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
Vvi2g252 . . . Bda08g00385 . . Bma07g01031 Bma14g00099 . . Cma02g00944 Cma15g01321 Car02g00693 Car15g01186 . . Cpe05g00769 . . . . . . . . . . . . . . . . Cone6ag0800 . . Csa05g00160 Chy09g01338 . Blo03g00798 . Bda07g00155 . Bpe08g00905 Bpe11g00373 . . . Cmo02g00953 Cmo15g01384 . . . . . . Bhi12g00081 . . . . . Lcy12g1514 Cla01g00142 . . . . . . . . . Cme09g01885
Vvi2g253 . . Bda06g01087 Bda08g00753 Bpe05g00385 . . . . Cmo16g00658 . . . . . Cpe14g00513 . . . . . . . . Cla07g00788 Cam07g0851 Cec07g0904 Cco07g0886 Clacu07g0826 Cmu07g0829 Cre07g1187 Cone8ag0557 Cone12ag0556 . . . . . Cme07g01643 . . . . . . Bma05g00535 Bma12g00421 . . . . Cma16g00604 . . . . . . . . . . . . . . . . . . . Csa04g00584 Chy07g01227 .
Vvi2g254 . . . . Bpe05g00386 . Bma07g01033 . . . Cma02g00945 Cma15g01322 Car02g00694 Car15g01187 . . Cpe05g00768 . . . . . . . . . . . . . . . Cone12ag0581 . . . Csa05g00159 Chy09g01339 . . . . Bda09g00635 Bpe08g00906 . Bma05g00537 . . Cmo02g00954 Cmo15g01385 . . . . . . Bhi12g00080 . . Lac11g1903 Hepe06g1432 . Lcy12g1511 Cla01g00141 Cam01g0146 Cec01g0142 Cco01g0147 Clacu01g0141 Cmu01g0141 Cre09g2365 Lsi09g00132 . . Cme09g01886
Vvi2g255 . . . . . . . Bma14g00703 . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0590 Cone12ag0580 . . . . . . . . Bda07g00483 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g256 . . . Bda08g00752 Bpe05g00387 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0587 Cone12ag0579 . . . . . . . . . . . . Bma05g00538 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g257 . . . Bda08g00751 Bpe05g00390 . . . Cmo06g00541 . Cma02g00946 Cma15g01323 Car02g00695 Car15g01188 . . Cpe05g00767 . . . . . . . . . . . . . . . . . . . Csa05g00158 Chy09g01340 . . . . . . . Bma05g00539 Bma12g00420 . Cmo02g00955 Cmo15g01386 Cma06g00538 . Car06g00476 . Cpe08g00954 . Bhi12g00079 . . . . . Lcy12g1510 Cla01g00140 Cam01g0145 . . Clacu01g0140 Cmu01g0140 Cre09g2366 Lsi09g00131 . . Cme09g01887
Vvi2g258 . . . . Bpe05g00391 . . Bma14g00098 . . . Cma15g01324 Car02g00696 Car15g01189 . . . . . . . . . . . . . . . . . Cone8ag0586 Cone12ag0578 . . . Csa05g00157 Chy09g01341 . Blo03g00342 Blo19g00134 . Bda09g00634 Bpe08g00907 Bpe11g00374 . . . . Cmo15g01388 . . . . . . Bhi12g00077 . . . . . Lcy12g1509 Cla01g00139 Cam01g0144 Cec01g0141 Cco01g0146 Clacu01g0139 Cmu01g0139 Cre09g2367 Lsi09g00130 . . Cme09g01888
Vvi2g259 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g260 Blo02g01125 . Bda06g01089 Bda08g00750 Bpe05g00392 . . . . . Cma02g00947 Cma15g01326 Car02g00697 Car15g01191 . . Cpe05g00766 . . . . . . . . . . . . . . Cone8ag0561 . . . . Csa05g00156 Chy09g01342 . . . . . . . Bma05g00540 Bma12g00419 . Cmo02g00956 Cmo15g01390 . . . . . . Bhi12g00075 . . . . . Lcy12g1508 Cla01g00138 Cam01g0142 Cec01g0140 Cco01g0144 Clacu01g0138 Cmu01g0138 Cre09g2368 Lsi09g00129 . . Cme09g01889
Vvi2g261 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 38751463 38756687 + Bda022861.1 Bda06g01087 1087
6 38847849 38850868 - Bda022865.1 Bda06g01089 1089
7 1909280 1910646 - Bda025222.1 Bda07g00155 155
7 6067217 6068560 - Bda025585.1 Bda07g00483 483
8 4013790 4014740 - Bda024831.1 Bda08g00385 385
8 9350650 9353619 + Bda029238.1 Bda08g00750 750
8 9390556 9401593 - Bda029239.1 Bda08g00751 751
8 9430169 9436362 - Bda029240.1 Bda08g00752 752
8 9555056 9555601 + Bda029243.1 Bda08g00753 753
9 9300908 9302540 + Bda031265.1 Bda09g00634 634
9 9302882 9306084 - Bda031266.1 Bda09g00635 635
12 2211382 2215965 + XM_039050951.1 Bhi12g00075 75
12 2219248 2223225 + XM_039050953.1 Bhi12g00077 77
12 2224080 2232375 - XM_039050949.1 Bhi12g00079 79
12 2340101 2348081 - XM_039019641.1 Bhi12g00080 80
12 2485271 2486909 + XM_039019787.1 Bhi12g00081 81
2 42531761 42533192 - BLOR10855 Blo02g01125 1125
3 7392899 7410841 - BLOR11523 Blo03g00342 342
3 33190114 33191461 + BLOR11979 Blo03g00798 798
19 3897438 3899394 + BLOR09477 Blo19g00134 134
5 28213022 28213567 - Bma021497.1 Bma05g00535 535
5 28732416 28766005 + Bma021500.1 Bma05g00537 537
5 28923044 28929228 + Bma021501.1 Bma05g00538 538
5 29051357 29061238 + Bma021502.1 Bma05g00539 539
5 29107140 29110178 - Bma021503.1 Bma05g00540 540
7 41597762 41599075 - Bma026221.1 Bma07g01031 1031
7 41786114 41816252 + Bma026227.1 Bma07g01033 1033
12 9453780 9456895 + Bma007400.1 Bma12g00419 419
12 9459698 9471084 - Bma007401.1 Bma12g00420 420
12 9640714 9641301 - Bma007407.1 Bma12g00421 421
14 1352807 1354018 + Bma010504.1 Bma14g00098 98
14 1370119 1371486 + Bma010505.1 Bma14g00099 99
14 7670777 7671474 - Bma011158.1 Bma14g00703 703
5 18105219 18105764 - Bpe017802.1 Bpe05g00385 385
5 18142131 18161505 + Bpe017803.1 Bpe05g00386 386
5 18169758 18175956 + Bpe017804.1 Bpe05g00387 387
5 18190128 18199059 + Bpe017807.1 Bpe05g00390 390
5 18199802 18200989 - Bpe017808.1 Bpe05g00391 391
5 18212326 18215368 - Bpe017809.1 Bpe05g00392 392
8 11491250 11492556 - Bpe023029.1 Bpe08g00905 905
8 11523507 11528075 + Bpe026157 Bpe08g00906 906
8 11529337 11530419 - Bpe023030.1 Bpe08g00907 907
11 2829163 2830522 - Bpe003747.1 Bpe11g00373 373
11 2847089 2847862 - Bpe003748.1 Bpe11g00374 374
1 1735098 1739168 + CaPI482276_01g001420.1 Cam01g0142 142
1 1741885 1744320 + CaPI482276_01g001440.1 Cam01g0144 144
1 1746226 1754925 - CaPI482276_01g001450.1 Cam01g0145 145
1 1758888 1767850 - CaPI482276_01g001460.1 Cam01g0146 146
7 21249107 21249784 + CaPI482276_07g008510.1 Cam07g0851 851
2 5142132 5143573 - Carg08530-RA Car02g00693 693
2 5150201 5154251 + Carg08529-RA Car02g00694 694
2 5154884 5165728 + Carg08528-RA Car02g00695 695
2 5165374 5170650 - Carg08527-RA Car02g00696 696
2 5171128 5175802 - Carg08526-RA Car02g00697 697
6 2633187 2643056 + Carg16228-RA Car06g00476 476
15 9250989 9252293 - Carg21310-RA Car15g01186 1186
15 9261943 9265898 + Carg21311-RA Car15g01187 1187
15 9267994 9279398 + Carg21312-RA Car15g01188 1188
15 9282082 9283940 - Carg21313-RA Car15g01189 1189
15 9285329 9289017 - Carg21315-RA Car15g01191 1191
1 1300523 1304573 + CcPI632755_01g001440.1 Cco01g0144 144
1 1307302 1309767 + CcPI632755_01g001460.1 Cco01g0146 146
1 1311629 1333324 - CcPI632755_01g001470.1 Cco01g0147 147
7 20641342 20642001 + CcPI632755_07g008860.1 Cco07g0886 886
1 1323545 1327678 + CePI673135_01g001400.1 Cec01g0140 140
1 1330113 1332774 + CePI673135_01g001410.1 Cec01g0141 141
1 1335443 1356081 - CePI673135_01g001420.1 Cec01g0142 142
7 22437903 22438571 + CePI673135_07g009040.1 Cec07g0904 904
7 17057257 17057925 + Chy7G140570.1 Chy07g01227 1227
9 15227760 15229152 - Chy9G170540.1 Chy09g01338 1338
9 15252861 15258490 + Chy9G170550.1 Chy09g01339 1339
9 15260680 15268054 + Chy9G170560.1 Chy09g01340 1340
9 15271103 15272979 - Chy9G170570.1 Chy09g01341 1341
9 15274839 15283002 - Chy9G170580.1 Chy09g01342 1342
1 1346688 1350764 + ClG42_01g0013800.10 Clacu01g0138 138
1 1353412 1355842 + ClG42_01g0013900.10 Clacu01g0139 139
1 1358680 1366397 - ClG42_01g0014000.10 Clacu01g0140 140
1 1370382 1379181 - ClG42_01g0014100.10 Clacu01g0141 141
7 20922505 20923176 + ClG42_07g0082600.10 Clacu07g0826 826
1 1331456 1335532 + ClCG01G001420.2 Cla01g00138 138
1 1337950 1342433 + ClCG01G001430.1 Cla01g00139 139
1 1343451 1351719 - ClCG01G001440.2 Cla01g00140 140
1 1355517 1364534 - ClCG01G001450.2 Cla01g00141 141
1 1427279 1432200 + ClCG01G001460.1 Cla01g00142 142
7 22054408 22055079 + ClCG07G008260.1 Cla07g00788 788
2 5611976 5613683 - CmaCh02G009440.1 Cma02g00944 944
2 5619329 5623227 + CmaCh02G009450.1 Cma02g00945 945
2 5623467 5634009 + CmaCh02G009460.1 Cma02g00946 946
2 5633999 5644793 - CmaCh02G009470.1 Cma02g00947 947
6 2535326 2544436 + CmaCh06G005380.1 Cma06g00538 538
15 8291539 8293133 - CmaCh15G013210.1 Cma15g01321 1321
15 8303107 8307145 + CmaCh15G013220.1 Cma15g01322 1322
15 8308673 8322298 + CmaCh15G013230.1 Cma15g01323 1323
15 8322826 8326218 - CmaCh15G013240.1 Cma15g01324 1324
15 8328560 8335750 - CmaCh15G013260.1 Cma15g01326 1326
16 3114445 3115737 + CmaCh16G006040.1 Cma16g00604 604
7 22152063 22152985 + MELO3C016367.2.1 Cme07g01643 1643
9 22982179 22983951 - MELO3C005791.2.1 Cme09g01885 1885
9 23008379 23014495 + MELO3C005792.2.1 Cme09g01886 1886
9 23016520 23023642 + MELO3C005793.2.1 Cme09g01887 1887
9 23024256 23028532 - MELO3C005794.2.1 Cme09g01888 1888
9 23029201 23034415 - MELO3C005795.2.1 Cme09g01889 1889
2 5834017 5835790 - CmoCh02G009530.1 Cmo02g00953 953
2 5842345 5846377 + CmoCh02G009540.1 Cmo02g00954 954
2 5847075 5858904 + CmoCh02G009550.1 Cmo02g00955 955
2 5860353 5868195 - CmoCh02G009560.1 Cmo02g00956 956
6 2610506 2620668 + CmoCh06G005410.1 Cmo06g00541 541
15 9417269 9418780 - CmoCh15G013840.1 Cmo15g01384 1384
15 9428590 9432898 + CmoCh15G013850.1 Cmo15g01385 1385
15 9435007 9447488 + CmoCh15G013860.1 Cmo15g01386 1386
15 9448617 9450969 - CmoCh15G013880.1 Cmo15g01388 1388
15 9452877 9460257 - CmoCh15G013900.1 Cmo15g01390 1390
16 3250160 3250834 + CmoCh16G006580.1 Cmo16g00658 658
1 1292364 1296440 + CmPI595203_01g001380.1 Cmu01g0138 138
1 1299086 1301507 + CmPI595203_01g001390.1 Cmu01g0139 139
1 1304327 1312045 - CmPI595203_01g001400.1 Cmu01g0140 140
1 1316030 1324831 - CmPI595203_01g001410.1 Cmu01g0141 141
7 21136400 21137071 + CmPI595203_07g008290.1 Cmu07g0829 829
6 4067642 4071004 + Conep06aG0082400.1 Cone6ag0800 800
8 4286560 4287492 - Conep08aG0057800.1 Cone8ag0557 557
8 4346564 4350392 - Conep08aG0058200.1 Cone8ag0561 561
8 4914570 4918103 + Conep08aG0060700.1 Cone8ag0586 586
8 4919698 4930073 - Conep08aG0060800.1 Cone8ag0587 587
8 4950653 4956285 + Conep08aG0061100.1 Cone8ag0590 590
12 4003797 4004466 - Conep12aG0057700.1 Cone12ag0556 556
12 4310689 4312937 + Conep12aG0059900.1 Cone12ag0578 578
12 4373716 4386717 - Conep12aG0060000.1 Cone12ag0579 579
12 4405542 4410396 + Conep12aG0060100.1 Cone12ag0580 580
12 4492977 4501138 - Conep12aG0060200.1 Cone12ag0581 581
5 4739053 4747397 + Cp4.1LG05g07690.1 Cpe05g00766 766
5 4748206 4759769 - Cp4.1LG05g07720.1 Cpe05g00767 767
5 4760201 4764484 - Cp4.1LG05g07730.1 Cpe05g00768 768
5 4770851 4772261 + Cp4.1LG05g07660.1 Cpe05g00769 769
8 7491564 7501935 - Cp4.1LG08g09530.1 Cpe08g00954 954
14 3244756 3245427 + Cp4.1LG14g02130.1 Cpe14g00513 513
7 24735270 24735947 + CrPI670011_07g011870.1 Cre07g1187 1187
9 42962892 42971872 + CrPI670011_09g023650.1 Cre09g2365 2365
9 42978190 42986867 + CrPI670011_09g023660.1 Cre09g2366 2366
9 42988748 42991188 - CrPI670011_09g023670.1 Cre09g2367 2367
9 42993942 42997993 - CrPI670011_09g023680.1 Cre09g2368 2368
4 3847053 3847721 - CsaV3_4G005840.1 Csa04g00584 584
5 862504 867879 + CsaV3_5G001560.1 Csa05g00156 156
5 868576 872917 + CsaV3_5G001570.1 Csa05g00157 157
5 870602 881652 - CsaV3_5G001580.1 Csa05g00158 158
5 883181 889960 - CsaV3_5G001590.1 Csa05g00159 159
5 913416 915221 + CsaV3_5G001600.1 Csa05g00160 160
6 64767012 64776029 - Hsped.06g14320.1 Hepe06g1432 1432
11 34322042 34327725 - Lag0032541.1 Lac11g1903 1903
12 34634824 34639096 + Maker00029471 Lcy12g1508 1508
12 34649036 34653224 + Maker00029260 Lcy12g1509 1509
12 34653955 34667424 - Maker00029188 Lcy12g1510 1510
12 34691670 34699516 - Maker00029355 Lcy12g1511 1511
12 34817197 34818880 + Maker00029330 Lcy12g1514 1514
9 1247180 1251791 + Lsi09G001290.1 Lsi09g00129 129
9 1253990 1257939 + Lsi09G001300.1 Lsi09g00130 130
9 1258203 1267925 - Lsi09G001310.1 Lsi09g00131 131
9 1284130 1285195 - Lsi09G001320.1 Lsi09g00132 132
2 2347215 2348922 - Vvi2g252 Vvi2g252 252
2 2356707 2357477 - Vvi2g253 Vvi2g253 253
2 2368433 2370940 + Vvi2g254 Vvi2g254 254
2 2372079 2385499 - Vvi2g255 Vvi2g255 255
2 2386823 2397387 + Vvi2g256 Vvi2g256 256
2 2398998 2409960 + Vvi2g257 Vvi2g257 257
2 2410590 2413708 - Vvi2g258 Vvi2g258 258
2 2414502 2415924 + Vvi2g259 Vvi2g259 259
2 2417891 2422350 - Vvi2g260 Vvi2g260 260
2 2425762 2427048 - Vvi2g261 Vvi2g261 261
       

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