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
Vvi2g682 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g683 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g684 . . . . . . Bma07g00926 Bma14g00159 . . Cma02g01621 . Car02g01380 . . . Cpe05g00170 . . . . . . . . . . . . . . . . . . . . Chy04g00106 . Blo03g00868 Blo19g00195 . Bda09g00731 Bpe08g00827 Bpe11g00328 . . . Cmo02g01666 Cmo19g00243 . . . . . Cpe15g00204 Bhi05g00481 . . . . . . . . . . . . . . Csa03g04597 . Cme04g00130
Vvi2g685 . . . . . . Bma07g00925 Bma14g00160 . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0472 . . . . . . Blo03g00870 Blo19g00196 . Bda09g00737 Bpe08g00826 Bpe11g00327 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g686 . . . . . . Bma07g00924 . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0478 . . . . . . . . Blo19g00197 . . Bpe08g00825 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g687 . . . . . . Bma07g00922 . . . Cma02g01623 . Car02g01382 . . . Cpe05g00169 . . . . . . . . . . . . . . Cone8ag0479 . . . . . Chy04g00108 . . Blo19g00198 . . Bpe08g00824 . . . Sed01g4122 Cmo02g01668 Cmo19g00241 . . . . . Cpe15g00202 Bhi05g00477 Tan07g1993 Cmetu04g2583 Lac11g2429 Hepe06g1786 . Lcy12g1959 . . . . . . . . Csa03g04595 . Cme04g00132
Vvi2g688 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g689 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma06g00872 . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g690 . Blo03g00119 Bda06g01271 . . Bpe07g00216 . . . . . . . . Sed13g0485 . . Bhi11g00020 Tan01g2206 Cmetu06g0815 . . Mch10g1675 . Cla10g00146 Cam10g0141 Cec10g0151 Cco10g0151 Clacu10g0145 Cmu10g0992 Cre10g0403 Cone8ag0607 . . . Lsi07g01181 . . Cme06g02459 . . . . . . . Bma12g00215 . . . . . . . . . . . . . . . . . . . . . . . . Csa03g00155 Chy06g02154 .
Vvi2g691 . . . . . . Bma07g00921 Bma14g00161 . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0480 Cone12ag0475 . . . . Chy04g00109 . . Blo19g00199 Bda07g00089 . . Bpe11g00326 . . Sed01g4123 . Cmo19g00240 . . . . . Cpe15g00201 Bhi05g00476 Tan07g1994 Cmetu04g3095 Lac11g2430 Hepe06g1787 . Lcy12g1960 Cla09g01108 Cam09g1162 Cec09g1170 Cco09g1185 . . Cre09g1123 . Csa03g04593 . Cme04g00133
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 43287934 43290785 - Bda023116.1 Bda06g01271 1271
7 1120284 1121794 + Bda025147.1 Bda07g00089 89
9 12626323 12627111 + Bda031423.1 Bda09g00731 731
9 12741016 12743129 + Bda031432.1 Bda09g00737 737
5 10079919 10082576 + XM_039032545.1 Bhi05g00476 476
5 10091729 10094281 - XM_039032433.1 Bhi05g00477 477
5 10149760 10153184 + XM_039032810.1 Bhi05g00481 481
11 324057 327761 - XM_039049400.1 Bhi11g00020 20
3 3547650 3551292 - BLOR11300 Blo03g00119 119
3 34500474 34502429 - BLOR12049 Blo03g00868 868
3 34521836 34526632 - BLOR12051 Blo03g00870 870
19 8781561 8783247 - BLOR09538 Blo19g00195 195
19 8823078 8825348 - BLOR09539 Blo19g00196 196
19 8860199 8863543 + BLOR09540 Blo19g00197 197
19 8915739 8916694 + BLOR09541 Blo19g00198 198
19 8917179 8919208 - BLOR09542 Blo19g00199 199
7 33455775 33457807 + Bma031385 Bma07g00921 921
7 33458463 33459366 - Bma026024.1 Bma07g00922 922
7 33527520 33530023 - Bma031386 Bma07g00924 924
7 33532834 33534801 + Bma026027.1 Bma07g00925 925
7 33647025 33648381 + Bma026030.1 Bma07g00926 926
12 2841157 2844408 + Bma007103.1 Bma12g00215 215
14 2170671 2172866 - Bma010566.1 Bma14g00159 159
14 2176602 2178333 - Bma010567.1 Bma14g00160 160
14 2179366 2180987 - Bma010568.1 Bma14g00161 161
7 1521277 1524657 + Bpe021027.1 Bpe07g00216 216
8 10345491 10346408 - Bpe022946.2 Bpe08g00824 824
8 10364861 10367267 - Bpe022947.2 Bpe08g00825 825
8 10371365 10373498 + Bpe022948.1 Bpe08g00826 826
8 10378936 10380314 + Bpe022949.1 Bpe08g00827 827
11 2390692 2392367 + Bpe003700.1 Bpe11g00326 326
11 2394483 2396226 + Bpe003701.1 Bpe11g00327 327
11 2403220 2405378 + Bpe003702.1 Bpe11g00328 328
9 12386076 12388191 + CaPI482276_09g011620.1 Cam09g1162 1162
10 3034865 3038265 - CaPI482276_10g001410.1 Cam10g0141 141
2 9095410 9097897 - Carg08847-RA Car02g01380 1380
2 9101034 9102238 + Carg08849-RA Car02g01382 1382
9 11751176 11753290 + CcPI632755_09g011850.1 Cco09g1185 1185
10 1451951 1455349 - CcPI632755_10g001510.1 Cco10g0151 151
9 11815294 11817402 + CePI673135_09g011700.1 Cec09g1170 1170
10 1465249 1468673 - CePI673135_10g001510.1 Cec10g0151 151
4 982987 985179 - Chy4G068240.1 Chy04g00106 106
4 993554 994576 + Chy4G068260.1 Chy04g00108 108
4 996534 998546 - Chy4G068270.1 Chy04g00109 109
6 25853771 25856729 + Chy6G126820.1 Chy06g02154 2154
10 1762462 1765863 - ClG42_10g0014500.10 Clacu10g0145 145
9 12021583 12024445 + ClCG09G011770.1 Cla09g01108 1108
10 1509091 1512797 - ClCG10G001470.1 Cla10g00146 146
2 9197161 9199765 - CmaCh02G016210.1 Cma02g01621 1621
2 9202359 9203742 + CmaCh02G016230.1 Cma02g01623 1623
6 5086398 5088174 + CmaCh06G008720.1 Cma06g00872 872
4 982510 985968 - MELO3C003423.2.1 Cme04g00130 130
4 993054 994537 + MELO3C003424.2.1 Cme04g00132 132
4 995418 998131 - MELO3C003425.2.1 Cme04g00133 133
6 31608798 31612128 - MELO3C013841.2.1 Cme06g02459 2459
4 32457090 32458393 - PI0006769.1 Cmetu04g2583 2583
4 32452709 32455443 + PI0014749.1 Cmetu04g3095 3095
6 29796355 29799340 + PI0015781.1 Cmetu06g0815 815
2 9571806 9573926 - CmoCh02G016660.1 Cmo02g01666 1666
2 9577093 9578100 + CmoCh02G016680.1 Cmo02g01668 1668
19 1702176 1705275 + CmoCh19G002400.1 Cmo19g00240 240
19 1706439 1707762 - CmoCh19G002410.1 Cmo19g00241 241
19 1715049 1718045 + CmoCh19G002430.1 Cmo19g00243 243
10 1913633 1917020 - CmPI595203_10g009920.1 Cmu10g0992 992
8 3247628 3250187 + Conep08aG0049900.1 Cone8ag0478 478
8 3257541 3259077 + Conep08aG0050000.1 Cone8ag0479 479
8 3261648 3265985 - Conep08aG0050100.1 Cone8ag0480 480
8 5722439 5726446 - Conep08aG0062800.1 Cone8ag0607 607
12 3037681 3041315 - Conep12aG0049100.1 Cone12ag0472 472
12 3072728 3075205 - Conep12aG0049400.1 Cone12ag0475 475
5 899558 900810 - Cp4.1LG05g00170.1 Cpe05g00169 169
5 903363 906629 + Cp4.1LG05g00270.1 Cpe05g00170 170
15 1684662 1687889 + Cp4.1LG15g01920.1 Cpe15g00201 201
15 1689155 1690432 - Cp4.1LG15g02090.1 Cpe15g00202 202
15 1698361 1701580 + Cp4.1LG15g02030.1 Cpe15g00204 204
9 11963698 11965810 + CrPI670011_09g011230.1 Cre09g1123 1123
10 2879179 2882579 - CrPI670011_10g004030.1 Cre10g0403 403
3 1185458 1188728 - CsaV3_3G001550.1 Csa03g00155 155
3 39979129 39982235 + CsaV3_3G048990.1 Csa03g04593 4593
3 39984549 39986150 - CsaV3_3G049010.1 Csa03g04595 4595
3 39993692 39997220 + CsaV3_3G049030.1 Csa03g04597 4597
6 68923160 68924835 + Hsped.06g17860.1 Hepe06g1786 1786
6 68927210 68929797 - Hsped.06g17870.1 Hepe06g1787 1787
11 40501405 40502408 + Lag0033067.1 Lac11g2429 2429
11 40504539 40505649 - Lag0033068.1 Lac11g2430 2430
12 40943423 40944860 + Maker00037998 Lcy12g1959 1959
12 40946421 40951388 - Maker00038230 Lcy12g1960 1960
7 17325604 17329303 - Lsi07G011810.1 Lsi07g01181 1181
10 16814721 16818791 + MC10g1330 Mch10g1675 1675
1 70059387 70060818 + Sed0010075.1 Sed01g4122 4122
1 70061804 70064892 - Sed0005698.1 Sed01g4123 4123
13 3318889 3322218 - Sed0009079.1 Sed13g0485 485
1 26157000 26160947 + Tan0013954.1 Tan01g2206 2206
7 71622313 71623577 + Tan0003934.1 Tan07g1993 1993
7 71625106 71628150 - Tan0001142.1 Tan07g1994 1994
2 7717271 7720036 + Vvi2g682 Vvi2g682 682
2 7767916 7770109 + Vvi2g683 Vvi2g683 683
2 7805764 7810149 - Vvi2g684 Vvi2g684 684
2 7838287 7840566 - Vvi2g685 Vvi2g685 685
2 7852462 7858844 + Vvi2g686 Vvi2g686 686
2 7864282 7866175 + Vvi2g687 Vvi2g687 687
2 7866502 7876163 + Vvi2g688 Vvi2g688 688
2 7878001 7879125 + Vvi2g689 Vvi2g689 689
2 7879595 7885136 + Vvi2g690 Vvi2g690 690
2 7886691 7889892 - Vvi2g691 Vvi2g691 691
       

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