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
Vvi17g706 Blo04g00740 . . . . . . . Cmo13g00928 Cmo18g00119 . . . . . Cpe20g00227 . . . . . . . . . . . . . . . Cone2ag0889 Cone16ag0121 . . Lsi02g00353 Csa01g00829 Chy12g01288 Cme12g01714 . . . Bda14g00819 . Bpe15g00630 . . Sed08g2488 . . Cma13g00902 Cma18g00151 Car13g00742 Car18g00145 Cpe09g01042 . Bhi08g01579 Tan05g2035 Cmetu12g0872 Lac10g0425 Hepe07g2245 . . Cla01g01391 Cam01g1452 Cec01g1487 . Clacu01g1476 Cmu01g1371 Cre01g1286 . . . .
Vvi17g707 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g708 . Blo16g00214 . . . . . . . Cmo18g00120 . . . . . . . . . . . . . . . . . . . . . . Cone16ag0120 . . Lsi02g00354 Csa01g00830 . Cme12g01713 . . . . . . . . Sed08g2490 . . . . . Car18g00146 Cpe09g01041 . Bhi08g01580 Tan05g2034 Cmetu12g1497 Lac10g0426 . . . Cla01g01390 Cam01g1451 Cec01g1486 . Clacu01g1475 Cmu01g1370 Cre01g1285 . . . .
Vvi17g709 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g710 . . . Bda15g00742 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g711 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g712 . . Bda06g00584 . Bpe12g00586 . . Bma12g01029 . Cmo18g00121 Cma10g00139 Cma11g00106 Car10g00130 Car11g00105 Sed08g0143 . Cpe04g01545 Bhi02g00419 Tan09g2224 Cmetu02g2070 . Hepe09g0187 . . Cla06g01648 Cam06g1833 Cec06g1882 Cco06g1888 Clacu06g1792 Cmu06g1734 Cre06g2552 Cone2ag0890 Cone16ag0119 . . Lsi02g00356 Csa01g00832 Chy12g01286 Cme12g01711 Blo13g00049 . . . Bpe07g00825 . . Bma08g00102 Sed01g1676 Cmo10g00145 Cmo11g00108 . Cma18g00152 . Car18g00147 Cpe09g01039 . Bhi08g01582 Tan05g2031 Cmetu12g1608 Lac10g0427 . . . Cla01g01389 Cam01g1449 Cec01g1485 . Clacu01g1472 Cmu01g1367 Cre01g1284 Lsi06g01536 Csa01g00167 Chy02g02564 Cme02g01953
Vvi17g713 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone2ag0138 Cone16ag0916 Lsi02g00357 Csa01g00833 Chy12g01285 Cme12g01710 . . . . . . . . Sed08g2492 . . . Cma18g00156 . Car18g00149 Cpe09g01038 . Bhi08g01585 Tan05g2030 Cmetu12g1860 Lac10g0429 Hepe07g2243 . . Cla01g01388 Cam01g1447 Cec01g1483 . Clacu01g1470 Cmu01g1365 Cre01g1282 . . . .
Vvi17g714 . . Bda06g00585 . . . . Bma12g01030 . . Cma10g00138 . Car10g00129 . Sed08g0142 . . Bhi02g00421 Tan09g2226 Cmetu02g1382 . Hepe09g0188 . . Cla06g01649 Cam06g1834 Cec06g1883 Cco06g1889 Clacu06g1793 Cmu06g1735 Cre06g2553 . . Cone13ag0129 . . . . . . . . . Bpe07g00826 . . . . Cmo10g00144 . . . . . . Cpe18g00835 . . . . . . . . . . . . . . Lsi06g01537 Csa01g00166 Chy02g02565 Cme02g01954
Vvi17g715 . Blo16g00216 . . . Bpe13g00255 Bma06g00207 . Cmo13g00927 . . . Car10g00128 Car11g00104 Sed08g0141 Cpe20g00228 Cpe04g01546 Bhi02g00422 Tan09g2227 Cmetu04g2397 . Hepe09g0189 . . Cla06g01650 . Cec06g1884 Cco06g1890 Clacu06g1794 Cmu06g1736 Cre06g2554 . . . . . Csa01g00834 Chy12g01284 Cme12g01709 Blo13g00050 . . . . . . Bma08g00173 Sed08g2493 Cmo10g00143 . Cma13g00900 Cma18g00157 Car13g00740 Car18g00150 Cpe09g01036 . Bhi08g01586 Tan05g2029 Cmetu12g1291 Lac10g0430 Hepe07g2242 . . Cla01g01284 Cam01g1444 Cec01g1482 Cco01g1445 Clacu01g1351 Cmu01g1255 Cre01g1281 . Csa01g00165 Chy02g02566 Cme02g01955
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 8075696 8078055 + Bda023846.1 Bda06g00584 584
6 8081980 8085611 + Bda023847.1 Bda06g00585 585
14 6290107 6296226 - Bda027589.1 Bda14g00819 819
15 10900169 10900807 + Bda012598.1 Bda15g00742 742
2 7760052 7764754 + XM_039024320.1 Bhi02g00419 419
2 7832576 7837352 + XM_039022992.1 Bhi02g00421 421
2 7837683 7838589 - XM_039022996.1 Bhi02g00422 422
8 45380952 45393206 + XM_039038450.1 Bhi08g01579 1579
8 45395557 45396709 + XM_039039315.1 Bhi08g01580 1580
8 45434143 45438753 + XM_039039313.1 Bhi08g01582 1582
8 45452997 45456868 + XM_039039310.1 Bhi08g01585 1585
8 45575033 45575997 - XM_039038852.1 Bhi08g01586 1586
4 6933465 6939028 - BLOR13652 Blo04g00740 740
13 741623 750439 + BLOR05330 Blo13g00049 49
13 751530 752045 - BLOR05331 Blo13g00050 50
16 4803435 4806615 - BLOR07462 Blo16g00214 214
16 4814382 4816266 - BLOR07464 Blo16g00216 216
6 2490202 2490699 - Bma022821.1 Bma06g00207 207
8 1218007 1218620 + Bma027102.1 Bma08g00102 102
8 2152025 2152546 + Bma027174.1 Bma08g00173 173
12 42378687 42380854 + Bma008377.1 Bma12g01029 1029
12 42381619 42382164 + Bma008378.1 Bma12g01030 1030
7 14513346 14515780 + Bpe021670.1 Bpe07g00825 825
7 14516891 14520812 + Bpe021671.1 Bpe07g00826 826
12 11635503 11637607 + Bpe005849.1 Bpe12g00586 586
13 10507931 10508434 + Bpe006376.1 Bpe13g00255 255
15 17122298 17128890 + Bpe001562.1 Bpe15g00630 630
1 28016368 28016868 + CaPI482276_01g014440.1 Cam01g1444 1444
1 28063991 28065046 - CaPI482276_01g014470.1 Cam01g1447 1447
1 28080195 28080446 - CaPI482276_01g014490.1 Cam01g1449 1449
1 28087264 28088053 - CaPI482276_01g014510.1 Cam01g1451 1451
1 28095251 28100852 - CaPI482276_01g014520.1 Cam01g1452 1452
6 29357770 29361492 + CaPI482276_06g018330.1 Cam06g1833 1833
6 29363682 29368198 + CaPI482276_06g018340.1 Cam06g1834 1834
10 606794 607309 + Carg10360-RA Car10g00128 128
10 607822 612021 - Carg10361-RA Car10g00129 129
10 612080 615080 - Carg10362-RA Car10g00130 130
11 595269 597706 + Carg18140-RA Car11g00104 104
11 599731 601455 - Carg18141-RA Car11g00105 105
13 8468553 8469047 + Carg07690-RA Car13g00740 740
13 8472947 8478633 - Carg07692-RA Car13g00742 742
18 791037 797420 + Carg06710-RA Car18g00145 145
18 798350 799461 + Carg06711-RA Car18g00146 146
18 804328 808680 + Carg06712-RA Car18g00147 147
18 812550 813626 + Carg06714-RA Car18g00149 149
18 815798 816289 - Carg06716-RA Car18g00150 150
1 26212037 26212537 - CcPI632755_01g014450.1 Cco01g1445 1445
6 29072707 29079584 + CcPI632755_06g018880.1 Cco06g1888 1888
6 29081873 29086404 + CcPI632755_06g018890.1 Cco06g1889 1889
6 29087228 29087728 - CcPI632755_06g018900.1 Cco06g1890 1890
1 29492423 29492923 + CePI673135_01g014820.1 Cec01g1482 1482
1 29495593 29496648 - CePI673135_01g014830.1 Cec01g1483 1483
1 29511551 29511802 - CePI673135_01g014850.1 Cec01g1485 1485
1 29518649 29519437 - CePI673135_01g014860.1 Cec01g1486 1486
1 29526412 29532533 - CePI673135_01g014870.1 Cec01g1487 1487
6 32135868 32139298 + CePI673135_06g018820.1 Cec06g1882 1882
6 32141371 32145894 + CePI673135_06g018830.1 Cec06g1883 1883
6 32146729 32147229 - CePI673135_06g018840.1 Cec06g1884 1884
2 28872185 28875931 + Chy2G048310.1 Chy02g02564 2564
2 28876912 28881308 + Chy2G048320.1 Chy02g02565 2565
2 28882145 28882796 - Chy2G048330.1 Chy02g02566 2566
12 17350415 17351029 + Chy12G218840.1 Chy12g01284 1284
12 17352743 17353804 - Chy12G218850.1 Chy12g01285 1285
12 17358159 17360618 - Chy12G218860.1 Chy12g01286 1286
12 17367381 17372355 - Chy12G218880.1 Chy12g01288 1288
1 24787939 24788439 - ClG42_01g0135100.10 Clacu01g1351 1351
1 26809990 26811051 - ClG42_01g0147000.10 Clacu01g1470 1470
1 26827255 26827506 - ClG42_01g0147200.10 Clacu01g1472 1472
1 26834229 26835013 - ClG42_01g0147500.10 Clacu01g1475 1475
1 26844649 26850303 - ClG42_01g0147600.10 Clacu01g1476 1476
6 28413925 28417349 + ClG42_06g0179200.10 Clacu06g1792 1792
6 28419729 28424239 + ClG42_06g0179300.10 Clacu06g1793 1793
6 28425082 28425582 - ClG42_06g0179400.10 Clacu06g1794 1794
1 26119026 26119526 - ClCG01G012990.1 Cla01g01284 1284
1 28264637 28268082 - ClCG01G014020.2 Cla01g01388 1388
1 28271005 28282371 - ClCG01G014030.1 Cla01g01389 1389
1 28291355 28292581 - ClCG01G014050.1 Cla01g01390 1390
1 28301515 28307898 - ClCG01G014060.1 Cla01g01391 1391
6 29994371 29998310 + ClCG06G016850.2 Cla06g01648 1648
6 30000460 30005091 + ClCG06G016860.1 Cla06g01649 1649
6 30005829 30006329 - ClCG06G016870.1 Cla06g01650 1650
10 619940 623897 - CmaCh10G001380.1 Cma10g00138 138
10 624176 627338 - CmaCh10G001390.1 Cma10g00139 139
11 567722 571767 - CmaCh11G001060.1 Cma11g00106 106
13 7229351 7229845 + CmaCh13G009000.1 Cma13g00900 900
13 7233456 7240404 - CmaCh13G009020.1 Cma13g00902 902
18 773293 781159 + CmaCh18G001510.1 Cma18g00151 151
18 784204 789012 + CmaCh18G001520.1 Cma18g00152 152
18 792975 794081 + CmaCh18G001560.1 Cma18g00156 156
18 796423 796917 - CmaCh18G001570.1 Cma18g00157 157
2 25816321 25820800 + MELO3C017107.2.1 Cme02g01953 1953
2 25821307 25826094 + MELO3C017106.2.1 Cme02g01954 1954
2 25826182 25827122 - MELO3C017105.2.1 Cme02g01955 1955
12 23924612 23925637 + MELO3C002250.2.1 Cme12g01709 1709
12 23926529 23927981 - MELO3C002249.2.1 Cme12g01710 1710
12 23931486 23935024 - MELO3C002248.2.1 Cme12g01711 1711
12 23938864 23940879 - MELO3C002246.2.1 Cme12g01713 1713
12 23941236 23947338 - MELO3C002245.2.1 Cme12g01714 1714
2 24157448 24163351 + PI0002407.1 Cmetu02g1382 1382
2 24152302 24156476 + PI0015835.1 Cmetu02g2070 2070
4 31705915 31706223 + PI0018299.1 Cmetu04g2397 2397
12 2334544 2340171 + PI0006876.1 Cmetu12g0872 872
12 2357434 2358546 - PI0006272.1 Cmetu12g1291 1291
12 2341239 2341960 + PI0021356.1 Cmetu12g1497 1497
12 2346468 2350441 + PI0012298.1 Cmetu12g1608 1608
12 2353185 2355969 + PI0025139.1 Cmetu12g1860 1860
10 659816 661939 + CmoCh10G001430.1 Cmo10g00143 143
10 662653 666501 - CmoCh10G001440.1 Cmo10g00144 144
10 666675 669958 - CmoCh10G001450.1 Cmo10g00145 145
11 564373 568243 - CmoCh11G001080.1 Cmo11g00108 108
13 8166979 8167473 + CmoCh13G009270.1 Cmo13g00927 927
13 8171363 8177014 - CmoCh13G009280.1 Cmo13g00928 928
18 834269 840462 + CmoCh18G001190.1 Cmo18g00119 119
18 840999 842941 + CmoCh18G001200.1 Cmo18g00120 120
18 846140 851926 + CmoCh18G001210.1 Cmo18g00121 121
1 25129052 25129552 - CmPI595203_01g012550.1 Cmu01g1255 1255
1 27153983 27155044 - CmPI595203_01g013650.1 Cmu01g1365 1365
1 27171252 27171503 - CmPI595203_01g013670.1 Cmu01g1367 1367
1 27178228 27179012 - CmPI595203_01g013700.1 Cmu01g1370 1370
1 27188644 27194298 - CmPI595203_01g013710.1 Cmu01g1371 1371
6 28317191 28320607 + CmPI595203_06g017340.1 Cmu06g1734 1734
6 28322986 28327496 + CmPI595203_06g017350.1 Cmu06g1735 1735
6 28328339 28328839 - CmPI595203_06g017360.1 Cmu06g1736 1736
2 734605 735285 + Conep02aG0014300.1 Cone2ag0138 138
2 34779935 34784765 + Conep02aG0191900.1 Cone2ag0889 889
2 34785894 34788782 + Conep02aG0192000.1 Cone2ag0890 890
13 750449 755183 + Conep13aG0013400.1 Cone13ag0129 129
16 678645 681124 - Conep16aG0012100.1 Cone16ag0119 119
16 681758 684845 - Conep16aG0012200.1 Cone16ag0120 120
16 685432 689843 - Conep16aG0012300.1 Cone16ag0121 121
16 9419287 9419916 - Conep16aG0328500.1 Cone16ag0916 916
4 12115701 12119614 + Cp4.1LG04g15400.1 Cpe04g01545 1545
4 12120385 12122185 - Cp4.1LG04g15480.1 Cpe04g01546 1546
9 9096808 9097302 + Cp4.1LG09g10300.1 Cpe09g01036 1036
9 9099483 9100556 - Cp4.1LG09g10350.1 Cpe09g01038 1038
9 9104252 9107791 - Cp4.1LG09g10420.1 Cpe09g01039 1039
9 9112537 9113977 - Cp4.1LG09g10360.1 Cpe09g01041 1041
9 9115289 9121412 - Cp4.1LG09g10380.1 Cpe09g01042 1042
18 7713205 7720535 + Cp4.1LG18g08320.1 Cpe18g00835 835
20 1306482 1313815 + Cp4.1LG20g02270.1 Cpe20g00227 227
20 1315291 1315785 - Cp4.1LG20g02380.1 Cpe20g00228 228
1 26065579 26066079 + CrPI670011_01g012810.1 Cre01g1281 1281
1 26068842 26069897 - CrPI670011_01g012820.1 Cre01g1282 1282
1 26084664 26084915 - CrPI670011_01g012840.1 Cre01g1284 1284
1 26091729 26092516 - CrPI670011_01g012850.1 Cre01g1285 1285
1 26099532 26105757 - CrPI670011_01g012860.1 Cre01g1286 1286
6 33136237 33139671 + CrPI670011_06g025520.1 Cre06g2552 2552
6 33141910 33146444 + CrPI670011_06g025530.1 Cre06g2553 2553
6 33147255 33149261 - CrPI670011_06g025540.1 Cre06g2554 2554
1 1073205 1073732 + CsaV3_1G001650.1 Csa01g00165 165
1 1074574 1078901 - CsaV3_1G001660.1 Csa01g00166 166
1 1079886 1082105 - CsaV3_1G001670.1 Csa01g00167 167
1 5225014 5230219 + CsaV3_1G008290.1 Csa01g00829 829
1 5231334 5232025 + CsaV3_1G008300.1 Csa01g00830 830
1 5236841 5240042 + CsaV3_1G008320.1 Csa01g00832 832
1 5242398 5244998 + CsaV3_1G008330.1 Csa01g00833 833
1 5245867 5247302 - CsaV3_1G008340.1 Csa01g00834 834
7 66819880 66820829 + Hsped.07g22420.1 Hepe07g2242 2242
7 66828032 66829367 - Hsped.07g22430.1 Hepe07g2243 2243
7 66848013 66853682 - Hsped.07g22450.1 Hepe07g2245 2245
9 1480349 1482991 + Hsped.09g01870.1 Hepe09g0187 187
9 1484373 1489083 + Hsped.09g01880.1 Hepe09g0188 188
9 1489678 1491709 - Hsped.09g01890.1 Hepe09g0189 189
10 3344055 3349954 + Lag0024470.1 Lac10g0425 425
10 3351735 3352456 + Lag0024471.1 Lac10g0426 426
10 3354229 3361004 + Lag0024472.1 Lac10g0427 427
10 3369126 3370175 + Lag0024474.1 Lac10g0429 429
10 3376530 3377027 - Lag0024475.1 Lac10g0430 430
2 3027143 3033018 + Lsi02G003530.1 Lsi02g00353 353
2 3034545 3035495 + Lsi02G003540.1 Lsi02g00354 354
2 3040865 3045632 + Lsi02G003560.1 Lsi02g00356 356
2 3051094 3052149 + Lsi02G003570.1 Lsi02g00357 357
6 25731757 25736907 + Lsi06G015360.1 Lsi06g01536 1536
6 25738978 25743577 + Lsi06G015370.1 Lsi06g01537 1537
1 12143219 12147087 - Sed0027253.2 Sed01g1676 1676
8 806954 807445 + Sed0019889.1 Sed08g0141 141
8 808299 813157 - Sed0009148.1 Sed08g0142 142
8 815104 820198 - Sed0013619.1 Sed08g0143 143
8 37755829 37761507 + Sed0022411.1 Sed08g2488 2488
8 37762820 37764734 + Sed0016611.2 Sed08g2490 2490
8 37768709 37771195 + Sed0001847.1 Sed08g2492 2492
8 37772623 37773324 - Sed0006170.1 Sed08g2493 2493
5 70411248 70412284 + Tan0003984.1 Tan05g2029 2029
5 70497903 70502890 - Tan0001805.1 Tan05g2030 2030
5 70504082 70508022 - Tan0017284.1 Tan05g2031 2031
5 70515609 70516449 - Tan0019751.1 Tan05g2034 2034
5 70531569 70537820 - Tan0014748.1 Tan05g2035 2035
9 72231120 72235417 + Tan0018647.1 Tan09g2224 2224
9 72239656 72243805 + Tan0015091.1 Tan09g2226 2226
9 72244488 72244997 - Tan0016647.1 Tan09g2227 2227
17 8873381 8880106 + Vvi17g706 Vvi17g706 706
17 8880241 8883008 - Vvi17g707 Vvi17g707 707
17 8898830 8901421 + Vvi17g708 Vvi17g708 708
17 8903186 8905249 - Vvi17g709 Vvi17g709 709
17 8909527 8910724 - Vvi17g710 Vvi17g710 710
17 8922763 8924925 + Vvi17g711 Vvi17g711 711
17 8952003 8971372 + Vvi17g712 Vvi17g712 712
17 8971970 8977390 + Vvi17g713 Vvi17g713 713
17 8977899 8986870 + Vvi17g714 Vvi17g714 714
17 8987334 8987805 - Vvi17g715 Vvi17g715 715
       

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