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
Vvi17g726 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g727 . . . . . . . . Cmo13g00923 . . . . . . Cpe20g00233 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed08g1387 . . Cma13g00895 . . . Cpe09g01033 . Bhi08g01593 Tan05g2023 Cmetu04g2527 Lac10g0436 Hepe07g2235 . . . . . . . . . . . . .
Vvi17g728 . . Bda06g00589 . . . . Bma12g01032 . . Cma10g00131 Cma11g00103 Car10g00123 Car11g00101 . . Cpe04g01549 Bhi02g00433 . . . . . . Cla06g01655 Cam06g1839 Cec06g1890 Cco06g1895 Clacu06g1799 Cmu06g1741 Cre06g2559 Cone2ag0900 Cone16ag0112 . . . . . . . Blo15g00272 . . Bpe07g00831 Bpe15g00632 . . . Cmo10g00138 Cmo11g00102 . . . . . Cpe18g00839 . . . . . . . . . . . . . . Lsi06g01545 Csa01g00159 Chy02g02571 Cme02g01961
Vvi17g729 . . . . . Bpe13g00224 Bma06g00229 . . . . . . . . . . . . . . . . . . . . . . . . . Cone16ag0110 . . Lsi02g00364 Csa01g00841 Chy12g01276 Cme12g01703 . . Bda11g01637 . . . . . Sed08g2498 . . . Cma18g00161 . Car18g00154 . . Bhi08g01595 Tan05g2021 Cmetu12g1885 Lac10g0437 Hepe07g2234 . . Cla01g01291 Cam01g1438 Cec01g1473 Cco01g1453 Clacu01g1358 Cmu01g1261 Cre01g1272 . . . .
Vvi17g730 . . Bda06g00590 . . . . . . . Cma10g00130 . Car10g00122 . Sed08g0134 . . Bhi02g00434 Tan09g2235 Cmetu02g1681 . Hepe09g0194 . . Cla06g01656 Cam06g1840 Cec06g1891 Cco06g1896 Clacu06g1800 Cmu06g1742 Cre06g2560 . . Cone13ag0134 . . . . . . . . . Bpe07g00832 . . . . Cmo10g00137 . . . . . . Cpe18g00840 . . . . . . . . . . . . . . Lsi06g01546 Csa01g00158 Chy02g02572 Cme02g01962
Vvi17g731 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g732 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g733 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g734 . . . . Bpe12g00592 . . . Cmo13g00922 . . . . . . Cpe20g00234 . . . . . . . . . . . . . . . . Cone16ag0109 . . Lsi02g00365 Csa01g00842 Chy12g01275 Cme12g01701 Blo13g00055 . . . . . . . . . . Cma13g00894 . Car13g00735 . . . Bhi08g01596 . . Lac10g0438 Hepe07g2233 . . . . . . . . . . . . .
Vvi17g735 . . . . Bpe12g00593 . . . . Cmo18g00124 Cma10g00129 Cma11g00101 Car10g00121 Car11g00100 Sed08g0132 Cpe20g00235 . Bhi02g00435 Tan09g2237 Cmetu02g1086 . Hepe09g0195 . . Cla06g01657 Cam06g1842 Cec06g1893 Cco06g1898 Clacu06g1802 . Cre06g2561 . . . Cone19ag0136 . Csa01g00843 Chy12g01273 . . . . . . . . Bma08g00169 . Cmo10g00136 Cmo11g00101 . . Car13g00734 Car18g00155 Cpe09g01032 Cpe18g00841 Bhi08g01598 . . Lac10g0440 . . . Cla01g01293 Cam01g1437 Cec01g1471 Cco01g1455 Clacu01g1360 Cmu01g1265 Cre01g1271 Lsi06g01547 Csa01g00157 Chy02g02573 Cme02g01963
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 8123710 8126731 - Bda023853.1 Bda06g00589 589
6 8129055 8130485 - Bda023854.1 Bda06g00590 590
11 50322436 50323121 + Bda008527.1 Bda11g01637 1637
2 8068134 8071818 - XM_039024043.1 Bhi02g00433 433
2 8141409 8143776 - XM_039022682.1 Bhi02g00434 434
2 8209428 8214886 + XM_039024178.1 Bhi02g00435 435
8 45633999 45635209 + XM_039039982.1 Bhi08g01593 1593
8 45826424 45826949 + XM_039037903.1 Bhi08g01595 1595
8 45916569 45922051 + XM_039037606.1 Bhi08g01596 1596
8 45922834 45927367 + XM_039039496.1 Bhi08g01598 1598
13 822264 829594 + BLOR05336 Blo13g00055 55
15 2938354 2941021 + BLOR06666 Blo15g00272 272
6 2688572 2689371 - Bma022847.1 Bma06g00229 229
8 2071303 2084598 - Bma027169.1 Bma08g00169 169
12 42403872 42405468 - Bma008380.1 Bma12g01032 1032
7 14539087 14541799 - Bpe021675.1 Bpe07g00831 831
7 14543304 14544734 - Bpe021676.1 Bpe07g00832 832
12 11674743 11677127 + Bpe005855.1 Bpe12g00592 592
12 11677914 11681692 + Bpe005856.1 Bpe12g00593 593
13 10254027 10254779 + Bpe006346.1 Bpe13g00224 224
15 17134552 17136135 + Bpe001564.2 Bpe15g00632 632
1 27918874 27924097 - CaPI482276_01g014370.1 Cam01g1437 1437
1 27953336 27954201 + CaPI482276_01g014380.1 Cam01g1438 1438
6 29420180 29423455 - CaPI482276_06g018390.1 Cam06g1839 1839
6 29431787 29433753 - CaPI482276_06g018400.1 Cam06g1840 1840
6 29442595 29447045 + CaPI482276_06g018420.1 Cam06g1842 1842
10 569970 574855 - Carg10353-RA Car10g00121 121
10 577631 579775 + Carg10354-RA Car10g00122 122
10 582369 585125 + Carg10355-RA Car10g00123 123
11 574218 578975 - Carg18136-RA Car11g00100 100
11 579938 582577 + Carg18137-RA Car11g00101 101
13 8446837 8449583 - Carg07684-RA Car13g00734 734
13 8450425 8451878 - Carg07685-RA Car13g00735 735
18 831274 832373 - Carg06720-RA Car18g00154 154
18 834119 837567 + Carg06721-RA Car18g00155 155
1 26273585 26274333 - CcPI632755_01g014530.1 Cco01g1453 1453
1 26310369 26313628 + CcPI632755_01g014550.1 Cco01g1455 1455
6 29138663 29141929 - CcPI632755_06g018950.1 Cco06g1895 1895
6 29161058 29163025 - CcPI632755_06g018960.1 Cco06g1896 1896
6 29172697 29178357 + CcPI632755_06g018980.1 Cco06g1898 1898
1 29377307 29380558 - CePI673135_01g014710.1 Cec01g1471 1471
1 29421055 29421791 + CePI673135_01g014730.1 Cec01g1473 1473
6 32198222 32201486 - CePI673135_06g018900.1 Cec06g1890 1890
6 32209783 32211750 - CePI673135_06g018910.1 Cec06g1891 1891
6 32221457 32225896 + CePI673135_06g018930.1 Cec06g1893 1893
2 28921622 28924822 - Chy2G048380.1 Chy02g02571 2571
2 28931274 28933214 - Chy2G048390.1 Chy02g02572 2572
2 28940268 28944725 + Chy2G048400.1 Chy02g02573 2573
12 17310095 17312848 - Chy12G218730.1 Chy12g01273 1273
12 17313294 17317221 - Chy12G218750.1 Chy12g01275 1275
12 17318785 17324800 + Chy12G218760.1 Chy12g01276 1276
1 24846635 24847383 - ClG42_01g0135800.10 Clacu01g1358 1358
1 24895847 24899093 + ClG42_01g0136000.10 Clacu01g1360 1360
6 28476743 28480021 - ClG42_06g0179900.10 Clacu06g1799 1799
6 28488355 28490321 - ClG42_06g0180000.10 Clacu06g1800 1800
6 28499200 28504790 + ClG42_06g0180200.10 Clacu06g1802 1802
1 26185703 26186541 - ClCG01G013070.2 Cla01g01291 1291
1 26231130 26239892 + ClCG01G013080.1 Cla01g01293 1293
6 30061814 30065630 - ClCG06G016920.1 Cla06g01655 1655
6 30073683 30075649 - ClCG06G016930.1 Cla06g01656 1656
6 30084390 30090326 + ClCG06G016940.2 Cla06g01657 1657
10 583554 588734 - CmaCh10G001290.1 Cma10g00129 129
10 591156 593176 + CmaCh10G001300.1 Cma10g00130 130
10 595793 599651 + CmaCh10G001310.1 Cma10g00131 131
11 543807 547607 - CmaCh11G001010.1 Cma11g00101 101
11 548654 552496 + CmaCh11G001030.1 Cma11g00103 103
13 7207400 7212799 - CmaCh13G008940.1 Cma13g00894 894
13 7213377 7214510 - CmaCh13G008950.1 Cma13g00895 895
18 815402 816661 - CmaCh18G001610.1 Cma18g00161 161
2 25864064 25867810 - MELO3C017099.2.1 Cme02g01961 1961
2 25880269 25882378 - MELO3C017098.2.1 Cme02g01962 1962
2 25888628 25892848 + MELO3C017097.2.1 Cme02g01963 1963
12 23884631 23892341 - MELO3C002259.2.1 Cme12g01701 1701
12 23896846 23898161 + MELO3C002257.2.1 Cme12g01703 1703
2 24222799 24228786 + PI0016980.1 Cmetu02g1086 1086
2 24213575 24215764 - PI0028802.1 Cmetu02g1681 1681
4 9332955 9336881 + PI0028856.1 Cmetu04g2527 2527
12 2386625 2386944 - PI0006969.1 Cmetu12g1885 1885
10 625356 629571 - CmoCh10G001360.1 Cmo10g00136 136
10 632421 634453 + CmoCh10G001370.1 Cmo10g00137 137
10 636719 640290 + CmoCh10G001380.1 Cmo10g00138 138
11 539352 543306 - CmoCh11G001010.1 Cmo11g00101 101
11 544268 547797 + CmoCh11G001020.1 Cmo11g00102 102
13 8143395 8148936 - CmoCh13G009220.1 Cmo13g00922 922
13 8149813 8150942 - CmoCh13G009230.1 Cmo13g00923 923
18 879086 883521 + CmoCh18G001240.1 Cmo18g00124 124
1 25187824 25188572 - CmPI595203_01g012610.1 Cmu01g1261 1261
1 25235381 25238624 + CmPI595203_01g012650.1 Cmu01g1265 1265
6 28379710 28382988 - CmPI595203_06g017410.1 Cmu06g1741 1741
6 28391323 28393289 - CmPI595203_06g017420.1 Cmu06g1742 1742
2 34824127 34827250 - Conep02aG0193000.1 Cone2ag0900 900
13 774562 776833 - Conep13aG0013900.1 Cone13ag0134 134
16 641785 644564 - Conep16aG0011100.1 Cone16ag0109 109
16 646153 646926 + Conep16aG0011200.1 Cone16ag0110 110
16 657816 660885 + Conep16aG0011400.1 Cone16ag0112 112
19 730622 736253 + Conep19aG0014200.1 Cone19ag0136 136
4 12135714 12139619 - Cp4.1LG04g15530.1 Cpe04g01549 1549
9 9074155 9079026 - Cp4.1LG09g10390.1 Cpe09g01032 1032
9 9086670 9087846 - Cp4.1LG09g10410.1 Cpe09g01033 1033
18 7743553 7747532 - Cp4.1LG18g08430.1 Cpe18g00839 839
18 7749667 7752366 - Cp4.1LG18g08420.1 Cpe18g00840 840
18 7755223 7759989 + Cp4.1LG18g08340.1 Cpe18g00841 841
20 1338736 1339871 + Cp4.1LG20g02330.1 Cpe20g00233 233
20 1340456 1341920 + Cp4.1LG20g02290.1 Cpe20g00234 234
20 1342753 1345854 + Cp4.1LG20g02320.1 Cpe20g00235 235
1 25962521 25971197 - CrPI670011_01g012710.1 Cre01g1271 1271
1 25999751 26000587 + CrPI670011_01g012720.1 Cre01g1272 1272
6 33198767 33202015 - CrPI670011_06g025590.1 Cre06g2559 2559
6 33210896 33212863 - CrPI670011_06g025600.1 Cre06g2560 2560
6 33222737 33228261 + CrPI670011_06g025610.1 Cre06g2561 2561
1 1012940 1016683 - CsaV3_1G001570.1 Csa01g00157 157
1 1023562 1026285 + CsaV3_1G001580.1 Csa01g00158 158
1 1031695 1035610 + CsaV3_1G001590.1 Csa01g00159 159
1 5269733 5277552 - CsaV3_1G008410.1 Csa01g00841 841
1 5278262 5281460 + CsaV3_1G008420.1 Csa01g00842 842
1 5282234 5286307 + CsaV3_1G008430.1 Csa01g00843 843
7 66765843 66768261 - Hsped.07g22330.1 Hepe07g2233 2233
7 66780465 66781786 + Hsped.07g22340.1 Hepe07g2234 2234
7 66788211 66789482 - Hsped.07g22350.1 Hepe07g2235 2235
9 1538557 1540623 - Hsped.09g01940.1 Hepe09g0194 194
9 1548748 1554792 + Hsped.09g01950.1 Hepe09g0195 195
10 3408462 3409762 + Lag0024481.1 Lac10g0436 436
10 3417202 3418357 - Lag0024482.1 Lac10g0437 437
10 3447677 3449678 + Lag0024483.1 Lac10g0438 438
10 3452271 3455200 + Lag0024485.1 Lac10g0440 440
2 3105894 3106817 - Lsi02G003640.1 Lsi02g00364 364
2 3123066 3131555 + Lsi02G003650.1 Lsi02g00365 365
6 25801745 25805609 - Lsi06G015450.1 Lsi06g01545 1545
6 25815711 25817854 - Lsi06G015460.1 Lsi06g01546 1546
6 25828898 25833037 + Lsi06G015470.1 Lsi06g01547 1547
8 743362 750340 - Sed0006960.1 Sed08g0132 132
8 766125 766815 + Sed0010486.1 Sed08g0134 134
8 28384001 28386171 + Sed0010967.1 Sed08g1387 1387
8 37801803 37804153 - Sed0012989.1 Sed08g2498 2498
5 70344372 70346416 + Tan0008412.1 Tan05g2021 2021
5 70363640 70364813 - Tan0009901.1 Tan05g2023 2023
9 72337190 72339317 - Tan0022734.1 Tan09g2235 2235
9 72350026 72355203 + Tan0004034.2 Tan09g2237 2237
17 9127963 9162243 + Vvi17g726 Vvi17g726 726
17 9162805 9164179 + Vvi17g727 Vvi17g727 727
17 9166427 9172256 - Vvi17g728 Vvi17g728 728
17 9199302 9201475 - Vvi17g729 Vvi17g729 729
17 9221631 9223623 - Vvi17g730 Vvi17g730 730
17 9224790 9239797 - Vvi17g731 Vvi17g731 731
17 9253867 9254795 - Vvi17g732 Vvi17g732 732
17 9255818 9255998 - Vvi17g733 Vvi17g733 733
17 9257909 9260120 + Vvi17g734 Vvi17g734 734
17 9272856 9280462 + Vvi17g735 Vvi17g735 735
       

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