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
Vvi2g412 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g413 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0367 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g414 . . . . . . . . . . Cma02g01490 . Car02g01248 . . . Cpe05g00301 . . . . . . . . . . . . . . . . . Cone15ag0129 . Csa05g00332 Chy09g01177 . . . . . . . . . . Cmo02g01529 . . . . . . . Bhi12g00186 . . Lac11g2149 Hepe06g1593 . Lcy12g1710 Cla01g00309 Cam01g0321 Cec01g0312 Cco01g0329 Clacu01g0322 Cmu01g0307 . Lsi09g00317 . . Cme09g01710
Vvi2g415 Blo02g01093 Blo03g00190 Bda06g00067 Bda08g00535 Bpe05g00625 Bpe07g00131 . . Cmo06g00748 Cmo16g01064 . . . . Sed03g1298 Cpe14g00839 . Bhi11g00356 Tan01g1947 Cmetu06g1625 . Hepe06g1209 Mch10g1479 . Cla10g00329 Cam10g0341 Cec10g0356 Cco10g0348 Clacu10g0342 Cmu10g1180 Cre10g0588 . Cone12ag0331 Cone6ag0741 Cone9ag0745 Lsi07g01377 . . Cme06g02665 . . . . . . Bma05g00802 Bma12g00107 . . . Cma06g00725 Cma16g01025 Car06g00646 Car16g00976 Cpe08g00792 . . . . . . . . . . . . . . . . Csa03g00349 Chy06g01974 .
Vvi2g416 . . . . . . Bma07g01629 Bma14g00579 . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0740 Cone9ag0744 . . . . . Blo19g00306 Bda07g00504 Bda09g00062 Bpe08g01471 Bpe11g00690 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g417 . . . . . . Bma07g01628 . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0332 . . . . . . Blo03g00376 Blo19g00304 Bda07g00505 . . Bpe11g00692 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g418 Blo02g01092 Blo03g00189 Bda06g00066 Bda08g00536 Bpe05g00624 Bpe07g00132 . . . . Cma02g01491 Cma15g01190 Car02g01249 Car15g01078 . . Cpe05g00300 . . . . . . . . . . . . . . . . . . . Csa05g00333 Chy09g01176 . . . . . . . . Bma12g00108 . Cmo02g01530 Cmo15g01253 . . . . . Cpe13g00184 Bhi12g00185 . . Lac11g2151 Hepe06g1594 . Lcy12g1711 Cla01g00310 Cam01g0322 Cec01g0313 Cco01g0330 Clacu01g0323 Cmu01g0308 Cre09g2202 Lsi09g00318 . . Cme09g01709
Vvi2g419 . Blo03g00188 Bda06g00065 . . Bpe07g00133 . . Cmo06g00749 . . . . . Sed09g0098 . . Bhi11g00355 Tan01g1948 Cmetu11g2416 . Hepe06g1205 . . Cla10g00328 Cam10g0340 Cec10g0355 Cco10g0347 Clacu10g0341 Cmu10g1179 Cre10g0587 . . . . Lsi07g01376 . . Cme06g02664 . . . . . . . Bma12g00109 . . . Cma06g00726 . Car06g00647 . Cpe08g00791 . . . . . . . . . . . . . . . . Csa03g00348 Chy06g01975 .
Vvi2g420 . . . . . . Bma07g01627 Bma14g00577 . . Cma02g01492 Cma15g01189 Car02g01251 Car15g01077 . . Cpe05g00299 . . . . . . . . . . . . . . . . Cone6ag0737 Cone9ag0742 . Csa05g00334 Chy09g01175 . Blo03g00378 Blo19g00301 Bda07g00506 Bda09g00064 Bpe08g01469 Bpe11g00693 . . . Cmo02g01531 Cmo15g01252 . . . . . Cpe13g00185 Bhi12g00327 . . Lac11g2153 Hepe06g1595 . Lcy12g1713 Cla01g00313 Cam01g0323 Cec01g0315 Cco01g0332 Clacu01g0325 Cmu01g0309 Cre09g2201 Lsi09g00319 . . Cme09g01708
Vvi2g421 . . . . . . Bma07g01626 . . . Cma02g01493 Cma15g01187 Car02g01253 Car15g01076 . . Cpe05g00297 . . . . . . . . . . . . . . . . Cone6ag0736 Cone9ag0741 . Csa05g00335 Chy09g01174 . . Blo19g00300 . Bda09g00065 Bpe08g01468 . . . . Cmo02g01532 Cmo15g01251 . . . . . Cpe13g00186 Bhi12g00329 . . Lac11g2154 Hepe06g1596 . Lcy12g1714 Cla01g00315 Cam01g0325 Cec01g0317 Cco01g0334 Clacu01g0327 Cmu01g0311 Cre09g2200 Lsi09g00320 . . Cme09g01707
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 656717 670335 + Bda023235.1 Bda06g00065 65
6 672261 673663 + Bda023236.1 Bda06g00066 66
6 675607 679981 - Bda023237.1 Bda06g00067 67
7 6434007 6435203 + Bda025610.1 Bda07g00504 504
7 6451469 6454925 + Bda025612.1 Bda07g00505 505
7 6463810 6466635 - Bda025613.1 Bda07g00506 506
8 5355490 5366771 + Bda033809 Bda08g00535 535
8 5367402 5368789 - Bda024992.1 Bda08g00536 536
9 1242750 1243925 + Bda030586.1 Bda09g00062 62
9 1265540 1268983 - Bda030588.1 Bda09g00064 64
9 1288999 1297062 - Bda030589.2 Bda09g00065 65
11 8467626 8474462 + XM_039048949.1 Bhi11g00355 355
11 8492279 8497071 - XM_039047100.1 Bhi11g00356 356
12 5611394 5613155 + XM_039020064.1 Bhi12g00185 185
12 5615627 5617540 - XM_039018374.1 Bhi12g00186 186
12 9196888 9200532 - XM_039020029.1 Bhi12g00327 327
12 9386630 9397703 - XM_039018686.1 Bhi12g00329 329
2 41768613 41770006 + BLOR10822 Blo02g01092 1092
2 41773686 41777906 - BLOR10823 Blo02g01093 1093
3 4527683 4532744 + BLOR11369 Blo03g00188 188
3 4534251 4535641 + BLOR11370 Blo03g00189 189
3 4536954 4541364 - BLOR11371 Blo03g00190 190
3 8717712 8721856 + BLOR11557 Blo03g00376 376
3 8848352 8848705 - BLOR11559 Blo03g00378 378
19 19246847 19254594 + BLOR09643 Blo19g00300 300
19 19356768 19360017 + BLOR09644 Blo19g00301 301
19 19494997 19498649 - BLOR09647 Blo19g00304 304
19 19546337 19547494 - BLOR09649 Blo19g00306 306
5 45301656 45305837 - Bma021905.1 Bma05g00802 802
7 51849850 51856086 + Bma026923.2 Bma07g01626 1626
7 51860220 51864225 + Bma026924.1 Bma07g01627 1627
7 51870529 51879351 - Bma026925.2 Bma07g01628 1628
7 51889012 51890169 - Bma026926.1 Bma07g01629 1629
12 1711636 1716015 + Bma006979.1 Bma12g00107 107
12 1718200 1719598 - Bma006980.1 Bma12g00108 108
12 1720156 1725923 - Bma006981.2 Bma12g00109 109
14 6216736 6219355 + Bma011012.1 Bma14g00577 577
14 6236461 6237384 - Bma011014.1 Bma14g00579 579
5 20159924 20163465 + Bpe018040.1 Bpe05g00624 624
5 20164082 20168063 - Bpe018041.1 Bpe05g00625 625
7 931789 936097 + Bpe020943.1 Bpe07g00131 131
7 938045 939442 - Bpe020944.1 Bpe07g00132 132
7 940188 947822 - Bpe020945.1 Bpe07g00133 133
8 15395608 15401255 + Bpe023580.1 Bpe08g01468 1468
8 15405169 15408464 + Bpe023581.1 Bpe08g01469 1469
8 15429333 15430490 - Bpe023583.1 Bpe08g01471 1471
11 5321711 5322715 + Bpe004046.1 Bpe11g00690 690
11 5329393 5333329 + Bpe004048.1 Bpe11g00692 692
11 5336908 5339732 - Bpe004049.1 Bpe11g00693 693
1 3586385 3588582 + CaPI482276_01g003210.1 Cam01g0321 321
1 3590755 3592500 - CaPI482276_01g003220.1 Cam01g0322 322
1 3604617 3607822 - CaPI482276_01g003230.1 Cam01g0323 323
1 3622422 3637420 - CaPI482276_01g003250.1 Cam01g0325 325
10 5529311 5535226 + CaPI482276_10g003400.1 Cam10g0340 340
10 5538663 5543037 - CaPI482276_10g003410.1 Cam10g0341 341
2 8436304 8438202 + Carg02500-RA Car02g01248 1248
2 8438753 8440010 - Carg02499-RA Car02g01249 1249
2 8444055 8444876 - Carg02497-RA Car02g01251 1251
2 8450956 8455818 - Carg02495-RA Car02g01253 1253
6 3870308 3874483 + Carg21636-RA Car06g00646 646
6 3875202 3881769 - Carg21635-RA Car06g00647 647
15 8447004 8456116 + Carg16666-RA Car15g01076 1076
15 8459115 8469596 + Carg16665-RA Car15g01077 1077
15 8470945 8472921 + Carg16664-RA Car15g01078 1078
16 8123891 8128932 + Carg25207-RA Car16g00976 976
1 3229315 3231512 + CcPI632755_01g003290.1 Cco01g0329 329
1 3234365 3235739 - CcPI632755_01g003300.1 Cco01g0330 330
1 3249957 3253159 - CcPI632755_01g003320.1 Cco01g0332 332
1 3267349 3277062 - CcPI632755_01g003340.1 Cco01g0334 334
10 4019268 4025266 + CcPI632755_10g003470.1 Cco10g0347 347
10 4028817 4033189 - CcPI632755_10g003480.1 Cco10g0348 348
1 3199845 3201755 + CePI673135_01g003120.1 Cec01g0312 312
1 3203738 3205576 - CePI673135_01g003130.1 Cec01g0313 313
1 3219474 3222683 - CePI673135_01g003150.1 Cec01g0315 315
1 3236775 3246296 - CePI673135_01g003170.1 Cec01g0317 317
10 4190904 4196854 + CePI673135_10g003550.1 Cec10g0355 355
10 4200384 4204781 - CePI673135_10g003560.1 Cec10g0356 356
6 23778245 23782470 + Chy6G125020.1 Chy06g01974 1974
6 23784904 23790489 - Chy6G125030.1 Chy06g01975 1975
9 13933841 13941665 + Chy9G168900.1 Chy09g01174 1174
9 13952596 13956084 + Chy9G168910.1 Chy09g01175 1175
9 13960820 13962172 + Chy9G168920.1 Chy09g01176 1176
9 13964593 13966515 - Chy9G168930.1 Chy09g01177 1177
1 3198568 3200478 + ClG42_01g0032200.10 Clacu01g0322 322
1 3202897 3204289 - ClG42_01g0032300.10 Clacu01g0323 323
1 3218047 3221254 - ClG42_01g0032500.10 Clacu01g0325 325
1 3235576 3245367 - ClG42_01g0032700.10 Clacu01g0327 327
10 4306257 4312176 + ClG42_10g0034100.10 Clacu10g0341 341
10 4315689 4320193 - ClG42_10g0034200.10 Clacu10g0342 342
1 3291622 3293532 + ClCG01G003210.1 Cla01g00309 309
1 3295358 3297653 - ClCG01G003220.1 Cla01g00310 310
1 3311245 3314780 - ClCG01G003250.1 Cla01g00313 313
1 3329016 3340037 - ClCG01G003270.2 Cla01g00315 315
10 4258401 4263668 + ClCG10G003480.1 Cla10g00328 328
10 4282314 4287093 - ClCG10G003490.2 Cla10g00329 329
2 8518632 8520530 + CmaCh02G014900.1 Cma02g01490 1490
2 8520812 8522762 - CmaCh02G014910.1 Cma02g01491 1491
2 8524124 8527441 - CmaCh02G014920.1 Cma02g01492 1492
2 8530513 8539498 - CmaCh02G014930.1 Cma02g01493 1493
6 3674832 3679289 + CmaCh06G007250.1 Cma06g00725 725
6 3679605 3686675 - CmaCh06G007260.1 Cma06g00726 726
15 7515430 7524406 + CmaCh15G011870.1 Cma15g01187 1187
15 7530904 7534873 + CmaCh15G011890.1 Cma15g01189 1189
15 7537134 7538933 + CmaCh15G011900.1 Cma15g01190 1190
16 7883533 7888273 + CmaCh16G010250.1 Cma16g01025 1025
6 33733869 33740048 + MELO3C014016.2.1 Cme06g02664 2664
6 33742193 33746823 - MELO3C014017.2.1 Cme06g02665 2665
9 21702545 21711342 + MELO3C005619.2.1 Cme09g01707 1707
9 21722415 21731186 + MELO3C005620.2.1 Cme09g01708 1708
9 21735522 21737501 + MELO3C005621.2.1 Cme09g01709 1709
9 21738915 21740849 - MELO3C005622.2.1 Cme09g01710 1710
6 27929339 27934157 + PI0010041.1 Cmetu06g1625 1625
11 154117 163467 - PI0016187.1 Cmetu11g2416 2416
2 8891366 8893261 + CmoCh02G015290.1 Cmo02g01529 1529
2 8893555 8895412 - CmoCh02G015300.1 Cmo02g01530 1530
2 8896584 8899700 - CmoCh02G015310.1 Cmo02g01531 1531
2 8903143 8910360 - CmoCh02G015320.1 Cmo02g01532 1532
6 3892768 3897474 + CmoCh06G007480.1 Cmo06g00748 748
6 3897532 3904640 - CmoCh06G007490.1 Cmo06g00749 749
15 8591946 8601097 + CmoCh15G012510.1 Cmo15g01251 1251
15 8604183 8607980 + CmoCh15G012520.1 Cmo15g01252 1252
15 8609533 8611762 + CmoCh15G012530.1 Cmo15g01253 1253
16 7471630 7476423 + CmoCh16G010640.1 Cmo16g01064 1064
1 3154727 3156637 + CmPI595203_01g003070.1 Cmu01g0307 307
1 3159062 3160456 - CmPI595203_01g003080.1 Cmu01g0308 308
1 3174113 3177326 - CmPI595203_01g003090.1 Cmu01g0309 309
1 3191633 3201429 - CmPI595203_01g003110.1 Cmu01g0311 311
10 4447374 4453293 + CmPI595203_10g011790.1 Cmu10g1179 1179
10 4456804 4461157 - CmPI595203_10g011800.1 Cmu10g1180 1180
6 3717026 3721769 + Conep06aG0075900.1 Cone6ag0736 736
6 3726221 3729297 + Conep06aG0076000.1 Cone6ag0737 737
6 3733009 3734677 - Conep06aG0076300.1 Cone6ag0740 740
6 3735422 3739397 - Conep06aG0076400.1 Cone6ag0741 741
8 2162391 2166335 + Conep08aG0038300.1 Cone8ag0367 367
9 3520893 3525702 + Conep09aG0075800.1 Cone9ag0741 741
9 3527506 3530565 + Conep09aG0075900.1 Cone9ag0742 742
9 3534491 3536064 - Conep09aG0076100.1 Cone9ag0744 744
9 3536878 3540695 - Conep09aG0076200.1 Cone9ag0745 745
12 1805629 1809551 + Conep12aG0034600.1 Cone12ag0331 331
12 1811510 1815640 + Conep12aG0034700.1 Cone12ag0332 332
15 598587 600482 + Conep15aG0013100.1 Cone15ag0129 129
5 1663130 1670591 + Cp4.1LG05g03840.1 Cpe05g00297 297
5 1679524 1682979 + Cp4.1LG05g03900.1 Cpe05g00299 299
5 1683976 1685880 + Cp4.1LG05g03780.1 Cpe05g00300 300
5 1685995 1687890 - Cp4.1LG05g03620.1 Cpe05g00301 301
8 6274287 6280943 + Cp4.1LG08g07820.1 Cpe08g00791 791
8 6281006 6285728 - Cp4.1LG08g07890.1 Cpe08g00792 792
13 1442721 1445102 - Cp4.1LG13g01860.1 Cpe13g00184 184
13 1447129 1451193 - Cp4.1LG13g01870.1 Cpe13g00185 185
13 1453637 1463509 - Cp4.1LG13g01880.1 Cpe13g00186 186
14 6813133 6817879 + Cp4.1LG14g08320.1 Cpe14g00839 839
9 41111258 41121021 + CrPI670011_09g022000.1 Cre09g2200 2200
9 41135487 41138674 + CrPI670011_09g022010.1 Cre09g2201 2201
9 41153068 41154447 + CrPI670011_09g022020.1 Cre09g2202 2202
10 5361748 5367684 + CrPI670011_10g005870.1 Cre10g0587 587
10 5370623 5375602 - CrPI670011_10g005880.1 Cre10g0588 588
3 2867950 2874258 + CsaV3_3G003480.1 Csa03g00348 348
3 2876197 2881174 - CsaV3_3G003490.1 Csa03g00349 349
5 2106404 2108886 + CsaV3_5G003320.1 Csa05g00332 332
5 2110220 2112261 - CsaV3_5G003330.1 Csa05g00333 333
5 2116274 2120560 - CsaV3_5G003340.1 Csa05g00334 334
5 2129969 2138348 - CsaV3_5G003350.1 Csa05g00335 335
6 61581699 61588243 + Hsped.06g12050.1 Hepe06g1205 1205
6 61615622 61620636 - Hsped.06g12090.1 Hepe06g1209 1209
6 66726220 66728604 + Hsped.06g15930.1 Hepe06g1593 1593
6 66729979 66731846 - Hsped.06g15940.1 Hepe06g1594 1594
6 66740123 66744630 - Hsped.06g15950.1 Hepe06g1595 1595
6 66757219 66765565 - Hsped.06g15960.1 Hepe06g1596 1596
11 37543639 37545552 + Lag0032787.1 Lac11g2149 2149
11 37555570 37556851 - Lag0032789.1 Lac11g2151 2151
11 37576346 37579638 - Lag0032791.1 Lac11g2153 2153
11 37591645 37598835 - Lag0032792.1 Lac11g2154 2154
12 37626310 37630886 + Maker00003073 Lcy12g1710 1710
12 37636465 37638301 - Maker00003063 Lcy12g1711 1711
12 37656975 37660855 - Maker00003022 Lcy12g1713 1713
12 37669765 37677829 - Maker00003076 Lcy12g1714 1714
7 20013246 20019888 + Lsi07G013760.1 Lsi07g01376 1376
7 20021859 20026910 - Lsi07G013770.1 Lsi07g01377 1377
9 3283032 3284942 + Lsi09G003170.1 Lsi09g00317 317
9 3287975 3289918 - Lsi09G003180.1 Lsi09g00318 318
9 3295926 3299979 - Lsi09G003190.1 Lsi09g00319 319
9 3310707 3321290 - Lsi09G003200.1 Lsi09g00320 320
10 14747202 14753935 - MC10g1165 Mch10g1479 1479
3 8297660 8302902 - Sed0004891.1 Sed03g1298 1298
9 721980 728787 - Sed0001664.3 Sed09g0098 98
1 21407156 21412137 + Tan0005321.1 Tan01g1947 1947
1 21422153 21429390 - Tan0016773.1 Tan01g1948 1948
2 4105425 4105566 + Vvi2g412 Vvi2g412 412
2 4110678 4113795 + Vvi2g413 Vvi2g413 413
2 4120662 4122643 + Vvi2g414 Vvi2g414 414
2 4131460 4138394 + Vvi2g415 Vvi2g415 415
2 4139670 4141512 + Vvi2g416 Vvi2g416 416
2 4146731 4149948 + Vvi2g417 Vvi2g417 417
2 4150396 4152247 - Vvi2g418 Vvi2g418 418
2 4153190 4161632 - Vvi2g419 Vvi2g419 419
2 4164200 4172140 - Vvi2g420 Vvi2g420 420
2 4176704 4190754 - Vvi2g421 Vvi2g421 421
       

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