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
Vvi17g766 . . Bda06g00607 . . . . Bma12g01042 . . Cma10g00122 Cma11g00092 Car10g00110 Car11g00084 . . Cpe04g01562 Bhi02g00454 Tan09g2254 . . . . . Cla06g01666 Cam06g1851 Cec06g1903 Cco06g1908 Clacu06g1810 Cmu06g1751 Cre06g2570 Cone2ag0913 Cone16ag0095 . . . . . . . Blo15g00264 . . Bpe07g00845 . . . . Cmo10g00126 Cmo11g00091 . . . . . Cpe18g00847 . . . . . . . . . . . . . . Lsi06g01558 Csa01g00145 Chy02g02584 .
Vvi17g767 . . . Bda15g00553 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0146 . . . . . . . . . . . . Bma08g00098 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g768 . . . . . Bpe13g00245 Bma06g00215 . . Cmo18g00134 . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0147 Cone19ag0144 Lsi02g00380 Csa01g00859 Chy12g01262 Cme12g01687 . . Bda11g01658 . . . . . Sed08g2519 . . . Cma18g00176 . Car18g00166 Cpe09g01020 . Bhi08g01622 Tan05g1997 Cmetu12g1080 . Hepe07g2220 . . Cla01g01306 Cam01g1425 Cec01g1458 Cco01g1465 Clacu01g1371 Cmu01g1278 Cre01g1260 . . . .
Vvi17g769 . . . Bda15g00552 . . . . Cmo13g00911 Cmo18g00135 . . . . . . . . . . . . . . . . . . . . . Cone2ag0914 Cone16ag0094 . . . Csa01g00860 Chy12g01261 Cme12g01686 . . . . . . . Bma08g00097 Sed08g2520 . . Cma13g00880 Cma18g00177 Car13g00721 Car18g00167 Cpe09g01019 . Bhi08g01623 Tan05g1996 Cmetu12g1069 Lac10g0458 Hepe07g2219 . . Cla01g01307 Cam01g1423 Cec01g1457 Cco01g1466 Clacu01g1372 Cmu01g1280 Cre01g1259 . . . .
Vvi17g770 . . . . . . . . . . . . . . . Cpe20g00249 . . . . . . . . . . . . . . . Cone2ag0915 Cone16ag0093 . . Lsi02g00381 Csa01g00861 Chy12g01260 Cme12g01685 . . . . . . . . Sed08g2521 . . . . Car13g00720 . . . Bhi08g01624 Tan05g1995 Cmetu12g2030 Lac10g0459 Hepe07g2218 . . Cla01g01308 Cam01g1422 Cec01g1456 Cco01g1468 Clacu01g1373 Cmu01g1281 Cre01g1258 . . . .
Vvi17g771 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00382 Csa01g00862 . Cme12g01684 . . . Bda14g00807 . Bpe15g00641 Bma03g00778 . Sed01g1640 . . . . . Car18g00168 Cpe09g01018 . Bhi08g01625 Tan05g1994 Cmetu12g1182 Lac10g0460 Hepe07g2217 . . Cla01g01309 Cam01g1421 Cec01g1455 Cco01g1469 Clacu01g1374 Cmu01g1282 Cre01g1257 . . . .
Vvi17g772 . . . Bda15g00551 . . . . Cmo13g00910 Cmo18g00136 . Cma11g00091 . Car11g00083 Sed14g0033 Cpe20g00250 Cpe04g01563 Bhi02g00606 Tan09g2439 Cmetu02g1402 . . . . Cla06g01667 Cam06g1852 Cec06g1904 Cco06g1909 Clacu06g1811 Cmu06g1752 Cre06g2571 . . . . Lsi02g00383 Csa01g00863 Chy12g01259 Cme12g01683 . . . . . . . Bma08g00096 . . Cmo11g00090 Cma13g00879 Cma18g00178 Car13g00719 Car18g00169 Cpe09g01017 . Bhi08g01627 . . Lac10g0461 . . . Cla01g01310 Cam01g1420 . Cco01g1470 Clacu01g1375 Cmu01g1283 Cre01g1256 Lsi06g01560 Csa01g00144 Chy02g02585 .
Vvi17g773 . . . Bda15g00550 . . . . . . . . . Car11g00082 . . Cpe04g01564 . . . . . . . Cla06g01668 Cam06g1854 . . . Cmu06g1753 . . . . . . . . . . . . . . . . Bma08g00095 . . . . . . . . . . . . . . . . . . . . . . . Lsi06g01561 Csa01g00143 . Cme02g01983
Vvi17g774 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g775 . . . . . . . Bma12g01043 . . . Cma11g00090 . Car11g00081 Sed08g0112 . Cpe04g01565 Bhi02g00459 Tan09g2259 Cmetu02g0570 . Hepe09g0209 . . Cla06g01669 Cam06g1857 Cec06g1905 Cco06g1911 Clacu06g1813 Cmu06g1754 Cre06g2572 . . . . . . . . . Blo15g00263 . . Bpe07g00846 . . . . . Cmo11g00089 . . . . . . . . . . . . . . . . . . . . . Csa01g00142 Chy02g02586 Cme02g01984
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 8269940 8275292 - Bda023873.1 Bda06g00607 607
11 50684128 50686208 - Bda033159 Bda11g01658 1658
14 6209551 6211615 + Bda027575.2 Bda14g00807 807
15 8647777 8652926 - Bda012387.1 Bda15g00550 550
15 8660698 8663070 + Bda012388.1 Bda15g00551 551
15 8664027 8664877 - Bda012389.1 Bda15g00552 552
15 8666053 8669247 - Bda012390.1 Bda15g00553 553
2 8838800 8843265 + XM_039022971.1 Bhi02g00454 454
2 8857790 8864434 + XM_039023318.1 Bhi02g00459 459
2 11636867 11637845 - XM_039024024.1 Bhi02g00606 606
8 46239647 46242469 - XM_039037823.1 Bhi08g01622 1622
8 46247248 46252523 + XM_039039806.1 Bhi08g01623 1623
8 46263008 46267434 + XM_039038219.1 Bhi08g01624 1624
8 46268006 46270014 - XM_039038220.1 Bhi08g01625 1625
8 46270633 46275442 - XM_039038217.1 Bhi08g01627 1627
15 2813309 2822589 - BLOR06657 Blo15g00263 263
15 2823776 2828525 + BLOR06658 Blo15g00264 264
3 7188670 7189988 + Bma017082.1 Bma03g00778 778
6 2571011 2572673 + Bma022829.1 Bma06g00215 215
8 1177722 1186482 - Bma027095.1 Bma08g00095 95
8 1193693 1195856 + Bma027096.1 Bma08g00096 96
8 1196714 1197603 - Bma027097.1 Bma08g00097 97
8 1198705 1201933 - Bma027098.1 Bma08g00098 98
12 42472205 42474897 - Bma008388.1 Bma12g01042 1042
12 42477558 42483243 + Bma008389.1 Bma12g01043 1043
7 14604388 14609141 - Bpe021689.1 Bpe07g00845 845
7 14610751 14616448 + Bpe021690.1 Bpe07g00846 846
13 10410667 10412742 - Bpe024934 Bpe13g00245 245
15 17199761 17201785 - Bpe001574.1 Bpe15g00641 641
1 27732851 27738611 + CaPI482276_01g014200.1 Cam01g1420 1420
1 27745452 27746904 + CaPI482276_01g014210.1 Cam01g1421 1421
1 27748458 27751726 - CaPI482276_01g014220.1 Cam01g1422 1422
1 27758137 27762439 - CaPI482276_01g014230.1 Cam01g1423 1423
1 27767473 27769473 + CaPI482276_01g014250.1 Cam01g1425 1425
6 29591548 29600960 - CaPI482276_06g018510.1 Cam06g1851 1851
6 29603873 29605666 - CaPI482276_06g018520.1 Cam06g1852 1852
6 29610541 29613615 + CaPI482276_06g018540.1 Cam06g1854 1854
6 29621606 29631846 + CaPI482276_06g018570.1 Cam06g1857 1857
10 523840 528567 + Carg10342-RA Car10g00110 110
11 434693 439694 - Carg20219-RA Car11g00081 81
11 440410 444862 - Carg20220-RA Car11g00082 82
11 448316 450381 + Carg20221-RA Car11g00083 83
11 451453 456385 + Carg20222-RA Car11g00084 84
13 8366788 8379024 + Carg07669-RA Car13g00719 719
13 8375330 8383314 - Carg07670-RA Car13g00720 720
13 8383733 8385315 - Carg07671-RA Car13g00721 721
18 908280 911058 - Carg06732-RA Car18g00166 166
18 912231 913837 + Carg06733-RA Car18g00167 167
18 913800 916113 - Carg06734-RA Car18g00168 168
18 917692 927438 - Carg06735-RA Car18g00169 169
1 26477261 26480876 - CcPI632755_01g014650.1 Cco01g1465 1465
1 26483266 26486738 + CcPI632755_01g014660.1 Cco01g1466 1466
1 26493219 26496516 + CcPI632755_01g014680.1 Cco01g1468 1468
1 26498130 26499577 - CcPI632755_01g014690.1 Cco01g1469 1469
1 26504741 26512045 - CcPI632755_01g014700.1 Cco01g1470 1470
6 29330793 29336133 - CcPI632755_06g019080.1 Cco06g1908 1908
6 29339121 29340910 - CcPI632755_06g019090.1 Cco06g1909 1909
6 29344686 29367777 + CcPI632755_06g019110.1 Cco06g1911 1911
1 29178589 29190939 + CePI673135_01g014550.1 Cec01g1455 1455
1 29192500 29195794 - CePI673135_01g014560.1 Cec01g1456 1456
1 29210669 29215082 - CePI673135_01g014570.1 Cec01g1457 1457
1 29219081 29223122 + CePI673135_01g014580.1 Cec01g1458 1458
6 32392468 32400804 - CePI673135_06g019030.1 Cec06g1903 1903
6 32405027 32408405 - CePI673135_06g019040.1 Cec06g1904 1904
6 32410348 32425650 + CePI673135_06g019050.1 Cec06g1905 1905
2 29078245 29083640 - Chy2G048510.1 Chy02g02584 2584
2 29085645 29087249 - Chy2G048520.1 Chy02g02585 2585
2 29089402 29095973 + Chy2G048530.1 Chy02g02586 2586
12 17185906 17194842 + Chy12G218590.1 Chy12g01259 1259
12 17196049 17199101 - Chy12G218600.1 Chy12g01260 1260
12 17200370 17204134 - Chy12G218610.1 Chy12g01261 1261
12 17205919 17207981 + Chy12G218620.1 Chy12g01262 1262
1 25049794 25053459 - ClG42_01g0137100.10 Clacu01g1371 1371
1 25056735 25060928 + ClG42_01g0137200.10 Clacu01g1372 1372
1 25067190 25070487 + ClG42_01g0137300.10 Clacu01g1373 1373
1 25072028 25073482 - ClG42_01g0137400.10 Clacu01g1374 1374
1 25081215 25088411 - ClG42_01g0137500.10 Clacu01g1375 1375
6 28652143 28657577 - ClG42_06g0181000.10 Clacu06g1810 1810
6 28660490 28662283 - ClG42_06g0181100.10 Clacu06g1811 1811
6 28667260 28682633 + ClG42_06g0181300.10 Clacu06g1813 1813
1 26407628 26410248 - ClCG01G013230.1 Cla01g01306 1306
1 26414987 26419684 + ClCG01G013240.2 Cla01g01307 1307
1 26425771 26429588 + ClCG01G013250.1 Cla01g01308 1308
1 26430422 26432412 - ClCG01G013260.1 Cla01g01309 1309
1 26439971 26445707 - ClCG01G013270.2 Cla01g01310 1310
6 30245455 30251674 - ClCG06G017060.1 Cla06g01666 1666
6 30251664 30257123 - ClCG06G017070.2 Cla06g01667 1667
6 30261499 30270102 + ClCG06G017080.2 Cla06g01668 1668
6 30277487 30283372 + ClCG06G017090.2 Cla06g01669 1669
10 538265 543400 + CmaCh10G001220.1 Cma10g00122 122
11 437936 447202 - CmaCh11G000900.1 Cma11g00090 90
11 449164 451690 + CmaCh11G000910.1 Cma11g00091 91
11 452326 460287 + CmaCh11G000920.1 Cma11g00092 92
13 7133144 7139226 + CmaCh13G008790.1 Cma13g00879 879
13 7139943 7145706 - CmaCh13G008800.1 Cma13g00880 880
18 890133 892774 - CmaCh18G001760.1 Cma18g00176 176
18 893905 894756 + CmaCh18G001770.1 Cma18g00177 177
18 895429 907944 - CmaCh18G001780.1 Cma18g00178 178
2 26093307 26094436 + MELO3C026289.2.1 Cme02g01983 1983
2 26100998 26107940 + MELO3C026288.2.1 Cme02g01984 1984
12 23760338 23767746 + MELO3C002277.2.1 Cme12g01683 1683
12 23768497 23770999 + MELO3C002276.2.1 Cme12g01684 1684
12 23771297 23775048 - MELO3C002275.2.1 Cme12g01685 1685
12 23775985 23779816 - MELO3C002274.2.1 Cme12g01686 1686
12 23781047 23783699 + MELO3C002273.2.1 Cme12g01687 1687
2 24387191 24393824 + PI0007182.1 Cmetu02g0570 570
2 25215074 25219235 + PI0009555.1 Cmetu02g1402 1402
12 2514221 2519216 + PI0026525.1 Cmetu12g1069 1069
12 2510703 2513180 - PI0008339.1 Cmetu12g1080 1080
12 2524445 2526890 - PI0002584.1 Cmetu12g1182 1182
12 2520317 2524268 + PI0006383.1 Cmetu12g2030 2030
10 575039 580691 + CmoCh10G001260.1 Cmo10g00126 126
11 428955 439025 - CmoCh11G000890.1 Cmo11g00089 89
11 441678 443938 + CmoCh11G000900.1 Cmo11g00090 90
11 445132 452553 + CmoCh11G000910.1 Cmo11g00091 91
13 8067891 8071975 + CmoCh13G009100.1 Cmo13g00910 910
13 8072203 8078658 - CmoCh13G009110.1 Cmo13g00911 911
18 955571 958354 - CmoCh18G001340.1 Cmo18g00134 134
18 959837 962196 + CmoCh18G001350.1 Cmo18g00135 135
18 961787 976669 - CmoCh18G001360.1 Cmo18g00136 136
1 25389189 25391190 - CmPI595203_01g012780.1 Cmu01g1278 1278
1 25396132 25400315 + CmPI595203_01g012800.1 Cmu01g1280 1280
1 25406577 25409877 + CmPI595203_01g012810.1 Cmu01g1281 1281
1 25411422 25412874 - CmPI595203_01g012820.1 Cmu01g1282 1282
1 25420605 25426345 - CmPI595203_01g012830.1 Cmu01g1283 1283
6 28554061 28559484 - CmPI595203_06g017510.1 Cmu06g1751 1751
6 28562246 28565027 - CmPI595203_06g017520.1 Cmu06g1752 1752
6 28568968 28577223 + CmPI595203_06g017530.1 Cmu06g1753 1753
6 28585034 28595678 + CmPI595203_06g017540.1 Cmu06g1754 1754
2 34921770 34926774 - Conep02aG0194300.1 Cone2ag0913 913
2 34927962 34929470 + Conep02aG0194400.1 Cone2ag0914 914
2 34931058 34934825 + Conep02aG0194500.1 Cone2ag0915 915
13 917214 921152 + Conep13aG0015100.1 Cone13ag0146 146
13 922256 924751 - Conep13aG0015200.1 Cone13ag0147 147
16 522454 525797 - Conep16aG0009400.1 Cone16ag0093 93
16 526863 528356 - Conep16aG0009500.1 Cone16ag0094 94
16 529173 535019 + Conep16aG0009600.1 Cone16ag0095 95
19 798744 800766 - Conep19aG0015000.1 Cone19ag0144 144
4 12239308 12244214 - Cp4.1LG04g15590.1 Cpe04g01562 1562
4 12245573 12247445 - Cp4.1LG04g15660.1 Cpe04g01563 1563
4 12250525 12255224 + Cp4.1LG04g15560.1 Cpe04g01564 1564
4 12255837 12261272 + Cp4.1LG04g15570.1 Cpe04g01565 1565
9 8982240 8992406 + Cp4.1LG09g10210.1 Cpe09g01017 1017
9 8994341 8996163 + Cp4.1LG09g10220.1 Cpe09g01018 1018
9 8995832 8998062 - Cp4.1LG09g10280.1 Cpe09g01019 1019
9 8997222 9002330 + Cp4.1LG09g10170.1 Cpe09g01020 1020
18 7802718 7807919 - Cp4.1LG18g08500.1 Cpe18g00847 847
20 1408479 1417432 + Cp4.1LG20g02490.1 Cpe20g00249 249
20 1414709 1422106 - Cp4.1LG20g02570.1 Cpe20g00250 250
1 25756895 25762643 + CrPI670011_01g012560.1 Cre01g1256 1256
1 25775302 25776773 + CrPI670011_01g012570.1 Cre01g1257 1257
1 25778169 25781444 - CrPI670011_01g012580.1 Cre01g1258 1258
1 25787493 25791855 - CrPI670011_01g012590.1 Cre01g1259 1259
1 25795284 25799409 + CrPI670011_01g012600.1 Cre01g1260 1260
6 33376363 33381756 - CrPI670011_06g025700.1 Cre06g2570 2570
6 33384668 33387451 - CrPI670011_06g025710.1 Cre06g2571 2571
6 33393137 33409748 + CrPI670011_06g025720.1 Cre06g2572 2572
1 857651 864545 - CsaV3_1G001420.1 Csa01g00142 142
1 865316 871226 - CsaV3_1G001430.1 Csa01g00143 143
1 873509 875943 + CsaV3_1G001440.1 Csa01g00144 144
1 877495 883604 + CsaV3_1G001450.1 Csa01g00145 145
1 5384516 5387094 - CsaV3_1G008590.1 Csa01g00859 859
1 5388084 5391760 + CsaV3_1G008600.1 Csa01g00860 860
1 5392808 5396825 + CsaV3_1G008610.1 Csa01g00861 861
1 5396802 5399161 - CsaV3_1G008620.1 Csa01g00862 862
1 5400262 5406638 - CsaV3_1G008630.1 Csa01g00863 863
7 66559170 66561646 + Hsped.07g22170.1 Hepe07g2217 2217
7 66562778 66566321 - Hsped.07g22180.1 Hepe07g2218 2218
7 66570343 66573763 - Hsped.07g22190.1 Hepe07g2219 2219
7 66576778 66579438 + Hsped.07g22200.1 Hepe07g2220 2220
9 1739042 1745186 + Hsped.09g02090.1 Hepe09g0209 209
10 3600716 3602711 + Lag0024503.1 Lac10g0458 458
10 3612146 3618345 + Lag0024504.1 Lac10g0459 459
10 3620040 3621622 - Lag0024505.1 Lac10g0460 460
10 3623885 3629633 - Lag0024506.1 Lac10g0461 461
2 3276580 3279600 - Lsi02G003800.1 Lsi02g00380 380
2 3283178 3292594 + Lsi02G003810.1 Lsi02g00381 381
2 3292955 3295021 - Lsi02G003820.1 Lsi02g00382 382
2 3296518 3303229 - Lsi02G003830.1 Lsi02g00383 383
6 26000569 26006842 - Lsi06G015580.1 Lsi06g01558 1558
6 26008360 26011714 - Lsi06G015600.1 Lsi06g01560 1560
6 26015326 26030144 + Lsi06G015610.1 Lsi06g01561 1561
1 11918620 11920761 + Sed0020369.1 Sed01g1640 1640
8 665718 672743 - Sed0001292.4 Sed08g0112 112
8 37929524 37933149 - Sed0005243.1 Sed08g2519 2519
8 37934344 37937866 + Sed0017346.1 Sed08g2520 2520
8 37939014 37943895 + Sed0012780.1 Sed08g2521 2521
14 409978 410769 - Sed0013533.1 Sed14g0033 33
5 69855063 69857203 + Tan0020705.1 Tan05g1994 1994
5 69857581 69861907 - Tan0010407.1 Tan05g1995 1995
5 69878532 69880969 - Tan0015643.1 Tan05g1996 1996
5 69882361 69885091 + Tan0017361.1 Tan05g1997 1997
9 72630917 72636295 - Tan0017425.1 Tan09g2254 2254
9 72658889 72665464 + Tan0010145.1 Tan09g2259 2259
9 73955219 73956066 + Tan0019973.1 Tan09g2439 2439
17 9899394 9906902 - Vvi17g766 Vvi17g766 766
17 9907477 9915574 + Vvi17g767 Vvi17g767 767
17 9915828 9919405 - Vvi17g768 Vvi17g768 768
17 9922869 9924825 + Vvi17g769 Vvi17g769 769
17 9936624 9941415 + Vvi17g770 Vvi17g770 770
17 9941523 9942662 - Vvi17g771 Vvi17g771 771
17 9949637 9964293 - Vvi17g772 Vvi17g772 772
17 9989634 10000315 + Vvi17g773 Vvi17g773 773
17 10011351 10014827 + Vvi17g774 Vvi17g774 774
17 10037581 10071108 + Vvi17g775 Vvi17g775 775
       

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