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
Vvi17g666 Blo04g00791 Blo16g00165 . . . Bpe13g00315 Bma06g00149 . . . . . . Car11g00188 Sed08g0276 . . Bhi02g00094 Tan09g2043 Cmetu02g1345 . Hepe09g0274 . . Cla06g01538 Cam06g1697 Cec06g1759 Cco06g1758 Clacu06g1664 Cmu06g1610 Cre06g2423 . . . . . . . . . . Bda11g01731 Bda14g00882 . Bpe15g00579 Bma03g00852 . . . . . . . . . Cpe18g00708 . . . . . . . . . . . . . . Lsi06g01411 Csa01g00296 Chy02g02441 Cme02g01828
Vvi17g667 . . Bda06g00521 . Bpe12g00524 . . Bma12g00964 . . . . . Car11g00189 Sed08g0277 . Cpe04g01458 Bhi02g00093 Tan09g2042 Cmetu02g0517 . Hepe09g0275 . . Cla06g01537 Cam06g1696 Cec06g1758 Cco06g1757 Clacu06g1663 Cmu06g1609 Cre06g2422 . . . . . . . . . Blo15g00339 . . Bpe07g00755 . . Bma08g00242 . . Cmo11g00212 . . . . . . . . . . . . . . . . . . . . Lsi06g01410 Csa01g00297 Chy02g02440 Cme02g01827
Vvi17g668 . Blo16g00164 . . . Bpe13g00316 . . Cmo13g01119 . . . . . . . . . . . . . . . . . . . . . . Cone2ag0798 Cone16ag0211 . . Lsi02g00120 Csa01g00601 Chy12g01496 Cme12g01940 . . Bda11g01732 . . . . . Sed01g2295 . . Cma13g01073 . Car13g00909 Car18g00003 . . Bhi08g01082 Tan05g2359 Cmetu12g0766 Lac10g0150 Hepe07g2461 . . Cla04g01152 Cam04g1210 Cec01g1721 Cco01g1766 Clacu04g1237 Cmu04g1216 Cre01g1512 . . . .
Vvi17g669 . . . . . . . . . . Cma10g00157 . . Car11g00119 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo10g00169 Cmo11g00126 . . . . . . . . . . . . . . . . . . . . . Csa01g00189 . .
Vvi17g670 . . Bda06g00570 . Bpe12g00572 . . Bma12g01020 Cmo13g00939 . . . . . . . . . . . . . . . . . . . . . . . Cone16ag0132 . . . . Chy12g01303 Cme12g01728 . Blo15g00285 . . . . . . . . . Cma13g00912 Cma18g00142 Car13g00752 Car18g00136 Cpe09g01049 . . . . . . . . Cla01g01402 Cam01g1464 Cec01g1507 . Clacu01g1490 Cmu01g1384 Cre01g1300 . . . .
Vvi17g671 . . . . . . Bma06g00193 . . Cmo18g00111 . . . . . Cpe20g00216 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi08g01440 . . . . . . . . . . . . . . . . .
Vvi17g672 Blo04g00752 . . Bda15g00706 Bpe12g00497 . . . . . . . . . Sed08g0179 . Cpe04g01530 Bhi02g00380 Tan09g2185 Cmetu02g0204 . Hepe09g0159 . . Cla06g01627 Cam06g1808 Cec06g1859 Cco06g1865 Clacu06g1768 Cmu06g1711 Cre06g2530 Cone2ag0877 . Cone13ag0104 . Lsi02g00340 Csa01g00811 . . Blo13g00036 . Bda11g01577 . Bpe07g00811 Bpe15g00619 . . . . . . . . . . Cpe18g00819 . . . . . . . . . . . . . . Lsi06g01508 . Chy02g02541 Cme02g01925
Vvi17g673 . . . . . . . . . . . . Car10g00152 . . . . . . . . . . . . . . . . . . Cone2ag0776 Cone16ag0254 . Cone19ag0110 . . . . . . . . . . . Bma08g00193 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g674 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g675 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 7478794 7481976 - Bda023776.1 Bda06g00521 521
6 7977515 7980452 + Bda023832.2 Bda06g00570 570
11 48986958 48988049 - Bda008447.1 Bda11g01577 1577
11 51953752 51955201 + Bda008628.2 Bda11g01731 1731
11 51956727 51965278 - Bda033166 Bda11g01732 1732
14 6814763 6815730 + Bda027660.1 Bda14g00882 882
15 10471975 10474420 - Bda012560.1 Bda15g00706 706
2 1778198 1781690 - XM_039022790.1 Bhi02g00093 93
2 1784470 1787304 - XM_039024346.1 Bhi02g00094 94
2 7200800 7203087 - XM_039022349.1 Bhi02g00380 380
8 35032970 35038119 + XM_039039690.1 Bhi08g01082 1082
8 42443271 42450837 - XM_039038275.1 Bhi08g01440 1440
4 7094119 7110105 + BLOR13664 Blo04g00752 752
4 7932250 7933733 + BLOR13703 Blo04g00791 791
13 551486 552862 - BLOR05317 Blo13g00036 36
15 3116203 3119715 - BLOR06679 Blo15g00285 285
15 4088092 4091311 + BLOR06733 Blo15g00339 339
16 3775839 3784242 + BLOR07412 Blo16g00164 164
16 3784352 3785695 - BLOR07413 Blo16g00165 165
3 8202002 8203017 + Bma017168.1 Bma03g00852 852
6 1950268 1951197 - Bma022768.1 Bma06g00149 149
6 2360548 2364353 - Bma022808.1 Bma06g00193 193
8 2310372 2313320 - Bma027196.1 Bma08g00193 193
8 2989413 2992555 + Bma027253.1 Bma08g00242 242
12 41612761 41616633 - Bma008306.1 Bma12g00964 964
12 42265889 42271199 + Bma008368.2 Bma12g01020 1020
7 14079346 14082568 - Bpe021601.1 Bpe07g00755 755
7 14433413 14434933 - Bpe021656.1 Bpe07g00811 811
12 10783517 10784583 - Bpe024895 Bpe12g00497 497
12 11107744 11110870 - Bpe005787.1 Bpe12g00524 524
12 11533435 11537064 + Bpe005836.1 Bpe12g00572 572
13 11017692 11019134 + Bpe006442.1 Bpe13g00315 315
13 11023369 11025408 - Bpe006443.1 Bpe13g00316 316
15 16759547 16760295 - Bpe001512.1 Bpe15g00579 579
15 17053693 17060813 - Bpe001552.1 Bpe15g00619 619
1 28225612 28229663 - CaPI482276_01g014640.1 Cam01g1464 1464
4 26144083 26149069 + CaPI482276_04g012100.1 Cam04g1210 1210
6 28355730 28358847 - CaPI482276_06g016960.1 Cam06g1696 1696
6 28360252 28361836 - CaPI482276_06g016970.1 Cam06g1697 1697
6 29162364 29164001 - CaPI482276_06g018080.1 Cam06g1808 1808
10 717498 736185 - Carg10384-RA Car10g00152 152
11 675397 678788 + Carg18156-RA Car11g00119 119
11 1078006 1079293 + Carg09201-RA Car11g00188 188
11 1080955 1084241 + Carg09200-RA Car11g00189 189
13 8531732 8535649 - Carg07702-RA Car13g00752 752
13 9413389 9418503 + Carg04762-RA Car13g00909 909
18 9820 15153 + Carg22783-RA Car18g00003 3
18 730659 732890 + Carg06701-RA Car18g00136 136
1 30395325 30400326 + CcPI632755_01g017660.1 Cco01g1766 1766
6 28059366 28062465 - CcPI632755_06g017570.1 Cco06g1757 1757
6 28063878 28065462 - CcPI632755_06g017580.1 Cco06g1758 1758
6 28876501 28878134 - CcPI632755_06g018650.1 Cco06g1865 1865
1 29661162 29665223 - CePI673135_01g015070.1 Cec01g1507 1507
1 31822566 31827547 + CePI673135_01g017210.1 Cec01g1721 1721
6 31119824 31122965 - CePI673135_06g017580.1 Cec06g1758 1758
6 31124372 31125956 - CePI673135_06g017590.1 Cec06g1759 1759
6 31941358 31942983 - CePI673135_06g018590.1 Cec06g1859 1859
2 28056017 28059440 - Chy2G047070.1 Chy02g02440 2440
2 28061270 28062807 - Chy2G047080.1 Chy02g02441 2441
2 28696908 28698472 - Chy2G048080.1 Chy02g02541 2541
12 17458191 17466905 - Chy12G219030.1 Chy12g01303 1303
12 18810214 18818933 + Chy12G220960.1 Chy12g01496 1496
1 26982790 26986837 - ClG42_01g0149000.10 Clacu01g1490 1490
4 26493629 26498728 + ClG42_04g0123700.10 Clacu04g1237 1237
6 27414588 27417697 - ClG42_06g0166300.10 Clacu06g1663 1663
6 27419105 27420687 - ClG42_06g0166400.10 Clacu06g1664 1664
6 28219281 28220918 - ClG42_06g0176800.10 Clacu06g1768 1768
1 28458020 28467904 - ClCG01G014170.2 Cla01g01402 1402
4 26727140 26736789 + ClCG04G011760.2 Cla04g01152 1152
6 28963821 28967228 - ClCG06G015600.1 Cla06g01537 1537
6 28968549 28971011 - ClCG06G015610.2 Cla06g01538 1538
6 29790728 29793146 - ClCG06G016600.1 Cla06g01627 1627
10 711917 715781 + CmaCh10G001570.1 Cma10g00157 157
13 7289414 7295357 - CmaCh13G009120.1 Cma13g00912 912
13 8111314 8116064 + CmaCh13G010730.1 Cma13g01073 1073
18 716952 720845 + CmaCh18G001420.1 Cma18g00142 142
2 25012380 25016613 - MELO3C017228.2.1 Cme02g01827 1827
2 25018511 25021593 - MELO3C017227.2.1 Cme02g01828 1828
2 25634711 25636549 - MELO3C017134.2.1 Cme02g01925 1925
12 24033989 24038282 - MELO3C002230.2.1 Cme12g01728 1728
12 25353516 25359223 + MELO3C002033.2.1 Cme12g01940 1940
2 23979168 23981508 - PI0011312.1 Cmetu02g0204 204
2 19309591 19310229 + PI0004777.1 Cmetu02g0517 517
2 23332659 23335483 - PI0019967.1 Cmetu02g1345 1345
12 779117 785037 - PI0011991.1 Cmetu12g0766 766
10 758189 762055 + CmoCh10G001690.1 Cmo10g00169 169
11 643950 646700 + CmoCh11G001260.1 Cmo11g00126 126
11 1048642 1052009 + CmoCh11G002120.1 Cmo11g00212 212
13 8228648 8233901 - CmoCh13G009390.1 Cmo13g00939 939
13 9127081 9131870 + CmoCh13G011190.1 Cmo13g01119 1119
18 769494 771306 - CmoCh18G001110.1 Cmo18g00111 111
1 27326510 27330558 - CmPI595203_01g013840.1 Cmu01g1384 1384
4 26675692 26680790 + CmPI595203_04g012160.1 Cmu04g1216 1216
6 27323659 27326771 - CmPI595203_06g016090.1 Cmu06g1609 1609
6 27328179 27329761 - CmPI595203_06g016100.1 Cmu06g1610 1610
6 28122849 28124486 - CmPI595203_06g017110.1 Cmu06g1711 1711
2 33726449 33741896 + Conep02aG0180300.1 Cone2ag0776 776
2 33999576 34003628 + Conep02aG0182600.1 Cone2ag0798 798
2 34685865 34687623 - Conep02aG0190700.1 Cone2ag0877 877
13 647998 650217 - Conep13aG0010900.1 Cone13ag0104 104
16 748561 751154 - Conep16aG0013400.1 Cone16ag0132 132
16 1412997 1415069 - Conep16aG0021500.1 Cone16ag0211 211
16 2793920 2805430 + Conep16aG0260300.1 Cone16ag0254 254
19 615318 618717 + Conep19aG0011600.1 Cone19ag0110 110
4 11631581 11635043 - Cp4.1LG04g14620.1 Cpe04g01458 1458
4 12028450 12030864 - Cp4.1LG04g15360.1 Cpe04g01530 1530
9 9176784 9180994 - Cp4.1LG09g10570.1 Cpe09g01049 1049
18 6984738 6987936 + Cp4.1LG18g06920.1 Cpe18g00708 708
18 7609958 7612542 - Cp4.1LG18g08280.1 Cpe18g00819 819
20 1232696 1239688 - Cp4.1LG20g02190.1 Cpe20g00216 216
1 26236595 26240656 - CrPI670011_01g013000.1 Cre01g1300 1300
1 28341803 28346810 + CrPI670011_01g015120.1 Cre01g1512 1512
6 32119016 32122244 - CrPI670011_06g024220.1 Cre06g2422 2422
6 32123644 32125228 - CrPI670011_06g024230.1 Cre06g2423 2423
6 32939380 32941017 - CrPI670011_06g025300.1 Cre06g2530 2530
1 1232528 1236547 + CsaV3_1G001890.1 Csa01g00189 189
1 1846663 1849602 + CsaV3_1G002960.1 Csa01g00296 296
1 1850827 1855075 + CsaV3_1G002970.1 Csa01g00297 297
1 3860780 3865989 - CsaV3_1G006010.1 Csa01g00601 601
1 5119221 5121677 - CsaV3_1G008110.1 Csa01g00811 811
7 68932519 68937862 + Hsped.07g24610.1 Hepe07g2461 2461
9 1260536 1263226 - Hsped.09g01590.1 Hepe09g0159 159
9 2347591 2349223 + Hsped.09g02740.1 Hepe09g0274 274
9 2352005 2355697 + Hsped.09g02750.1 Hepe09g0275 275
10 1129046 1134174 - Lag0024195.1 Lac10g0150 150
2 987684 1001029 - Lsi02G001200.1 Lsi02g00120 120
2 2890868 2893177 - Lsi02G003400.1 Lsi02g00340 340
6 24675472 24679035 - Lsi06G014100.1 Lsi06g01410 1410
6 24682832 24684864 - Lsi06G014110.1 Lsi06g01411 1411
6 25512275 25514241 - Lsi06G015080.1 Lsi06g01508 1508
1 17363819 17370390 + Sed0001151.1 Sed01g2295 2295
8 998775 1001531 + Sed0001396.1 Sed08g0179 179
8 1614325 1615922 + Sed0008450.1 Sed08g0276 276
8 1617414 1621932 + Sed0022878.1 Sed08g0277 277
5 74953226 74958635 + Tan0012865.1 Tan05g2359 2359
9 70931421 70934885 - Tan0008837.1 Tan09g2042 2042
9 70936655 70939143 - Tan0012977.1 Tan09g2043 2043
9 71903166 71905995 - Tan0020227.1 Tan09g2185 2185
17 8375782 8381026 + Vvi17g666 Vvi17g666 666
17 8383024 8387816 + Vvi17g667 Vvi17g667 667
17 8388647 8394515 - Vvi17g668 Vvi17g668 668
17 8408075 8412077 + Vvi17g669 Vvi17g669 669
17 8423633 8438742 - Vvi17g670 Vvi17g670 670
17 8441136 8447388 + Vvi17g671 Vvi17g671 671
17 8454311 8456118 + Vvi17g672 Vvi17g672 672
17 8459180 8463972 - Vvi17g673 Vvi17g673 673
17 8466167 8517606 - Vvi17g674 Vvi17g674 674
17 8528863 8536897 + Vvi17g675 Vvi17g675 675
       

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