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
Vvi17g776 . . . . . . . . . . Cma10g00121 . Car10g00108 . . . . Bhi02g00461 Tan09g2260 . . Hepe09g0210 . . Cla06g01670 Cam06g1859 Cec06g1908 Cco06g1913 Clacu06g1815 Cmu06g1756 Cre06g2573 . Cone16ag0091 . . . . . . . . . . . . . Bma08g00093 . Cmo10g00125 . . . . . . Cpe18g00848 . . . . . . . . . . . . . . Lsi06g01563 Csa01g00140 . Cme02g01985
Vvi17g777 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone2ag0917 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g778 Blo04g00730 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0150 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g779 . . . Bda15g00549 . . . . . . Cma10g00120 . Car10g00107 . . . . Bhi02g00472 Tan09g2262 . . Hepe09g0211 . . Cla06g01671 Cam06g1860 Cec06g1909 Cco06g1914 Clacu06g1816 Cmu06g1757 Cre06g2574 . . . Cone19ag0148 . . . . . . . . . . . . . Cmo10g00124 . . . . . . . . . . . . . . . . . . . . . . Csa01g00139 Chy02g02588 Cme02g01986
Vvi17g780 . . . . . . . Bma12g01044 Cmo13g00909 Cmo18g00138 . . . . . Cpe20g00251 . Bhi02g00474 . . . Hepe09g0212 . . Cla06g01672 . Cec06g1910 Cco06g1915 . . . Cone2ag0918 Cone16ag0089 . . Lsi02g00387 Csa01g00866 Chy12g01256 Cme12g01680 . . . . Bpe07g00847 . . Bma08g00092 . . . Cma13g00878 Cma18g00180 . Car18g00171 Cpe09g01015 . Bhi08g01637 . . . . . . Cla01g01312 Cam01g1417 Cec01g1450 Cco01g1473 Clacu01g1377 Cmu01g1287 Cre01g1254 . . . Cme02g01987
Vvi17g781 . . . . . . . . . . Cma10g00119 Cma11g00088 Car10g00106 Car11g00079 Sed08g0103 . Cpe04g01566 Bhi02g00478 Tan09g2266 Cmetu02g1512 . Hepe09g0213 . . Cla06g01673 Cam06g1861 Cec06g1911 Cco06g1916 Clacu06g1817 Cmu06g1758 Cre06g2575 . . . . . . . . . Blo15g00262 . . Bpe07g00848 . . . . Cmo10g00123 Cmo11g00088 . . . . . Cpe18g00849 . . . . . . . . . . . . . . Lsi06g01564 Csa01g00136 Chy02g02591 Cme02g01988
Vvi17g782 . . . . . . . . Cmo13g00908 . . . . . . Cpe20g00252 . . . . . . . . . . . . . . . Cone2ag0919 Cone16ag0088 . . Lsi02g00388 Csa01g00867 Chy12g01255 Cme12g01679 . . . . . . . . . . . Cma13g00875 . Car13g00717 . . . Bhi08g01639 . . . . . . . . . . . . . . . . .
Vvi17g783 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g784 . . Bda06g00608 . . . . . Cmo13g00907 . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00390 Csa01g00868 Chy12g01254 Cme12g01678 . . . . Bpe07g00849 . . . Sed01g1635 . . Cma13g00874 . Car13g00716 . . . Bhi08g01640 Tan05g1989 Cmetu12g1788 Lac10g0470 . . . Cla01g01314 . . Cco01g1476 Clacu01g1380 Cmu01g1290 . . . . .
Vvi17g785 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 8283768 8285309 - Bda023875.1 Bda06g00608 608
15 8558460 8564074 + Bda012384.1 Bda15g00549 549
2 9031014 9067752 + XM_039024022.1 Bhi02g00461 461
2 9222119 9225523 - XM_039023084.1 Bhi02g00472 472
2 9226408 9229961 - XM_039023420.1 Bhi02g00474 474
2 9231394 9241052 - XM_039023705.1 Bhi02g00478 478
8 46362947 46368249 - XM_039039569.1 Bhi08g01637 1637
8 46369303 46372269 + XM_039038785.1 Bhi08g01639 1639
8 46372258 46373630 - XM_039038787.1 Bhi08g01640 1640
4 6782624 6785496 - BLOR13642 Blo04g00730 730
15 2799117 2809127 + BLOR06656 Blo15g00262 262
8 1073790 1091352 + Bma027091.2 Bma08g00092 92
8 1118659 1153949 - Bma027092.1 Bma08g00093 93
12 42490790 42493245 - Bma008390.2 Bma12g01044 1044
7 14621855 14622474 - Bpe021691.1 Bpe07g00847 847
7 14626071 14632376 - Bpe021692.1 Bpe07g00848 848
7 14635700 14637213 - Bpe021693.1 Bpe07g00849 849
1 27712409 27717075 + CaPI482276_01g014170.1 Cam01g1417 1417
6 29640159 29660282 + CaPI482276_06g018590.1 Cam06g1859 1859
6 29662544 29666098 - CaPI482276_06g018600.1 Cam06g1860 1860
6 29667215 29680941 - CaPI482276_06g018610.1 Cam06g1861 1861
10 490808 500406 + Carg10338-RA Car10g00106 106
10 501196 504477 + Carg10339-RA Car10g00107 107
10 506521 514930 - Carg10340-RA Car10g00108 108
11 423467 432557 + Carg20217-RA Car11g00079 79
13 8362735 8364649 + Carg07666-RA Car13g00716 716
13 8363754 8365867 - Carg07667-RA Car13g00717 717
18 938042 942144 - Carg06737-RA Car18g00171 171
1 26527114 26531532 - CcPI632755_01g014730.1 Cco01g1473 1473
1 26537745 26538584 - CcPI632755_01g014760.1 Cco01g1476 1476
6 29374382 29387858 + CcPI632755_06g019130.1 Cco06g1913 1913
6 29390635 29393680 - CcPI632755_06g019140.1 Cco06g1914 1914
6 29394768 29398138 - CcPI632755_06g019150.1 Cco06g1915 1915
6 29400390 29408445 - CcPI632755_06g019160.1 Cco06g1916 1916
1 29147459 29152069 + CePI673135_01g014500.1 Cec01g1450 1450
6 32443829 32457541 + CePI673135_06g019080.1 Cec06g1908 1908
6 32460741 32464312 - CePI673135_06g019090.1 Cec06g1909 1909
6 32465469 32469017 - CePI673135_06g019100.1 Cec06g1910 1910
6 32478120 32486504 - CePI673135_06g019110.1 Cec06g1911 1911
2 29122124 29124536 - Chy2G048550.1 Chy02g02588 2588
2 29134124 29141736 - Chy2G048580.1 Chy02g02591 2591
12 17159928 17160686 + Chy12G218540.1 Chy12g01254 1254
12 17161079 17163012 - Chy12G218550.1 Chy12g01255 1255
12 17170887 17174806 + Chy12G218560.1 Chy12g01256 1256
1 25102920 25107352 - ClG42_01g0137700.10 Clacu01g1377 1377
1 25113491 25117489 - ClG42_01g0138000.10 Clacu01g1380 1380
6 28696431 28711105 + ClG42_06g0181500.10 Clacu06g1815 1815
6 28713367 28716921 - ClG42_06g0181600.10 Clacu06g1816 1816
6 28718037 28731769 - ClG42_06g0181700.10 Clacu06g1817 1817
1 26461824 26467131 - ClCG01G013290.1 Cla01g01312 1312
1 26471722 26479322 - ClCG01G013310.2 Cla01g01314 1314
6 30287083 30315269 + ClCG06G017100.2 Cla06g01670 1670
6 30315982 30321023 - ClCG06G017110.2 Cla06g01671 1671
6 30322094 30325535 - ClCG06G017120.1 Cla06g01672 1672
6 30327469 30337365 - ClCG06G017130.2 Cla06g01673 1673
10 508260 516662 + CmaCh10G001190.1 Cma10g00119 119
10 516779 520100 + CmaCh10G001200.1 Cma10g00120 120
10 520991 536558 - CmaCh10G001210.1 Cma10g00121 121
11 425970 436747 + CmaCh11G000880.1 Cma11g00088 88
13 7123516 7124521 + CmaCh13G008740.1 Cma13g00874 874
13 7124492 7126589 - CmaCh13G008750.1 Cma13g00875 875
13 7128928 7131022 + CmaCh13G008780.1 Cma13g00878 878
18 918318 922525 - CmaCh18G001800.1 Cma18g00180 180
2 26109608 26130893 + MELO3C026286.2.1 Cme02g01985 1985
2 26134324 26138092 - MELO3C026285.2.1 Cme02g01986 1986
2 26139435 26142587 - MELO3C026284.2.1 Cme02g01987 1987
2 26143349 26152960 - MELO3C026283.2.1 Cme02g01988 1988
12 23740870 23742172 + MELO3C002283.2.1 Cme12g01678 1678
12 23742279 23744361 - MELO3C002282.2.1 Cme12g01679 1679
12 23745458 23750902 + MELO3C002281.2.1 Cme12g01680 1680
2 24432095 24439675 - PI0003776.1 Cmetu02g1512 1512
12 2554062 2554907 - PI0026532.1 Cmetu12g1788 1788
10 544542 552836 + CmoCh10G001230.1 Cmo10g00123 123
10 552973 556995 + CmoCh10G001240.1 Cmo10g00124 124
10 558846 572663 - CmoCh10G001250.1 Cmo10g00125 125
11 417730 428893 + CmoCh11G000880.1 Cmo11g00088 88
13 8056406 8057286 + CmoCh13G009070.1 Cmo13g00907 907
13 8057496 8060231 - CmoCh13G009080.1 Cmo13g00908 908
13 8060380 8063293 + CmoCh13G009090.1 Cmo13g00909 909
18 986280 990305 - CmoCh18G001380.1 Cmo18g00138 138
1 25442640 25446761 - CmPI595203_01g012870.1 Cmu01g1287 1287
1 25452881 25456876 - CmPI595203_01g012900.1 Cmu01g1290 1290
6 28604117 28619500 + CmPI595203_06g017560.1 Cmu06g1756 1756
6 28620726 28624270 - CmPI595203_06g017570.1 Cmu06g1757 1757
6 28625398 28639030 - CmPI595203_06g017580.1 Cmu06g1758 1758
2 34938611 34941511 - Conep02aG0194700.1 Cone2ag0917 917
2 34950281 34953448 - Conep02aG0194800.1 Cone2ag0918 918
2 34955246 34956679 + Conep02aG0194900.1 Cone2ag0919 919
13 946347 949490 - Conep13aG0015500.1 Cone13ag0150 150
16 475148 478072 - Conep16aG0008900.1 Cone16ag0088 88
16 479602 483039 + Conep16aG0009000.1 Cone16ag0089 89
16 494670 500610 - Conep16aG0009200.1 Cone16ag0091 91
19 816031 819210 + Conep19aG0015400.1 Cone19ag0148 148
4 12261430 12272580 - Cp4.1LG04g15600.1 Cpe04g01566 1566
9 8966047 8971349 + Cp4.1LG09g10190.1 Cpe09g01015 1015
18 7809541 7823740 + Cp4.1LG18g08480.1 Cpe18g00848 848
18 7825274 7837499 - Cp4.1LG18g08530.1 Cpe18g00849 849
20 1423491 1427222 - Cp4.1LG20g02600.1 Cpe20g00251 251
20 1427434 1434183 + Cp4.1LG20g02450.1 Cpe20g00252 252
1 25736696 25740681 + CrPI670011_01g012540.1 Cre01g1254 1254
6 33418381 33439971 + CrPI670011_06g025730.1 Cre06g2573 2573
6 33440720 33445822 - CrPI670011_06g025740.1 Cre06g2574 2574
6 33446915 33460665 - CrPI670011_06g025750.1 Cre06g2575 2575
1 808666 816223 + CsaV3_1G001360.1 Csa01g00136 136
1 825303 831136 + CsaV3_1G001390.1 Csa01g00139 139
1 832560 854984 - CsaV3_1G001400.1 Csa01g00140 140
1 5416877 5422526 - CsaV3_1G008660.1 Csa01g00866 866
1 5422614 5426735 + CsaV3_1G008670.1 Csa01g00867 867
1 5424140 5426519 - CsaV3_1G008680.1 Csa01g00868 868
9 1753855 1785997 + Hsped.09g02100.1 Hepe09g0210 210
9 1795129 1798682 - Hsped.09g02110.1 Hepe09g0211 211
9 1799948 1803638 - Hsped.09g02120.1 Hepe09g0212 212
9 1805463 1813997 - Hsped.09g02130.1 Hepe09g0213 213
10 3651217 3652083 - Lag0024515.1 Lac10g0470 470
2 3315095 3320330 - Lsi02G003870.1 Lsi02g00387 387
2 3322247 3325681 + Lsi02G003890.1 Lsi02g00388 388
2 3326058 3327245 - Lsi02G003900.1 Lsi02g00390 390
6 26044394 26067023 + Lsi06G015630.1 Lsi06g01563 1563
6 26068330 26097867 - Lsi06G015640.1 Lsi06g01564 1564
1 11891729 11892481 + Sed0017974.1 Sed01g1635 1635
8 629056 639075 + Sed0016557.2 Sed08g0103 103
5 69796700 69797605 + Tan0017133.1 Tan05g1989 1989
9 72666687 72683609 + Tan0016560.1 Tan09g2260 2260
9 72687509 72691190 - Tan0010702.1 Tan09g2262 2262
9 72698578 72707822 - Tan0010412.1 Tan09g2266 2266
17 10124362 10160031 + Vvi17g776 Vvi17g776 776
17 10163868 10167001 - Vvi17g777 Vvi17g777 777
17 10170748 10178460 - Vvi17g778 Vvi17g778 778
17 10180665 10185047 - Vvi17g779 Vvi17g779 779
17 10194238 10198544 - Vvi17g780 Vvi17g780 780
17 10201723 10209064 - Vvi17g781 Vvi17g781 781
17 10235741 10240891 + Vvi17g782 Vvi17g782 782
17 10240919 10241875 + Vvi17g783 Vvi17g783 783
17 10241879 10248968 - Vvi17g784 Vvi17g784 784
17 10277073 10279848 - Vvi17g785 Vvi17g785 785
       

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