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
Vvi17g526 Blo04g00764 . . . . . . . Cmo13g00966 Cmo18g00094 . . . . . . . . . . . . . . . . . . . . . Cone2ag0855 . . . Lsi02g00304 Csa01g00783 Chy12g01332 Cme12g01761 . . . . . Bpe15g00609 . . . . . Cma13g00936 Cma18g00122 Car13g00776 Car18g00112 Cpe09g01070 . Bhi08g01398 . . . . . . Cla01g01432 . . . . . . . . . .
Vvi17g527 . . Bda06g00550 Bda15g00576 Bpe12g00553 . . Bma12g01001 . . Cma10g00183 Cma11g00152 Car10g00173 Car11g00142 Sed08g0205 . Cpe04g01507 Bhi02g00335 Tan09g2138 Cmetu02g1801 . Hepe09g0129 . . Cla06g01599 Cam06g1773 Cec06g1825 Cco06g1832 Clacu06g1736 Cmu06g1680 Cre06g2496 . . Cone13ag0080 Cone19ag0083 Lsi02g00303 . Chy12g01333 Cme12g01762 Blo13g00015 . . . Bpe07g00789 . . . Sed01g1823 . . . Cma18g00121 . Car18g00111 Cpe09g01071 Cpe18g00801 Bhi08g01396 Tan05g2096 Cmetu12g1502 Lac10g0362 Hepe07g2292 . . Cla01g01433 Cam01g1501 Cec01g1541 Cco01g1586 Clacu01g1525 Cmu01g1416 Cre01g1335 Lsi06g01475 Csa01g00224 Chy02g02508 Cme02g01894
Vvi17g528 Blo04g00765 . . . . . . . Cmo13g01169 . . . . . . Cpe20g00034 . . . . . . . . . . . . . . . . Cone16ag0157 . Cone19ag0082 Lsi02g00055 Csa01g00528 Chy12g01559 Cme12g02013 . . . Bda14g00843 . Bpe15g00608 Bma03g00821 . . . . Cma13g01118 . Car13g00952 . . . . . . . . . . Cla04g01214 Cam04g1280 Cec01g1789 Cco01g1835 Clacu04g1309 Cmu04g1284 Cre01g1575 . . . .
Vvi17g529 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0081 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g530 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g531 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g532 Blo04g00766 . Bda06g00549 Bda15g00598 Bpe12g00552 Bpe13g00284 Bma06g00180 . . . . . . . . . . . . . . . . . . . . . . . . Cone2ag0852 Cone16ag0158 . . . . . . Blo13g00014 . Bda11g01694 . Bpe07g00788 . . Bma08g00215 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g533 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g534 . Blo16g00189 . . . Bpe13g00285 Bma06g00179 . Cmo13g01174 . Cma10g00184 Cma11g00151 Car10g00174 Car11g00143 Sed08g0206 . . Bhi02g00334 Tan09g2137 Cmetu02g1078 . Hepe09g0128 . . Cla06g01598 Cam06g1772 Cec06g1824 Cco06g1831 Clacu06g1735 Cmu06g1679 Cre06g2495 Cone2ag0850 . Cone13ag0078 Cone19ag0078 Lsi02g00059 Csa01g00532 Chy12g01555 Cme12g02009 . . Bda11g01695 Bda14g00845 . Bpe15g00606 Bma03g00823 . . Cmo10g00201 Cmo11g00156 Cma13g01121 . Car13g00956 . . . . . . . . . . Cla04g01210 Cam04g1276 Cec01g1784 Cco01g1831 Clacu04g1305 Cmu04g1280 Cre01g1571 Lsi06g01474 Csa01g00225 Chy02g02507 Cme02g01893
Vvi17g535 . . . . . . . Bma12g01000 . . Cma10g00185 . Car10g00175 Car11g00145 . . Cpe04g01506 Bhi02g00333 Tan09g2136 . . Hepe09g0127 . . Cla06g01597 Cam06g1771 Cec06g1823 Cco06g1830 Clacu06g1734 Cmu06g1678 Cre06g2494 . . Cone13ag0077 Cone19ag0077 . . . . . . . . Bpe07g00787 . . . . Cmo10g00202 Cmo11g00157 . . . . . Cpe18g00800 . . . . . . . . . . . . . . Lsi06g01473 Csa01g00226 Chy02g02506 Cme02g01892
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 7759025 7761084 + Bda023807.1 Bda06g00549 549
6 7771362 7771956 + Bda023808.1 Bda06g00550 550
11 51087400 51088010 - Bda008590.1 Bda11g01694 1694
11 51091563 51092488 - Bda008591.1 Bda11g01695 1695
14 6510058 6511407 + Bda027616.1 Bda14g00843 843
14 6518046 6518816 - Bda027618.1 Bda14g00845 845
15 8977221 8977711 + Bda012420.1 Bda15g00576 576
15 9193734 9195493 - Bda012442.1 Bda15g00598 598
2 6153377 6155922 + XM_039023054.1 Bhi02g00333 333
2 6159914 6165040 + XM_039023359.1 Bhi02g00334 334
2 6191172 6191586 + XM_039024722.1 Bhi02g00335 335
8 41609374 41609913 + XM_039039691.1 Bhi08g01396 1396
8 41654245 41658783 + XM_039039521.1 Bhi08g01398 1398
4 7290714 7295086 - BLOR13676 Blo04g00764 764
4 7297218 7298567 + BLOR13677 Blo04g00765 765
4 7300235 7300962 - BLOR13678 Blo04g00766 766
13 203212 206390 + BLOR05295 Blo13g00014 14
13 237285 237711 + BLOR05296 Blo13g00015 15
16 4266519 4274973 + BLOR07437 Blo16g00189 189
3 7622815 7624164 + Bma017135.1 Bma03g00821 821
3 7629902 7630811 - Bma017136.1 Bma03g00823 823
6 2238573 2239171 + Bma022794.1 Bma06g00179 179
6 2241028 2241429 + Bma022795.1 Bma06g00180 180
8 2676920 2678629 - Bma027225.1 Bma08g00215 215
12 42086034 42086780 + Bma008347.1 Bma12g01000 1000
12 42105005 42105573 + Bma008349.1 Bma12g01001 1001
7 14297207 14297962 + Bpe021632.1 Bpe07g00787 787
7 14298673 14300709 + Bpe021633.1 Bpe07g00788 788
7 14308217 14308806 + Bpe021634.1 Bpe07g00789 789
12 11363311 11365133 + Bpe005816.1 Bpe12g00552 552
12 11388976 11389465 + Bpe005817.1 Bpe12g00553 553
13 10727734 10728344 - Bpe006409.1 Bpe13g00284 284
13 10730558 10731483 - Bpe006410.1 Bpe13g00285 285
15 16965142 16965982 + Bpe001540.1 Bpe15g00606 606
15 16972713 16974062 - Bpe001542.2 Bpe15g00608 608
15 16976102 16978801 + Bpe001543.1 Bpe15g00609 609
1 28550764 28551228 - CaPI482276_01g015010.1 Cam01g1501 1501
4 26632706 26633625 + CaPI482276_04g012760.1 Cam04g1276 1276
4 26654048 26655238 - CaPI482276_04g012800.1 Cam04g1280 1280
6 28893540 28903387 + CaPI482276_06g017710.1 Cam06g1771 1771
6 28903398 28906318 + CaPI482276_06g017720.1 Cam06g1772 1772
6 28916315 28916725 + CaPI482276_06g017730.1 Cam06g1773 1773
10 828138 828492 - Carg10405-RA Car10g00173 173
10 830956 833204 - Carg10406-RA Car10g00174 174
10 835504 836737 - Carg10407-RA Car10g00175 175
11 817594 817942 - Carg18179-RA Car11g00142 142
11 820099 820922 - Carg18180-RA Car11g00143 143
11 823608 824966 - Carg18182-RA Car11g00145 145
13 8646913 8649282 - Carg07726-RA Car13g00776 776
13 9648068 9649378 + Carg04719-RA Car13g00952 952
13 9657940 9658801 - Carg04716-RA Car13g00956 956
18 600955 601313 + Carg06676-RA Car18g00111 111
18 603712 607127 + Carg06677-RA Car18g00112 112
1 28568124 28568576 - CcPI632755_01g015860.1 Cco01g1586 1586
1 30902498 30903420 + CcPI632755_01g018310.1 Cco01g1831 1831
1 30934846 30936162 - CcPI632755_01g018350.1 Cco01g1835 1835
6 28600497 28610669 + CcPI632755_06g018300.1 Cco06g1830 1830
6 28610828 28613762 + CcPI632755_06g018310.1 Cco06g1831 1831
6 28623814 28624217 + CcPI632755_06g018320.1 Cco06g1832 1832
1 29997972 29998443 - CePI673135_01g015410.1 Cec01g1541 1541
1 32315495 32316426 + CePI673135_01g017840.1 Cec01g1784 1784
1 32344224 32346090 - CePI673135_01g017890.1 Cec01g1789 1789
6 31664546 31674215 + CePI673135_06g018230.1 Cec06g1823 1823
6 31674226 31677169 + CePI673135_06g018240.1 Cec06g1824 1824
6 31687227 31687635 + CePI673135_06g018250.1 Cec06g1825 1825
2 28496600 28498557 + Chy2G047730.1 Chy02g02506 2506
2 28499733 28501972 + Chy2G047740.1 Chy02g02507 2507
2 28508439 28508824 + Chy2G047750.1 Chy02g02508 2508
12 17663053 17666046 - Chy12G219320.1 Chy12g01332 1332
12 17673092 17673488 - Chy12G219330.1 Chy12g01333 1333
12 19171856 19172763 + Chy12G221550.1 Chy12g01555 1555
12 19186090 19187406 - Chy12G221590.1 Chy12g01559 1559
1 27333602 27334057 - ClG42_01g0152500.10 Clacu01g1525 1525
4 26989816 26990738 + ClG42_04g0130500.10 Clacu04g1305 1305
4 27010908 27012930 - ClG42_04g0130900.10 Clacu04g1309 1309
6 27948509 27958330 + ClG42_06g0173400.10 Clacu06g1734 1734
6 27958341 27961282 + ClG42_06g0173500.10 Clacu06g1735 1735
6 27971166 27971574 + ClG42_06g0173600.10 Clacu06g1736 1736
1 28808438 28812848 - ClCG01G014480.1 Cla01g01432 1432
1 28827396 28827851 - ClCG01G014490.2 Cla01g01433 1433
4 27244087 27245728 + ClCG04G012390.2 Cla04g01210 1210
4 27266679 27268995 - ClCG04G012430.1 Cla04g01214 1214
6 29512829 29521371 + ClCG06G016260.2 Cla06g01597 1597
6 29522323 29525879 + ClCG06G016280.2 Cla06g01598 1598
6 29535713 29536121 + ClCG06G016290.1 Cla06g01599 1599
10 839320 839970 - CmaCh10G001830.1 Cma10g00183 183
10 842053 845689 - CmaCh10G001840.1 Cma10g00184 184
10 845908 848411 - CmaCh10G001850.1 Cma10g00185 185
11 794669 800339 + CmaCh11G001510.1 Cma11g00151 151
11 801732 802403 + CmaCh11G001520.1 Cma11g00152 152
13 7403076 7406942 - CmaCh13G009360.1 Cma13g00936 936
13 8343049 8346874 + CmaCh13G011180.1 Cma13g01118 1118
13 8354129 8355953 - CmaCh13G011210.1 Cma13g01121 1121
18 593424 593963 + CmaCh18G001210.1 Cma18g00121 121
18 596575 600433 + CmaCh18G001220.1 Cma18g00122 122
2 25430915 25433113 + MELO3C017166.2.1 Cme02g01892 1892
2 25433842 25436964 + MELO3C017165.2.1 Cme02g01893 1893
2 25443034 25443948 + MELO3C017164.2.1 Cme02g01894 1894
12 24261612 24266020 - MELO3C002198.2.1 Cme12g01761 1761
12 24271172 24271788 - MELO3C002197.2.1 Cme12g01762 1762
12 25716463 25717909 + MELO3C001971.2.1 Cme12g02009 2009
12 25732093 25735886 - MELO3C001967.2.1 Cme12g02013 2013
2 23767409 23770670 + PI0014107.2 Cmetu02g1078 1078
2 23777619 23778018 + PI0019493.1 Cmetu02g1801 1801
12 2017571 2017964 + PI0003142.1 Cmetu12g1502 1502
10 901798 905183 - CmoCh10G002010.1 Cmo10g00201 201
10 905295 908009 - CmoCh10G002020.1 Cmo10g00202 202
11 787941 791075 - CmoCh11G001560.1 Cmo11g00156 156
11 791208 792606 - CmoCh11G001570.1 Cmo11g00157 157
13 8350701 8354528 - CmoCh13G009660.1 Cmo13g00966 966
13 9365833 9367143 + CmoCh13G011690.1 Cmo13g01169 1169
13 9375385 9376479 - CmoCh13G011740.1 Cmo13g01174 1174
18 640244 647760 + CmoCh18G000940.1 Cmo18g00094 94
1 27677379 27677835 - CmPI595203_01g014160.1 Cmu01g1416 1416
4 27171490 27172412 + CmPI595203_04g012800.1 Cmu04g1280 1280
4 27192317 27194612 - CmPI595203_04g012840.1 Cmu04g1284 1284
6 27856745 27865292 + CmPI595203_06g016780.1 Cmu06g1678 1678
6 27866579 27869524 + CmPI595203_06g016790.1 Cmu06g1679 1679
6 27879437 27879845 + CmPI595203_06g016800.1 Cmu06g1680 1680
2 34490064 34491548 + Conep02aG0188000.1 Cone2ag0850 850
2 34500870 34503312 + Conep02aG0188200.1 Cone2ag0852 852
2 34546743 34551671 + Conep02aG0188500.1 Cone2ag0855 855
13 471625 472995 + Conep13aG0008100.1 Cone13ag0077 77
13 474335 475824 + Conep13aG0008200.1 Cone13ag0078 78
13 490723 491288 + Conep13aG0008400.1 Cone13ag0080 80
16 932672 935294 + Conep16aG0016100.1 Cone16ag0157 157
16 946514 948664 - Conep16aG0016200.1 Cone16ag0158 158
19 467299 468745 + Conep19aG0008200.1 Cone19ag0077 77
19 469914 471140 + Conep19aG0008300.1 Cone19ag0078 78
19 479915 483357 - Conep19aG0008700.1 Cone19ag0081 81
19 484830 486139 + Conep19aG0008800.1 Cone19ag0082 82
19 489905 490423 + Conep19aG0008900.1 Cone19ag0083 83
4 11885804 11895724 + Cp4.1LG04g15050.1 Cpe04g01506 1506
4 11898257 11898605 + Cp4.1LG04g15040.1 Cpe04g01507 1507
9 9305884 9309667 - Cp4.1LG09g10740.1 Cpe09g01070 1070
9 9312154 9312663 - Cp4.1LG09g10720.1 Cpe09g01071 1071
18 7486873 7495586 + Cp4.1LG18g07840.1 Cpe18g00800 800
18 7497930 7498284 + Cp4.1LG18g07850.1 Cpe18g00801 801
20 159494 160804 - Cp4.1LG20g00310.1 Cpe20g00034 34
1 26551701 26552151 - CrPI670011_01g013350.1 Cre01g1335 1335
1 28837087 28838007 + CrPI670011_01g015710.1 Cre01g1571 1571
1 28857045 28859203 - CrPI670011_01g015750.1 Cre01g1575 1575
6 32670696 32680460 + CrPI670011_06g024940.1 Cre06g2494 2494
6 32680471 32683386 + CrPI670011_06g024950.1 Cre06g2495 2495
6 32693661 32694065 + CrPI670011_06g024960.1 Cre06g2496 2496
1 1440343 1441301 - CsaV3_1G002240.1 Csa01g00224 224
1 1447149 1449393 - CsaV3_1G002250.1 Csa01g00225 225
1 1450554 1451954 - CsaV3_1G002260.1 Csa01g00226 226
1 3496752 3499541 + CsaV3_1G005280.1 Csa01g00528 528
1 3511387 3513865 - CsaV3_1G005320.1 Csa01g00532 532
1 4953242 4957046 + CsaV3_1G007830.1 Csa01g00783 783
7 67257783 67258222 - Hsped.07g22920.1 Hepe07g2292 2292
9 1013728 1015539 + Hsped.09g01270.1 Hepe09g0127 127
9 1016114 1020437 + Hsped.09g01280.1 Hepe09g0128 128
9 1027592 1028002 + Hsped.09g01290.1 Hepe09g0129 129
10 2831610 2831964 + Lag0024407.1 Lac10g0362 362
2 527095 528411 + Lsi02G000550.1 Lsi02g00055 55
2 547142 549752 - Lsi02G000590.1 Lsi02g00059 59
2 2612683 2613381 + Lsi02G003030.1 Lsi02g00303 303
2 2620655 2625228 + Lsi02G003040.1 Lsi02g00304 304
6 25240732 25249743 + Lsi06G014730.1 Lsi06g01473 1473
6 25250184 25254287 + Lsi06G014740.1 Lsi06g01474 1474
6 25264807 25265495 + Lsi06G014750.1 Lsi06g01475 1475
1 13376357 13377590 + Sed0011093.1 Sed01g1823 1823
8 1167567 1167926 - Sed0011941.1 Sed08g0205 205
8 1171186 1175510 - Sed0023075.1 Sed08g0206 206
5 71429821 71430358 - Tan0016260.1 Tan05g2096 2096
9 71617144 71619961 + Tan0019690.3 Tan09g2136 2136
9 71626235 71631599 + Tan0009284.1 Tan09g2137 2137
9 71640222 71640593 + Tan0006398.1 Tan09g2138 2138
17 6427645 6432407 - Vvi17g526 Vvi17g526 526
17 6455524 6456835 - Vvi17g527 Vvi17g527 527
17 6456980 6469336 + Vvi17g528 Vvi17g528 528
17 6471883 6479479 + Vvi17g529 Vvi17g529 529
17 6493135 6493937 + Vvi17g530 Vvi17g530 530
17 6498769 6499583 + Vvi17g531 Vvi17g531 531
17 6500053 6505038 - Vvi17g532 Vvi17g532 532
17 6515380 6546950 - Vvi17g533 Vvi17g533 533
17 6553936 6556559 - Vvi17g534 Vvi17g534 534
17 6556967 6562182 - Vvi17g535 Vvi17g535 535
       

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