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
Vvi4g222 Blo01g01348 . Bda01g00709 . . . . Bma01g02136 . . . . . . . . . . . . . . . . Cla05g01786 Cam05g1905 Cec05g1916 Cco05g1979 Clacu05g1898 Cmu05g1779 Cre05g1907 Cone4ag1846 . . . Lsi04g02180 Csa03g04388 Chy04g00314 . . . . . . . . . . Cmo01g01600 . . . . . . . Bhi09g02331 Tan01g3714 . . . . . . . . . . . . . . . .
Vvi4g223 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g224 . Blo12g00706 . Bda03g00042 . . Bma04g00041 . . . Cma01g01604 . Car09g00443 . . . Cpe06g00379 . . . . . . . Cla05g01785 Cam05g1904 Cec05g1915 Cco05g1978 Clacu05g1897 Cmu05g1778 Cre05g1906 Cone4ag1845 Cone7ag1751 . . . Csa03g04387 Chy04g00315 . . . . . . Bpe04g00031 . . Sed09g1246 Cmo01g01651 Cmo09g00506 Cma09g00556 . . . . Cpe02g00374 Bhi09g02328 Tan01g3711 Cmetu01g0800 . Hepe01g2073 Mch11g0610 . . . . . . . . . . . Cme04g00288
Vvi4g225 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g226 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g227 . . . . . . . . . . . . . . Sed01g1290 . . Bhi04g01134 Tan02g2586 Cmetu03g0727 . Hepe10g0338 . Lcy13g1382 . . . . . . . . . . . . . . Cme03g01721 . . . . . . . . . . . . . . . . . . . . . . . . Cla08g01242 Cam08g1700 Cec08g1280 Cco08g1401 Clacu08g1396 . Cre08g1182 Lsi08g01104 Csa02g02294 . .
Vvi4g228 Blo01g01781 . . . . Bpe02g00296 . Bma01g02561 . . Cma01g01441 . . . . . . Bhi04g01133 . . . . . Lcy13g1381 . . . . . . . . . . . . . Chy04g00161 Cme03g01720 . . . . . . . . . Cmo01g01495 . . . . . . . . . . . . . . Cla08g01243 . . . . . . Lsi08g01105 Csa02g02295 . Cme04g00185
Vvi4g229 . . . . . . . . . . Cma01g01592 . . . Sed03g1505 . Cpe06g00493 Bhi04g01132 Tan02g2588 Cmetu03g0558 . Hepe10g0336 . Lcy13g1380 . . . . . . . . . Cone17ag1131 Cone20ag0617 . . . Cme03g01719 Blo17g00065 Blo18g00078 . . . . . . . Cmo01g01640 . Cma09g00546 . . . . Cpe02g00385 . . . . . . . Cla08g01244 Cam08g1702 Cec08g1282 Cco08g1403 Clacu08g1399 . Cre08g1184 Lsi08g01106 Csa02g02296 . Cme04g00308
Vvi4g230 . . . . . Bpe02g00276 . . . . Cma01g01591 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo18g00003 . . . . . . . Cmo01g01639 . Cma09g00545 . . . . Cpe02g00386 . . . . . . . . . . . . . . . Csa02g02327 . Cme04g00310
Vvi4g231 . . . . . . . . . . . . . . Sed01g1291 . . Bhi04g01129 Tan02g2590 Cmetu03g1692 . . . . . . . . . . . . . Cone17ag1096 Cone20ag0619 . . . Cme03g01717 . . . . . . . . . . . . . . . . . . . . . . . . Cla08g01246 Cam08g1704 Cec08g1284 Cco08g1405 Clacu08g1401 . Cre08g1186 Lsi08g01109 Csa02g02299 . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 34381503 34384059 + Bda002747.1 Bda01g00709 709
3 529938 535006 + Bda015976.2 Bda03g00042 42
4 27409675 27413605 + XM_039028139.1 Bhi04g01129 1129
4 27587033 27595130 + XM_039029485.1 Bhi04g01132 1132
4 27594927 27600201 - XM_039029487.1 Bhi04g01133 1133
4 27626271 27628781 + XM_039028454.1 Bhi04g01134 1134
9 64249509 64255566 - XM_039040197.1 Bhi09g02328 2328
9 64263266 64265983 - XM_039040895.1 Bhi09g02331 2331
1 51164173 51168020 + BLOR01348 Blo01g01348 1348
1 57544189 57549294 + BLOR01781 Blo01g01781 1781
12 25346899 25349443 + BLOR04725 Blo12g00706 706
17 484447 486646 + BLOR15886 Blo17g00065 65
18 74772 81406 - BLOR08491 Blo18g00003 3
18 648425 651546 - BLOR08566 Blo18g00078 78
1 77880512 77882692 + Bma002977.2 Bma01g02136 2136
1 83267949 83271228 + Bma003443.1 Bma01g02561 2561
4 402345 407543 + Bma018492.1 Bma04g00041 41
2 1848346 1853173 + Bpe008120.1 Bpe02g00276 276
2 1947261 1949355 + Bpe008139.1 Bpe02g00296 296
4 265862 276802 + Bpe025567 Bpe04g00031 31
5 27986493 27990888 - CaPI482276_05g019040.1 Cam05g1904 1904
5 27992904 27995304 - CaPI482276_05g019050.1 Cam05g1905 1905
8 23306290 23308729 - CaPI482276_08g017000.1 Cam08g1700 1700
8 23320672 23328964 - CaPI482276_08g017020.1 Cam08g1702 1702
8 23340058 23343782 - CaPI482276_08g017040.1 Cam08g1704 1704
9 2480503 2485029 - Carg02925-RA Car09g00443 443
5 28879374 28883752 - CcPI632755_05g019780.1 Cco05g1978 1978
5 28885946 28888124 - CcPI632755_05g019790.1 Cco05g1979 1979
8 25939909 25940667 - CcPI632755_08g014010.1 Cco08g1401 1401
8 25954408 25962696 - CcPI632755_08g014030.1 Cco08g1403 1403
8 25973672 25977412 - CcPI632755_08g014050.1 Cco08g1405 1405
5 31229507 31233943 - CePI673135_05g019150.1 Cec05g1915 1915
5 31236066 31238469 - CePI673135_05g019160.1 Cec05g1916 1916
8 24788190 24792143 - CePI673135_08g012800.1 Cec08g1280 1280
8 24802539 24810674 - CePI673135_08g012820.1 Cec08g1282 1282
8 24821792 24825451 - CePI673135_08g012840.1 Cec08g1284 1284
4 1427264 1432848 - Chy4G068790.1 Chy04g00161 161
4 2782409 2784554 + Chy4G070320.1 Chy04g00314 314
4 2785909 2790360 + Chy4G070330.1 Chy04g00315 315
5 28180775 28185139 - ClG42_05g0189700.10 Clacu05g1897 1897
5 28187067 28189467 - ClG42_05g0189800.10 Clacu05g1898 1898
8 24058387 24059145 - ClG42_08g0139600.10 Clacu08g1396 1396
8 24072478 24080923 - ClG42_08g0139900.10 Clacu08g1399 1399
8 24091916 24095502 - ClG42_08g0140100.10 Clacu08g1401 1401
5 29731184 29744685 - ClCG05G017420.2 Cla05g01785 1785
5 29746122 29748990 - ClCG05G017440.2 Cla05g01786 1786
8 25354093 25356541 - ClCG08G012440.1 Cla08g01242 1242
8 25364314 25369371 + ClCG08G012450.2 Cla08g01243 1243
8 25367269 25376954 - ClCG08G012460.2 Cla08g01244 1244
8 25387612 25391512 - ClCG08G012480.1 Cla08g01246 1246
1 10144088 10151031 - CmaCh01G014410.1 Cma01g01441 1441
1 10986688 10995203 - CmaCh01G015910.1 Cma01g01591 1591
1 10996190 11001277 + CmaCh01G015920.1 Cma01g01592 1592
1 11059657 11063571 + CmaCh01G016040.1 Cma01g01604 1604
9 2456786 2467803 - CmaCh09G005450.1 Cma09g00545 545
9 2467732 2473979 + CmaCh09G005460.1 Cma09g00546 546
9 2529295 2533065 + CmaCh09G005560.1 Cma09g00556 556
3 25770252 25773748 + MELO3C011167.2.1 Cme03g01717 1717
3 25778042 25786065 + MELO3C011165.2.1 Cme03g01719 1719
3 25784740 25789616 - MELO3C011164.2.1 Cme03g01720 1720
3 25795998 25798397 + MELO3C011163.2.1 Cme03g01721 1721
4 1393639 1398629 - MELO3C003471.2.1 Cme04g00185 185
4 2265520 2269863 - MELO3C003575.2.1 Cme04g00288 288
4 2396272 2401882 - MELO3C003595.2.1 Cme04g00308 308
4 2407696 2418021 + MELO3C003597.2.1 Cme04g00310 310
1 24924518 24927798 - PI0020437.1 Cmetu01g0800 800
3 3655307 3660932 - PI0009231.1 Cmetu03g0558 558
3 3639909 3642513 - PI0012857.1 Cmetu03g0727 727
3 3665990 3669988 - PI0020440.1 Cmetu03g1692 1692
1 11556825 11563238 - CmoCh01G014950.1 Cmo01g01495 1495
1 12257406 12261602 + CmoCh01G016000.1 Cmo01g01600 1600
1 12439564 12448538 - CmoCh01G016390.1 Cmo01g01639 1639
1 12449225 12454231 + CmoCh01G016400.1 Cmo01g01640 1640
1 12513159 12517001 + CmoCh01G016510.1 Cmo01g01651 1651
9 2356818 2361273 - CmoCh09G005060.1 Cmo09g00506 506
5 27899127 27903490 - CmPI595203_05g017780.1 Cmu05g1778 1778
5 27905420 27907813 - CmPI595203_05g017790.1 Cmu05g1779 1779
4 13273402 13276220 - Conep04aG0190400.1 Cone4ag1845 1845
4 13276949 13278378 - Conep04aG0190500.1 Cone4ag1846 1846
7 11576842 11580393 - Conep07aG0180400.1 Cone7ag1751 1751
17 8148030 8151737 - Conep17aG0112400.1 Cone17ag1096 1096
17 8366354 8367273 + Conep17aG0116000.1 Cone17ag1131 1131
20 3658029 3662908 - Conep20aG0063400.1 Cone20ag0617 617
20 3709213 3711381 + Conep20aG0063600.1 Cone20ag0619 619
2 2062339 2066177 - Cp4.1LG02g04890.1 Cpe02g00374 374
2 2125477 2130511 - Cp4.1LG02g04940.1 Cpe02g00385 385
2 2132726 2140208 + Cp4.1LG02g05000.1 Cpe02g00386 386
6 2160599 2165087 - Cp4.1LG06g04670.1 Cpe06g00379 379
6 2928124 2931041 - Cp4.1LG06g04980.1 Cpe06g00493 493
5 31226536 31230928 - CrPI670011_05g019060.1 Cre05g1906 1906
5 31232971 31235370 - CrPI670011_05g019070.1 Cre05g1907 1907
8 25098698 25099456 - CrPI670011_08g011820.1 Cre08g1182 1182
8 25113358 25121391 - CrPI670011_08g011840.1 Cre08g1184 1184
8 25132491 25136316 - CrPI670011_08g011860.1 Cre08g1186 1186
2 20496541 20499162 - CsaV3_2G031130.1 Csa02g02294 2294
2 20505222 20508617 + CsaV3_2G031140.1 Csa02g02295 2295
2 20507713 20515931 - CsaV3_2G031150.1 Csa02g02296 2296
2 20520268 20525369 - CsaV3_2G031180.1 Csa02g02299 2299
2 20700134 20706177 - CsaV3_2G031460.1 Csa02g02327 2327
3 38309690 38315065 - CsaV3_3G046930.1 Csa03g04387 4387
3 38315450 38318174 - CsaV3_3G046940.1 Csa03g04388 4388
1 85395267 85400887 - Hsped.01g20730.1 Hepe01g2073 2073
10 3619197 3630362 + Hsped.10g03360.1 Hepe10g0336 336
10 3639075 3641531 + Hsped.10g03380.1 Hepe10g0338 338
13 31945657 31956203 + Maker00025497 Lcy13g1380 1380
13 31955494 31958585 - Maker00025659 Lcy13g1381 1381
13 31978244 31982551 + Maker00025557 Lcy13g1382 1382
4 28886116 28894736 - Lsi04G021800.1 Lsi04g02180 2180
8 19695194 19695952 - Lsi08G011040.1 Lsi08g01104 1104
8 19706516 19710910 + Lsi08G011050.1 Lsi08g01105 1105
8 19710218 19720547 - Lsi08G011070.1 Lsi08g01106 1106
8 19730893 19735388 - Lsi08G011090.1 Lsi08g01109 1109
11 3937637 3942610 - MC11g0507 Mch11g0610 610
1 9637411 9640119 - Sed0022456.1 Sed01g1290 1290
1 9641011 9647528 - Sed0011676.1 Sed01g1291 1291
3 9616565 9625310 - Sed0025325.2 Sed03g1505 1505
9 36633176 36637362 - Sed0003394.1 Sed09g1246 1246
1 101949917 101954431 - Tan0007048.3 Tan01g3711 3711
1 101955998 101958502 - Tan0002176.2 Tan01g3714 3714
2 94514876 94517510 - Tan0020043.1 Tan02g2586 2586
2 94531178 94537457 - Tan0019913.1 Tan02g2588 2588
2 94558313 94562895 - Tan0001572.1 Tan02g2590 2590
4 2187373 2190925 + Vvi4g222 Vvi4g222 222
4 2193001 2196242 + Vvi4g223 Vvi4g223 223
4 2199113 2209197 + Vvi4g224 Vvi4g224 224
4 2209340 2214324 - Vvi4g225 Vvi4g225 225
4 2217046 2222194 - Vvi4g226 Vvi4g226 226
4 2241931 2243881 - Vvi4g227 Vvi4g227 227
4 2250743 2253524 + Vvi4g228 Vvi4g228 228
4 2258247 2263610 - Vvi4g229 Vvi4g229 229
4 2271264 2281988 + Vvi4g230 Vvi4g230 230
4 2283622 2287194 - Vvi4g231 Vvi4g231 231
       

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