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
Vvi4g152 . . Bda01g00637 . . Bpe02g00506 . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1696 . . . . Csa03g04408 . . . . . . . . Bma01g01315 Bma02g00060 . . . . . Car01g01194 . . . . . . . . . . . . . . . . . . . . .
Vvi4g153 . Blo12g01029 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag1613 Cone17ag0942 Cone20ag0285 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g154 . . Bda01g00638 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1697 . . Cone20ag0634 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g155 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag1766 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g156 . . . Bda03g00129 . . . Bma01g02199 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g157 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1858 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g158 Blo01g01555 . . Bda03g00127 . . Bma04g00114 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g159 Blo01g01448 . . . . . . Bma01g02198 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe04g00112 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g160 Blo01g01447 Blo12g01030 Bda01g00639 Bda03g00126 Bpe02g01249 Bpe02g00507 Bma04g00113 Bma01g02195 . . Cma01g01702 . Car09g00311 . . . Cpe06g00257 . . . . . . . Cla05g01625 Cam05g1735 Cec05g1743 Cco05g1800 Clacu05g1725 Cmu05g1609 Cre05g1738 Cone4ag1698 Cone7ag1614 Cone17ag0943 Cone20ag0286 Lsi04g01389 . . . . . Bda01g01004 . . Bpe04g00111 . . Sed05g1792 Cmo01g01809 Cmo09g00362 Cma09g00363 . Car01g01320 . . Cpe02g00289 Bhi09g03084 Tan01g3470 Cmetu07g2288 . Hepe01g1915 Mch11g0450 . . . . . . . . . . . Cme07g00178
Vvi4g161 . . . . Bpe02g01559 . . . . . . . Car09g00313 . . . Cpe06g00258 . . . . . . . Cla05g01626 . . . Clacu05g1726 . Cre05g1739 . . . . Lsi04g01388 . . . Blo17g00273 Blo18g00056 Bda01g01346 Bda13g01586 Bpe14g00280 . Bma01g00911 Bma02g00548 Sed05g1794 Cmo01g01810 . . . Car01g01319 . . Cpe02g00290 Bhi09g03083 Tan01g3471 Cmetu07g1629 . Hepe01g1916 Mch11g0451 . . . . . . . . . . . Cme07g00176
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 33361513 33362521 - Bda002662.1 Bda01g00637 637
1 33364871 33365602 + Bda002663.1 Bda01g00638 638
1 33404700 33407938 + Bda002665.1 Bda01g00639 639
1 43615071 43616824 + Bda003163.1 Bda01g01004 1004
1 49168364 49175417 + Bda003583.1 Bda01g01346 1346
3 1091466 1093968 - Bda016064.1 Bda03g00126 126
3 1111279 1113167 - Bda016066.1 Bda03g00127 127
3 1147399 1150186 + Bda016069.1 Bda03g00129 129
13 39389216 39395699 - Bda000454.2 Bda13g01586 1586
9 79576514 79584356 - XM_039043690.1 Bhi09g03083 3083
9 79614026 79618655 - XM_039042943.1 Bhi09g03084 3084
1 53384652 53387445 - BLOR01447 Blo01g01447 1447
1 53466763 53467680 - BLOR01448 Blo01g01448 1448
1 55304386 55306194 - BLOR01555 Blo01g01555 1555
12 28177597 28179055 - BLOR05048 Blo12g01029 1029
12 28183454 28185798 + BLOR05049 Blo12g01030 1030
17 2875946 2882745 - BLOR16094 Blo17g00273 273
18 388378 389592 + BLOR08544 Blo18g00056 56
1 8832035 8838184 - Bma001140.1 Bma01g00911 911
1 17983932 17993630 + Bma001634.2 Bma01g01315 1315
1 78842195 78845049 - Bma003041.1 Bma01g02195 2195
1 78884484 78885394 - Bma003044.1 Bma01g02198 2198
1 78891678 78892669 - Bma003045.1 Bma01g02199 2199
2 493419 494348 - Bma014515.1 Bma02g00060 60
2 11090189 11096617 + Bma015064.2 Bma02g00548 548
4 896739 899279 - Bma018559.2 Bma04g00113 113
4 901436 903338 - Bma018560.1 Bma04g00114 114
2 3286853 3287876 - Bpe008346.1 Bpe02g00506 506
2 3322244 3325105 + Bpe008347.1 Bpe02g00507 507
2 16014627 16016585 - Bpe009105.1 Bpe02g01249 1249
2 18592132 18598223 + Bpe009411.1 Bpe02g01559 1559
4 770643 773173 - Bpe014832.1 Bpe04g00111 111
4 783944 784946 + Bpe014834.1 Bpe04g00112 112
14 2801640 2807960 + Bpe006933.2 Bpe14g00280 280
5 25926002 25929730 + CaPI482276_05g017350.1 Cam05g1735 1735
1 11055619 11057586 - Carg21175-RA Car01g01194 1194
1 11798213 11806195 - Carg10718-RA Car01g01319 1319
1 11809529 11813183 - Carg10717-RA Car01g01320 1320
9 1721473 1724761 + Carg02790-RA Car09g00311 311
9 1731246 1735302 + Carg02792-RA Car09g00313 313
5 26718667 26722336 + CcPI632755_05g018000.1 Cco05g1800 1800
5 28993218 28996966 + CePI673135_05g017430.1 Cec05g1743 1743
5 26125734 26129436 + ClG42_05g0172500.10 Clacu05g1725 1725
5 26158642 26165548 + ClG42_05g0172600.10 Clacu05g1726 1726
5 27588169 27600191 + ClCG05G015720.2 Cla05g01625 1625
5 27630305 27637763 + ClCG05G015740.1 Cla05g01626 1626
1 11591206 11606912 - CmaCh01G017020.1 Cma01g01702 1702
9 1496454 1499825 + CmaCh09G003630.1 Cma09g00363 363
7 1168552 1179064 - MELO3C016912.2.1 Cme07g00176 176
7 1188048 1192518 - MELO3C016911.2.1 Cme07g00178 178
7 23574730 23582528 + PI0019853.1 Cmetu07g1629 1629
7 23562811 23567367 + PI0023649.1 Cmetu07g2288 2288
1 13283339 13287288 + CmoCh01G018090.1 Cmo01g01809 1809
1 13290894 13298362 + CmoCh01G018100.1 Cmo01g01810 1810
9 1567556 1571311 + CmoCh09G003620.1 Cmo09g00362 362
5 25845052 25848755 + CmPI595203_05g016090.1 Cmu05g1609 1609
4 12610302 12611394 - Conep04aG0175000.1 Cone4ag1696 1696
4 12621608 12623230 + Conep04aG0175100.1 Cone4ag1697 1697
4 12627629 12630918 + Conep04aG0175200.1 Cone4ag1698 1698
4 13328339 13331537 + Conep04aG0191700.1 Cone4ag1858 1858
7 10963165 10964265 - Conep07aG0166200.1 Cone7ag1613 1613
7 10970700 10973723 + Conep07aG0166300.1 Cone7ag1614 1614
7 11645922 11647867 - Conep07aG0181900.1 Cone7ag1766 1766
17 7372586 7374131 - Conep17aG0096900.1 Cone17ag0942 942
17 7389781 7392923 + Conep17aG0097000.1 Cone17ag0943 943
20 1277592 1278791 - Conep20aG0029800.1 Cone20ag0285 285
20 1285911 1288693 + Conep20aG0029900.1 Cone20ag0286 286
20 3811066 3815076 + Conep20aG0065200.1 Cone20ag0634 634
2 1494450 1498375 + Cp4.1LG02g05880.1 Cpe02g00289 289
2 1501554 1509293 + Cp4.1LG02g05910.1 Cpe02g00290 290
6 1374991 1378612 + Cp4.1LG06g02470.1 Cpe06g00257 257
6 1380671 1390164 + Cp4.1LG06g02590.1 Cpe06g00258 258
5 29087500 29091200 + CrPI670011_05g017380.1 Cre05g1738 1738
5 29108159 29116032 + CrPI670011_05g017390.1 Cre05g1739 1739
3 38433423 38436416 - CsaV3_3G047140.1 Csa03g04408 4408
1 83962545 83966864 + Hsped.01g19150.1 Hepe01g1915 1915
1 83978316 83986748 + Hsped.01g19160.1 Hepe01g1916 1916
4 21675063 21682316 - Lsi04G013880.1 Lsi04g01388 1388
4 21699031 21702924 - Lsi04G013890.1 Lsi04g01389 1389
11 2815475 2819985 + MC11g0362 Mch11g0450 450
11 2826063 2834349 + MC11g0363 Mch11g0451 451
5 31523952 31530059 + Sed0018261.1 Sed05g1792 1792
5 31539119 31546705 + Sed0000287.2 Sed05g1794 1794
1 99983338 99987824 + Tan0004904.2 Tan01g3470 3470
1 99997410 100007267 + Tan0006874.1 Tan01g3471 3471
4 1418710 1420503 - Vvi4g152 Vvi4g152 152
4 1439745 1447540 + Vvi4g153 Vvi4g153 153
4 1456411 1464354 + Vvi4g154 Vvi4g154 154
4 1464948 1466397 + Vvi4g155 Vvi4g155 155
4 1467630 1468488 + Vvi4g156 Vvi4g156 156
4 1473562 1476022 - Vvi4g157 Vvi4g157 157
4 1479600 1482518 + Vvi4g158 Vvi4g158 158
4 1483001 1484002 - Vvi4g159 Vvi4g159 159
4 1498312 1502167 + Vvi4g160 Vvi4g160 160
4 1514830 1524551 + Vvi4g161 Vvi4g161 161
       

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