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
Vvi17g636 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone16ag0133 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g637 . . . . . . . . . . Cma10g00228 . Car10g00213 Car11g00179 Sed08g0258 . Cpe04g01468 Bhi02g00695 Tan09g2054 Cmetu02g0232 . . . . Cla06g01548 Cam06g1709 Cec06g1769 Cco06g1770 Clacu06g1676 Cmu06g1622 Cre06g2435 Cone2ag0818 . . . . . . . . . . . . . . . . Cmo10g00240 Cmo11g00203 . . . . . Cpe18g00765 . . . . . . . . . . . . . . Lsi06g01423 Csa01g00281 Chy02g02453 .
Vvi17g638 . . . . . . . . . . Cma10g00229 . Car10g00214 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo10g00241 . . . . . . Cpe18g00764 . . . . . . . . . . . . . . . . . .
Vvi17g639 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g640 Blo04g00787 Blo16g00173 . . . Bpe13g00307 Bma06g00157 . Cmo13g01131 . . . . . . Cpe20g00066 . . . . . . . . . . . . . . . Cone2ag0816 Cone16ag0198 Cone13ag0041 Cone19ag0047 Lsi02g00108 Csa01g00588 Chy12g01510 Cme12g01954 . . Bda11g01717 Bda14g00869 . Bpe15g00586 Bma03g00846 . Sed08g2109 . . Cma13g01082 . Car13g00920 . . . Bhi08g01103 Tan05g2375 Cmetu12g1694 Lac10g0137 . . . Cla04g01165 Cam04g1224 Cec01g1735 Cco01g1781 Clacu04g1251 Cmu04g1229 Cre01g1525 . . . .
Vvi17g641 . Blo16g00172 . . . Bpe13g00308 Bma06g00156 . Cmo13g01129 . . . . . . Cpe20g00067 . . . . . . . . . . . . . . . Cone2ag0815 Cone16ag0199 . . Lsi02g00109 . Chy12g01508 Cme12g01953 . . Bda11g01718 . . . . . Sed08g2112 . . Cma13g01081 . Car13g00918 . . . Bhi08g01102 Tan05g2374 Cmetu12g0892 . Hepe07g2474 . . Cla04g01164 Cam04g1222 Cec01g1733 Cco01g1779 Clacu04g1249 Cmu04g1228 Cre01g1524 . . . .
Vvi17g642 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag1011 Cone8ag1038 Cone3ag1068 Cone10ag1081 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g643 Blo04g00788 . . . Bpe12g00459 . Bma06g00155 . Cmo13g01128 . . . . . . Cpe20g00068 . Bhi02g00694 Tan09g2052 Cmetu02g0330 . . . . Cla06g01547 Cam06g1708 Cec06g1768 Cco06g1769 Clacu06g1675 Cmu06g1621 Cre06g2434 Cone2ag0814 Cone16ag0200 . . Lsi02g00111 Csa01g00590 . Cme12g01952 . . Bda11g01719 Bda14g00871 . Bpe15g00585 Bma03g00847 Bma08g00280 Sed08g2114 . . Cma13g01080 . Car13g00917 . . . Bhi08g01100 Tan05g2372 Cmetu12g0960 Lac10g0140 Hepe07g2473 . . Cla04g01163 Cam04g1221 Cec01g1732 Cco01g1778 Clacu04g1248 Cmu04g1227 Cre01g1523 Lsi06g01422 Csa01g00282 Chy02g02452 Cme02g01838
Vvi17g644 . . . . . . . . . . . Cma11g00116 . . . . . . . . . . . . . . . . . . . . . Cone13ag0039 . . . . . . . . . . . . . . . Cmo11g00204 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g645 . . . . . . . Bma12g00971 . . . . . . . . . Bhi02g00693 . . . . . . Cla06g01546 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi06g01421 Csa01g00284 Chy02g02450 Cme02g01837
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 51597871 51603871 - Bda008614.2 Bda11g01717 1717
11 51607774 51611880 + Bda008615.1 Bda11g01718 1718
11 51627060 51629059 + Bda008616.2 Bda11g01719 1719
14 6710061 6716182 - Bda027645.1 Bda14g00869 869
14 6743680 6746860 + Bda027648.1 Bda14g00871 871
2 13957810 13962976 - XM_039022770.1 Bhi02g00693 693
2 13986178 13991679 - XM_039024407.1 Bhi02g00694 694
2 14028348 14036495 + XM_039024448.1 Bhi02g00695 695
8 35445870 35449585 - XM_039038707.1 Bhi08g01100 1100
8 35452106 35458203 - XM_039038992.1 Bhi08g01102 1102
8 35499800 35511233 + XM_039038782.1 Bhi08g01103 1103
4 7814896 7821985 - BLOR13699 Blo04g00787 787
4 7853777 7856935 + BLOR13700 Blo04g00788 788
16 3888732 3892917 - BLOR07420 Blo16g00172 172
16 3899301 3906122 + BLOR07421 Blo16g00173 173
3 8093615 8100640 - Bma017162.1 Bma03g00846 846
3 8104314 8147357 + Bma017163.1 Bma03g00847 847
6 2018170 2031228 - Bma022774.1 Bma06g00155 155
6 2032494 2036582 - Bma022775.1 Bma06g00156 156
6 2039657 2046451 + Bma022776.1 Bma06g00157 157
8 3794538 3799504 - Bma027301.1 Bma08g00280 280
12 41712128 41713508 - Bma008313.1 Bma12g00971 971
12 10338239 10343189 + Bpe005719.1 Bpe12g00459 459
13 10896116 10902942 - Bpe006433.2 Bpe13g00307 307
13 10908919 10912901 + Bpe006434.1 Bpe13g00308 308
15 16804672 16807857 - Bpe001519.1 Bpe15g00585 585
15 16811028 16817990 + Bpe001520.1 Bpe15g00586 586
4 26250434 26253607 - CaPI482276_04g012210.1 Cam04g1221 1221
4 26258178 26262807 - CaPI482276_04g012220.1 Cam04g1222 1222
4 26268026 26275519 + CaPI482276_04g012240.1 Cam04g1224 1224
6 28435908 28441368 - CaPI482276_06g017080.1 Cam06g1708 1708
6 28444049 28446503 + CaPI482276_06g017090.1 Cam06g1709 1709
10 1024385 1026645 - Carg17930-RA Car10g00213 213
10 1027044 1029832 + Carg17929-RA Car10g00214 214
11 1038249 1038868 - Carg09210-RA Car11g00179 179
13 9468214 9472055 - Carg04754-RA Car13g00917 917
13 9473137 9479912 - Carg04753-RA Car13g00918 918
13 9483168 9491057 + Carg04751-RA Car13g00920 920
1 30508468 30511640 - CcPI632755_01g017780.1 Cco01g1778 1778
1 30516185 30520821 - CcPI632755_01g017790.1 Cco01g1779 1779
1 30526013 30533530 + CcPI632755_01g017810.1 Cco01g1781 1781
6 28139738 28145130 - CcPI632755_06g017690.1 Cco06g1769 1769
6 28147497 28149899 + CcPI632755_06g017700.1 Cco06g1770 1770
1 31931727 31934898 - CePI673135_01g017320.1 Cec01g1732 1732
1 31938822 31943447 - CePI673135_01g017330.1 Cec01g1733 1733
1 31951620 31960725 + CePI673135_01g017350.1 Cec01g1735 1735
6 31209432 31214609 - CePI673135_06g017680.1 Cec06g1768 1768
6 31217200 31219727 + CePI673135_06g017690.1 Cec06g1769 1769
2 28120739 28124807 - Chy2G047170.1 Chy02g02450 2450
2 28130558 28133950 - Chy2G047190.1 Chy02g02452 2452
2 28134741 28157504 + Chy2G047200.1 Chy02g02453 2453
12 18888894 18900678 - Chy12G221080.1 Chy12g01508 1508
12 18906255 18917443 + Chy12G221100.1 Chy12g01510 1510
4 26606014 26609188 - ClG42_04g0124800.10 Clacu04g1248 1248
4 26613580 26618230 - ClG42_04g0124900.10 Clacu04g1249 1249
4 26623423 26630919 + ClG42_04g0125100.10 Clacu04g1251 1251
6 27499404 27499673 - ClG42_06g0167500.10 Clacu06g1675 1675
6 27502322 27503306 + ClG42_06g0167600.10 Clacu06g1676 1676
4 26843030 26846741 - ClCG04G011880.1 Cla04g01163 1163
4 26849780 26857969 - ClCG04G011890.2 Cla04g01164 1164
4 26858046 26872638 + ClCG04G011900.2 Cla04g01165 1165
6 29033908 29038597 - ClCG06G015700.1 Cla06g01546 1546
6 29044164 29051385 - ClCG06G015710.1 Cla06g01547 1547
6 29053848 29056612 + ClCG06G015720.1 Cla06g01548 1548
10 1014794 1017036 - CmaCh10G002280.1 Cma10g00228 228
10 1017355 1021073 + CmaCh10G002290.1 Cma10g00229 229
11 621168 625835 - CmaCh11G001160.1 Cma11g00116 116
13 8164516 8168723 - CmaCh13G010800.1 Cma13g01080 1080
13 8169628 8176718 - CmaCh13G010810.1 Cma13g01081 1081
13 8178841 8196305 + CmaCh13G010820.1 Cma13g01082 1082
2 25076406 25080142 - MELO3C017219.2.1 Cme02g01837 1837
2 25082929 25086322 - MELO3C017218.2.1 Cme02g01838 1838
12 25431148 25434741 - MELO3C002020.2.1 Cme12g01952 1952
12 25435988 25441811 - MELO3C002019.2.1 Cme12g01953 1953
12 25443765 25454259 + MELO3C002018.2.1 Cme12g01954 1954
2 23407852 23410656 + PI0024678.1 Cmetu02g0232 232
2 23400855 23404583 - PI0018533.1 Cmetu02g0330 330
12 695034 701048 + PI0000781.2 Cmetu12g0892 892
12 702484 706288 + PI0028674.1 Cmetu12g0960 960
12 682826 690193 - PI0026858.1 Cmetu12g1694 1694
10 1073803 1076120 - CmoCh10G002400.1 Cmo10g00240 240
10 1076404 1077789 + CmoCh10G002410.1 Cmo10g00241 241
11 1002369 1006024 - CmoCh11G002030.1 Cmo11g00203 203
11 1007530 1010472 + CmoCh11G002040.1 Cmo11g00204 204
13 9181718 9185488 - CmoCh13G011280.1 Cmo13g01128 1128
13 9186541 9194057 - CmoCh13G011290.1 Cmo13g01129 1129
13 9197321 9206392 + CmoCh13G011310.1 Cmo13g01131 1131
4 26787972 26791146 - CmPI595203_04g012270.1 Cmu04g1227 1227
4 26795535 26800183 - CmPI595203_04g012280.1 Cmu04g1228 1228
4 26805376 26812872 + CmPI595203_04g012290.1 Cmu04g1229 1229
6 27408365 27408634 - CmPI595203_06g016210.1 Cmu06g1621 1621
6 27411284 27412268 + CmPI595203_06g016220.1 Cmu06g1622 1622
2 34163321 34167516 - Conep02aG0184200.1 Cone2ag0814 814
2 34168907 34175472 - Conep02aG0184300.1 Cone2ag0815 815
2 34180047 34188670 + Conep02aG0184400.1 Cone2ag0816 816
2 34194734 34196453 + Conep02aG0184600.1 Cone2ag0818 818
3 29353861 29355429 + Conep03aG0157100.1 Cone3ag1068 1068
8 9577075 9580749 - Conep08aG0106600.1 Cone8ag1038 1038
10 7501998 7503540 + Conep10aG0110800.1 Cone10ag1081 1081
12 8540219 8542714 - Conep12aG0103900.1 Cone12ag1011 1011
13 230826 233535 - Conep13aG0004200.1 Cone13ag0039 39
13 242847 250441 + Conep13aG0004400.1 Cone13ag0041 41
16 757302 759112 + Conep16aG0013500.1 Cone16ag0133 133
16 1296614 1305926 - Conep16aG0020200.1 Cone16ag0198 198
16 1312882 1319125 + Conep16aG0020300.1 Cone16ag0199 199
16 1324958 1328614 + Conep16aG0020400.1 Cone16ag0200 200
19 304778 314739 + Conep19aG0005100.1 Cone19ag0047 47
4 11676932 11677365 + Cp4.1LG04g14740.1 Cpe04g01468 1468
18 7315014 7316493 - Cp4.1LG18g07790.1 Cpe18g00764 764
18 7316744 7319047 + Cp4.1LG18g07660.1 Cpe18g00765 765
20 324576 332529 - Cp4.1LG20g00640.1 Cpe20g00066 66
20 335732 342796 + Cp4.1LG20g00600.1 Cpe20g00067 67
20 343652 354919 + Cp4.1LG20g00610.1 Cpe20g00068 68
1 28453494 28457039 - CrPI670011_01g015230.1 Cre01g1523 1523
1 28461208 28465838 - CrPI670011_01g015240.1 Cre01g1524 1524
1 28471011 28478507 + CrPI670011_01g015250.1 Cre01g1525 1525
6 32199289 32204646 - CrPI670011_06g024340.1 Cre06g2434 2434
6 32205156 32211574 + CrPI670011_06g024350.1 Cre06g2435 2435
1 1774820 1777781 - CsaV3_1G002810.1 Csa01g00281 281
1 1778618 1781828 + CsaV3_1G002820.1 Csa01g00282 282
1 1788086 1791498 + CsaV3_1G002840.1 Csa01g00284 284
1 3757349 3775118 - CsaV3_1G005880.1 Csa01g00588 588
1 3780760 3791714 + CsaV3_1G005900.1 Csa01g00590 590
7 69050869 69054579 - Hsped.07g24730.1 Hepe07g2473 2473
7 69057003 69065823 - Hsped.07g24740.1 Hepe07g2474 2474
10 1029124 1033970 - Lag0024182.1 Lac10g0137 137
10 1048537 1051717 + Lag0024185.1 Lac10g0140 140
2 880656 891405 - Lsi02G001080.1 Lsi02g00108 108
2 891803 899906 + Lsi02G001090.1 Lsi02g00109 109
2 903077 907114 + Lsi02G001110.1 Lsi02g00111 111
6 24754847 24760856 - Lsi06G014210.1 Lsi06g01421 1421
6 24767325 24774029 - Lsi06G014220.1 Lsi06g01422 1422
6 24777605 24808206 + Lsi06G014230.1 Lsi06g01423 1423
8 1506733 1508757 - Sed0010236.1 Sed08g0258 258
8 35140794 35151532 - Sed0001778.2 Sed08g2109 2109
8 35152648 35158469 + Sed0026784.3 Sed08g2112 2112
8 35161487 35165170 + Sed0000797.2 Sed08g2114 2114
5 75095149 75098919 - Tan0000302.1 Tan05g2372 2372
5 75101708 75108635 - Tan0019385.2 Tan05g2374 2374
5 75136271 75146765 + Tan0005143.1 Tan05g2375 2375
9 71037574 71042012 - Tan0017714.1 Tan09g2052 2052
9 71049581 71052545 + Tan0013686.1 Tan09g2054 2054
17 7856333 7862567 - Vvi17g636 Vvi17g636 636
17 7897103 7901315 - Vvi17g637 Vvi17g637 637
17 7901599 7907555 + Vvi17g638 Vvi17g638 638
17 7909777 7916412 + Vvi17g639 Vvi17g639 639
17 7936597 7945392 - Vvi17g640 Vvi17g640 640
17 7961695 7972366 + Vvi17g641 Vvi17g641 641
17 7980104 7980632 - Vvi17g642 Vvi17g642 642
17 7994140 7998739 + Vvi17g643 Vvi17g643 643
17 8011742 8034743 + Vvi17g644 Vvi17g644 644
17 8035242 8037678 + Vvi17g645 Vvi17g645 645
       

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