cone20ag0047 . . . Cme03g01547 . Blo18g00759 . Bda01g01549 Bpe02g01745 . Bma01g00713 . . . . . Cma05g00334 Car05g00278 . . . . . . . . . . . . . . . . . Lsi08g01279 . Chy03g01055 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 34445562 34451810 + Bda002755.1 Bda01g00717 717
1 51409240 51415316 - Bda003816.2 Bda01g01549 1549
1 51435164 51438357 - Bda003819.3 Bda01g01551 1551
1 51447449 51448541 + Bda003822.1 Bda01g01554 1554
1 51449120 51451466 - Bda003823.1 Bda01g01555 1555
8 47250281 47253245 - Bda030127.1 Bda08g01178 1178
8 47362611 47365643 - Bda030129.1 Bda08g01180 1180
8 47527473 47531207 + Bda034042 Bda08g01183 1183
11 9326300 9330773 - Bda033067 Bda11g00955 955
4 2369941 2382671 - XM_039028493.1 Bhi04g00089 89
4 2384020 2391985 - XM_039030457.1 Bhi04g00090 90
4 2422502 2427556 - XM_039030487.1 Bhi04g00091 91
4 38922465 38936225 + XM_039028817.1 Bhi04g01547 1547
4 38922468 38936225 + XM_039028816.1 Bhi04g01548 1548
4 38979183 38986965 - XM_039029955.1 Bhi04g01549 1549
4 39243059 39245413 + XM_039028304.1 Bhi04g01553 1553
9 76495983 76504629 + XM_039041834.1 Bhi09g02935 2935
1 51314192 51321471 - BLOR01352 Blo01g01352 1352
1 56079624 56093609 - BLOR01618 Blo01g01618 1618
1 56096377 56110286 - BLOR01619 Blo01g01619 1619
17 21107723 21111811 - BLOR08264 Blo17g00718 718
17 21375177 21387057 - BLOR08267 Blo17g00721 721
17 21645693 21649274 + BLOR08269 Blo17g00723 723
18 20367321 20369588 + BLOR09239 Blo18g00751 751
18 20370173 20371195 - BLOR09240 Blo18g00752 752
18 20570392 20572411 - BLOR09242 Blo18g00754 754
18 20906782 20909421 + BLOR09245 Blo18g00757 757
18 20928526 20935687 + BLOR09247 Blo18g00759 759
1 6445378 6447824 + Bma000916.1 Bma01g00707 707
1 6448390 6449472 - Bma000917.1 Bma01g00708 708
1 6455111 6458361 + Bma000919.1 Bma01g00710 710
1 6495166 6507855 + Bma000921.1 Bma01g00712 712
1 6509155 6511376 + Bma000922.1 Bma01g00713 713
1 77039814 77041907 + Bma002921.1 Bma01g02099 2099
1 81526990 81531078 - Bma003265.1 Bma01g02393 2393
1 81534140 81542100 - Bma003266.1 Bma01g02394 2394
4 304387 305858 + Bma018474.1 Bma04g00023 23
2 2106622 2109526 + Bpe008165.1 Bpe02g00324 324
2 2111468 2114448 + Bpe008166.1 Bpe02g00325 325
2 2116700 2121003 + Bpe008167.1 Bpe02g00326 326
2 19839791 19846420 - Bpe009576.1 Bpe02g01745 1745
2 19859342 19862495 - Bpe009578.1 Bpe02g01747 1747
2 19869117 19870175 + Bpe025177 Bpe02g01749 1749
2 19870756 19873339 - Bpe009580.3 Bpe02g01750 1750
4 171750 173233 + Bpe014743.1 Bpe04g00016 16
5 5277572 5281333 - Bpe017554.1 Bpe05g00167 167
5 5611391 5614290 + Bpe017557.1 Bpe05g00170 170
5 25186261 25192059 + CaPI482276_05g016900.1 Cam05g1690 1690
8 20372177 20374188 - CaPI482276_08g014140.1 Cam08g1414 1414
8 20391028 20396078 + CaPI482276_08g014160.1 Cam08g1416 1416
8 24641175 24645635 + CaPI482276_08g018600.1 Cam08g1860 1860
8 24650531 24657259 + CaPI482276_08g018610.1 Cam08g1861 1861
8 24661058 24670741 + CaPI482276_08g018620.1 Cam08g1862 1862
1 13050626 13055277 - Carg21387-RA Car01g01568 1568
1 13056399 13058652 - Carg21386-RA Car01g01569 1569
5 1536900 1543365 - Carg09381-RA Car05g00278 278
5 1544185 1548971 - Carg09380-RA Car05g00279 279
5 8546291 8548566 - Carg21863-RA Car05g00876 876
5 8560063 8565069 + Carg21861-RA Car05g00878 878
5 8567869 8576963 - Carg21860-RA Car05g00879 879
5 8578040 8590823 + Carg21859-RA Car05g00880 880
9 308306 308632 + Carg08644-RA Car09g00061 61
12 4378419 4380556 + Carg17655-RA Car12g00647 647
5 25750667 25756075 + CcPI632755_05g017400.1 Cco05g1740 1740
8 22886167 22888233 - CcPI632755_08g011160.1 Cco08g1116 1116
8 22912074 22917181 + CcPI632755_08g011180.1 Cco08g1118 1118
8 27308556 27312998 + CcPI632755_08g015710.1 Cco08g1571 1571
8 27318283 27325033 + CcPI632755_08g015720.1 Cco08g1572 1572
8 27326823 27333840 + CcPI632755_08g015730.1 Cco08g1573 1573
5 28125720 28135293 + CePI673135_05g016930.1 Cec05g1693 1693
8 21738872 21740885 - CePI673135_08g009930.1 Cec08g0993 993
8 21759758 21764818 + CePI673135_08g009950.1 Cec08g0995 995
8 26167075 26171573 + CePI673135_08g014390.1 Cec08g1439 1439
8 26176905 26183831 + CePI673135_08g014400.1 Cec08g1440 1440
8 26183877 26192424 + CePI673135_08g014410.1 Cec08g1441 1441
3 8036438 8038531 + Chy3G055400.1 Chy03g00560 560
3 8869885 8880426 + Chy3G056160.1 Chy03g00636 636
3 14010954 14022706 - Chy3G060350.1 Chy03g01055 1055
7 3012560 3017461 - Chy7G132020.1 Chy07g00372 372
5 25369461 25374720 + ClG42_05g0167900.10 Clacu05g1679 1679
8 21143179 21145209 - ClG42_08g0111700.10 Clacu08g1117 1117
8 21161670 21166787 + ClG42_08g0111900.10 Clacu08g1119 1119
8 25385243 25389683 + ClG42_08g0155400.10 Clacu08g1554 1554
8 25394604 25401392 + ClG42_08g0155500.10 Clacu08g1555 1555
8 25403487 25414789 + ClG42_08g0155600.10 Clacu08g1556 1556
5 26791685 26796945 + ClCG05G015250.2 Cla05g01582 1582
8 22246331 22248340 - ClCG08G009600.1 Cla08g00965 965
8 22265004 22270303 + ClCG08G009620.2 Cla08g00967 967
8 26734092 26738534 + ClCG08G013910.2 Cla08g01387 1387
8 26743359 26750661 + ClCG08G013920.1 Cla08g01388 1388
8 26751994 26759343 + ClCG08G013930.2 Cla08g01389 1389
1 12826363 12831312 - CmaCh01G019960.1 Cma01g01996 1996
1 12832004 12834436 - CmaCh01G019970.1 Cma01g01997 1997
5 1447559 1455196 - CmaCh05G003340.1 Cma05g00334 334
5 1455822 1460483 - CmaCh05G003350.1 Cma05g00335 335
5 7982032 7984555 - CmaCh05G009940.1 Cma05g00994 994
5 7995006 8000790 + CmaCh05G009960.1 Cma05g00996 996
5 7997452 8012710 - CmaCh05G009970.1 Cma05g00997 997
5 8014630 8027286 + CmaCh05G009980.1 Cma05g00998 998
9 317328 329077 + CmaCh09G000720.1 Cma09g00072 72
12 3578859 3580761 + CmaCh12G006660.1 Cma12g00666 666
3 23106967 23109779 - MELO3C026549.2.1 Cme03g01359 1359
3 23128348 23130785 + MELO3C030285.2.1 Cme03g01363 1363
3 23128732 23137007 - MELO3C026552.2.1 Cme03g01364 1364
3 23139200 23142887 - MELO3C026553.2.1 Cme03g01365 1365
3 24569287 24576325 - MELO3C011330.2.1 Cme03g01547 1547
3 24576867 24581957 - MELO3C011329.2.1 Cme03g01548 1548
3 24584913 24589222 - MELO3C011328.2.1 Cme03g01549 1549
7 468307 473776 + MELO3C017005.2.1 Cme07g00076 76
3 6278505 6281791 + PI0023259.1 Cmetu03g1408 1408
3 4828401 4835108 + PI0000572.1 Cmetu03g2098 2098
1 14360794 14372141 - CmoCh01G020570.1 Cmo01g02057 2057
1 14373346 14375853 - CmoCh01G020580.1 Cmo01g02058 2058
5 1488210 1496341 - CmoCh05G003350.1 Cmo05g00335 335
5 1497718 1502296 - CmoCh05G003360.1 Cmo05g00336 336
5 8147409 8150161 - CmoCh05G010120.1 Cmo05g01012 1012
5 8162745 8169470 + CmoCh05G010140.1 Cmo05g01014 1014
5 8171550 8182733 - CmoCh05G010150.1 Cmo05g01015 1015
5 8197154 8201482 + CmoCh05G010180.1 Cmo05g01018 1018
9 325982 339052 + CmoCh09G000730.1 Cmo09g00073 73
12 3775333 3778471 + CmoCh12G006050.1 Cmo12g00605 605
5 25091033 25096292 + CmPI595203_05g015700.1 Cmu05g1570 1570
7 12274202 12278056 - Conep07aG0197700.1 Cone7ag1919 1919
17 9801776 9804250 - Conep17aG0147700.1 Cone17ag1436 1436
20 216335 219312 + Conep20aG0004400.1 Cone20ag0044 44
20 219359 221700 - Conep20aG0004500.1 Cone20ag0045 45
20 222539 225038 + Conep20aG0004600.1 Cone20ag0046 46
20 227026 230976 + Conep20aG0004700.1 Cone20ag0047 47
2 254097 259350 + Cp4.1LG02g08210.1 Cpe02g00049 49
2 6164890 6167328 + Cp4.1LG02g09070.1 Cpe02g00877 877
7 3902053 3904520 + Cp4.1LG07g05940.1 Cpe07g00581 581
11 6516233 6522417 + Cp4.1LG11g08010.1 Cpe11g00805 805
11 6524968 6530529 - Cp4.1LG11g08060.1 Cpe11g00806 806
11 6536622 6548663 + Cp4.1LG11g08130.1 Cpe11g00807 807
5 28283969 28289362 + CrPI670011_05g016870.1 Cre05g1687 1687
8 22124439 22126505 - CrPI670011_08g009010.1 Cre08g0901 901
8 22145020 22150081 + CrPI670011_08g009030.1 Cre08g0903 903
8 26445969 26450268 + CrPI670011_08g013380.1 Cre08g1338 1338
8 26455585 26462440 + CrPI670011_08g013390.1 Cre08g1339 1339
8 26464676 26476149 + CrPI670011_08g013400.1 Cre08g1340 1340
4 26031612 26037489 - CsaV3_4G037070.1 Csa04g02681 2681
1 87800210 87805577 - Hsped.01g23180.1 Hepe01g2318 2318
8 17859081 17864237 + Hsped.08g14660.1 Hepe08g1466 1466
8 17869294 17879560 + Hsped.08g14670.1 Hepe08g1467 1467
8 17877651 17881138 - Hsped.08g14680.1 Hepe08g1468 1468
8 18212044 18218015 + Hsped.08g14760.1 Hepe08g1476 1476
10 1951986 1959415 - Hsped.10g01930.1 Hepe10g0193 193
10 8944314 8946718 - Hsped.10g06750.1 Hepe10g0675 675
13 37605006 37613120 + Maker00034230 Lcy13g1873 1873
13 41356013 41362652 - Maker00025197 Lcy13g2242 2242
13 41400857 41403753 + Maker00025263 Lcy13g2246 2246
4 25115366 25121561 - Lsi04G017900.1 Lsi04g01790 1790
8 16428658 16431873 - Lsi08G008050.1 Lsi08g00805 805
8 16456518 16457354 + Lsi08G008090.1 Lsi08g00809 809
8 16461329 16466166 - Lsi08G008110.1 Lsi08g00811 811
8 16492986 16494456 - Lsi08G008140.1 Lsi08g00814 814
8 21160483 21165081 + Lsi08G012770.1 Lsi08g01277 1277
8 21170858 21176594 + Lsi08G012780.1 Lsi08g01278 1278
8 21178097 21183751 + Lsi08G012790.1 Lsi08g01279 1279
11 470294 479124 + MC11g0067 Mch11g0074 74
3 10713580 10719801 + Sed0022375.1 Sed03g1664 1664
8 32992598 32995041 + Sed0012631.1 Sed08g1824 1824
11 26915608 26924050 - Sed0027939.1 Sed11g1117 1117
1 116262375 116268131 - Tan0022526.2 Tan01g5072 5072
2 67263623 67266118 + Tan0012892.1 Tan02g1543 1543
2 67872133 67917336 - Tan0011023.1 Tan02g1549 1549
2 67872133 67875550 - Tan0011023.2 Tan02g1550 1550
2 96284772 96298577 + Tan0018920.1 Tan02g2797 2797
18 1270454 1281026 + Vvi18g130 Vvi18g130 130
18 1281189 1291984 - Vvi18g131 Vvi18g131 131
18 1303909 1307352 + Vvi18g132 Vvi18g132 132
18 1307368 1311229 - Vvi18g133 Vvi18g133 133
18 1319711 1322860 - Vvi18g134 Vvi18g134 134
18 1330119 1337723 + Vvi18g135 Vvi18g135 135
18 1343782 1349354 + Vvi18g136 Vvi18g136 136
18 1351278 1357082 + Vvi18g137 Vvi18g137 137
18 1357799 1364583 - Vvi18g138 Vvi18g138 138
18 1365466 1370757 + Vvi18g139 Vvi18g139 139
       

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