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
Vvi3g346 Blo02g00811 . . Bda08g00944 . . Bma05g00437 . . . Cma02g00379 Cma20g00831 Car02g00246 Car20g00716 . . . . . . . . . . . . . . . . . . Cone8ag1214 . . Lsi10g00394 . Chy11g00360 . . . . . . . . . . Cmo02g00386 Cmo20g00840 . . . . Cpe16g00258 Cpe05g01276 Bhi10g01979 Tan05g1273 . . Hepe08g0997 . . . . . . . . . . Csa02g01283 . Cme11g00137
Vvi3g347 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g348 . Blo15g00708 . . Bpe07g00418 . . Bma12g00501 . . Cma02g00382 Cma20g00832 Car02g00247 Car20g00717 . . . . . . . . . . . . . . . . . . Cone12ag0777 Cone6ag1649 Cone9ag1573 Lsi10g00392 . Chy11g00361 . . . . . . . . . Sed05g3527 Cmo02g00388 Cmo20g00841 . . . . Cpe16g00257 Cpe05g01275 Bhi10g01980 Tan05g1278 Cmetu11g2335 . Hepe08g0998 . . . . . . . . . . Csa02g01282 . Cme11g00136
Vvi3g349 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag1163 Cone8ag1212 . . . . . . Blo04g00521 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g350 . . . . . . . . . . Cma02g00383 Cma20g00834 Car02g00248 Car20g00720 . . . . . . . . . . . . . . . . . Cone12ag1162 Cone8ag1211 Cone3ag1175 Cone10ag0981 Lsi10g00391 . Chy11g00362 Cme01g01117 Blo04g00520 . . . . . . . Sed01g0288 Cmo02g00389 Cmo20g00842 . . . . Cpe16g00256 Cpe05g01274 Bhi10g01981 Tan05g1280 Cmetu11g2218 . Hepe08g0999 . . . . . . . . . . Csa02g01281 . Cme11g00135
Vvi3g351 . . . . . . . . . . Cma02g00384 Cma20g00835 Car02g00249 Car20g00721 . . . . . . . . . . . . . . . . . Cone12ag1161 Cone8ag1210 Cone3ag1174 Cone10ag0980 Lsi10g00390 . Chy11g00363 . Blo04g00519 . . . . . . . Sed01g0289 Cmo02g00390 Cmo20g00843 . . . . Cpe16g00255 Cpe05g01273 Bhi10g01982 Tan05g1281 Cmetu11g0971 . Hepe08g1000 . . . . . . . . . . Csa02g01280 . Cme11g00134
Vvi3g352 . . . . . . . . . . . Cma20g00836 . Car20g00722 . . . . . . . . . . . . . . . . . . . . . Lsi10g00389 . Chy11g00364 . . . . . . . . . Sed01g0290 . Cmo20g00844 . . . . Cpe16g00254 . Bhi10g01983 Tan05g1282 Cmetu11g0387 . . . . . . . . . . . . Csa02g01279 . Cme11g00133
Vvi3g353 Blo02g00809 Blo15g00707 . . Bpe07g00421 . . Bma12g00503 . . Cma02g00385 Cma20g00837 Car02g00250 Car20g00724 . . . . . . . . . . . . . . . . . Cone12ag1160 Cone8ag1209 Cone3ag1173 Cone10ag0979 Lsi10g00386 . Chy11g00365 . . . . . . . . . Sed01g0291 Cmo02g00391 Cmo20g00846 . . . . Cpe16g00253 Cpe05g01272 Bhi10g01985 Tan05g1284 Cmetu11g0118 . . . . . . . . . . . . Csa02g01278 . Cme11g00132
Vvi3g354 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g355 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 17708643 17712515 + Bda029590.1 Bda08g00944 944
10 49279916 49288915 - XM_039045897.1 Bhi10g01979 1979
10 49402659 49403901 - XM_039046979.1 Bhi10g01980 1980
10 49504981 49511291 + XM_039045275.1 Bhi10g01981 1981
10 49513190 49518261 - XM_039045276.1 Bhi10g01982 1982
10 49530406 49535480 + XM_039046840.1 Bhi10g01983 1983
10 49552228 49559105 + XM_039045668.1 Bhi10g01985 1985
2 28313665 28322290 - BLOR10539 Blo02g00809 809
2 28410261 28413976 + BLOR10541 Blo02g00811 811
4 4450161 4453964 + BLOR13431 Blo04g00519 519
4 4454564 4460068 - BLOR13432 Blo04g00520 520
4 4511551 4516316 + BLOR13433 Blo04g00521 521
15 22540291 22543419 - BLOR07101 Blo15g00707 707
15 22647720 22656685 + BLOR07102 Blo15g00708 708
5 14580891 14584759 - Bma021288.1 Bma05g00437 437
12 15596658 15597125 - Bma007558.1 Bma12g00501 501
12 15828715 15831402 + Bma007564.1 Bma12g00503 503
7 4429589 4430056 - Bpe021241.1 Bpe07g00418 418
7 4697761 4700432 + Bpe021245.1 Bpe07g00421 421
2 1665236 1669287 - Carg24150-RA Car02g00246 246
2 1676745 1677272 - Carg24151-RA Car02g00247 247
2 1689084 1693242 + Carg24152-RA Car02g00248 248
2 1694477 1700518 - Carg24153-RA Car02g00249 249
2 1703767 1708655 + Carg24154-RA Car02g00250 250
20 4139429 4144339 - Carg26788-RA Car20g00716 716
20 4156268 4156729 - Carg26787-RA Car20g00717 717
20 4200623 4206250 + Carg26467-RA Car20g00720 720
20 4207140 4211374 - Carg26468-RA Car20g00721 721
20 4215104 4220831 + Carg26469-RA Car20g00722 722
20 4224537 4226531 + Carg26471-RA Car20g00724 724
11 3289153 3291924 - Chy11G189400.1 Chy11g00360 360
11 3310947 3311426 - Chy11G189410.1 Chy11g00361 361
11 3336415 3343705 + Chy11G189420.1 Chy11g00362 362
11 3345724 3349496 - Chy11G189430.1 Chy11g00363 363
11 3355368 3361509 + Chy11G189440.1 Chy11g00364 364
11 3362419 3367773 + Chy11G189450.1 Chy11g00365 365
2 1912741 1916387 - CmaCh02G003790.1 Cma02g00379 379
2 1923569 1924162 - CmaCh02G003820.1 Cma02g00382 382
2 1934509 1939542 + CmaCh02G003830.1 Cma02g00383 383
2 1941775 1947641 - CmaCh02G003840.1 Cma02g00384 384
2 1947586 1956434 + CmaCh02G003850.1 Cma02g00385 385
20 3960402 3965605 - CmaCh20G008310.1 Cma20g00831 831
20 3976278 3976730 - CmaCh20G008320.1 Cma20g00832 832
20 3985464 3991424 + CmaCh20G008340.1 Cma20g00834 834
20 3991867 3996483 - CmaCh20G008350.1 Cma20g00835 835
20 4000058 4009116 + CmaCh20G008360.1 Cma20g00836 836
20 4009158 4015003 + CmaCh20G008370.1 Cma20g00837 837
1 14226295 14232921 + MELO3C013225.2.1 Cme01g01117 1117
11 1313255 1319901 - MELO3C023314.2.1 Cme11g00132 132
11 1322636 1327154 - MELO3C023315.2.1 Cme11g00133 133
11 1332044 1336680 + MELO3C023316.2.1 Cme11g00134 134
11 1338553 1345193 - MELO3C023317.2.1 Cme11g00135 135
11 1373467 1374442 + MELO3C023318.2.1 Cme11g00136 136
11 1392980 1396646 + MELO3C023319.2.1 Cme11g00137 137
11 27592337 27596764 - PI0002432.1 Cmetu11g0118 118
11 27601588 27606297 - PI0024656.1 Cmetu11g0387 387
11 27613575 27618549 + PI0000712.1 Cmetu11g0971 971
11 27636053 27642812 - PI0016330.1 Cmetu11g2218 2218
11 27667808 27668929 + PI0026720.1 Cmetu11g2335 2335
2 1980080 1983941 - CmoCh02G003860.1 Cmo02g00386 386
2 1992010 1992525 - CmoCh02G003880.1 Cmo02g00388 388
2 2003406 2009757 + CmoCh02G003890.1 Cmo02g00389 389
2 2009831 2016261 - CmoCh02G003900.1 Cmo02g00390 390
2 2017541 2027343 + CmoCh02G003910.1 Cmo02g00391 391
20 4206891 4211285 - CmoCh20G008400.1 Cmo20g00840 840
20 4223040 4223495 - CmoCh20G008410.1 Cmo20g00841 841
20 4232680 4238504 + CmoCh20G008420.1 Cmo20g00842 842
20 4240374 4244697 - CmoCh20G008430.1 Cmo20g00843 843
20 4248373 4256734 + CmoCh20G008440.1 Cmo20g00844 844
20 4258644 4260582 + CmoCh20G008460.1 Cmo20g00846 846
3 30386521 30390080 - Conep03aG0167800.1 Cone3ag1173 1173
3 30397100 30401049 + Conep03aG0168000.1 Cone3ag1174 1174
3 30402116 30407849 - Conep03aG0168100.1 Cone3ag1175 1175
6 12603613 12604113 + Conep06aG0171400.1 Cone6ag1649 1649
8 10262355 10266082 - Conep08aG0124600.1 Cone8ag1209 1209
8 10270462 10274233 + Conep08aG0124700.1 Cone8ag1210 1210
8 10274433 10278960 - Conep08aG0124800.1 Cone8ag1211 1211
8 10279714 10284976 - Conep08aG0124900.1 Cone8ag1212 1212
8 10296926 10299749 + Conep08aG0125100.1 Cone8ag1214 1214
9 11329068 11329574 + Conep09aG0162300.1 Cone9ag1573 1573
10 6587533 6591511 - Conep10aG0100500.1 Cone10ag0979 979
10 6604550 6613205 + Conep10aG0100600.1 Cone10ag0980 980
10 6613579 6619354 - Conep10aG0100700.1 Cone10ag0981 981
12 7122943 7123436 + Conep12aG0080000.1 Cone12ag0777 777
12 9232421 9240808 - Conep12aG0119900.1 Cone12ag1160 1160
12 9242558 9249660 + Conep12aG0120000.1 Cone12ag1161 1161
12 9249953 9254341 - Conep12aG0120100.1 Cone12ag1162 1162
12 9255223 9260295 - Conep12aG0120200.1 Cone12ag1163 1163
5 8864988 8869636 - Cp4.1LG05g12810.1 Cpe05g01272 1272
5 8872821 8879138 + Cp4.1LG05g12760.1 Cpe05g01273 1273
5 8880112 8885564 - Cp4.1LG05g12800.1 Cpe05g01274 1274
5 8896385 8896909 + Cp4.1LG05g12720.1 Cpe05g01275 1275
5 8903672 8908185 + Cp4.1LG05g12710.1 Cpe05g01276 1276
16 4546545 4552237 - Cp4.1LG16g02580.1 Cpe16g00253 253
16 4553032 4558756 - Cp4.1LG16g02550.1 Cpe16g00254 254
16 4563734 4569645 + Cp4.1LG16g02510.1 Cpe16g00255 255
16 4570028 4575761 - Cp4.1LG16g02570.1 Cpe16g00256 256
16 4585987 4586448 + Cp4.1LG16g02470.1 Cpe16g00257 257
16 4598125 4603877 + Cp4.1LG16g02490.1 Cpe16g00258 258
2 12434949 12442359 - CsaV3_2G014940.1 Csa02g01278 1278
2 12444125 12448921 - CsaV3_2G014950.1 Csa02g01279 1279
2 12453089 12458236 + CsaV3_2G014960.1 Csa02g01280 1280
2 12460321 12466969 - CsaV3_2G014970.1 Csa02g01281 1281
2 12483651 12485520 + CsaV3_2G014980.1 Csa02g01282 1282
2 12501857 12505634 + CsaV3_2G014990.1 Csa02g01283 1283
8 9443732 9447658 - Hsped.08g09970.1 Hepe08g0997 997
8 9465796 9466994 - Hsped.08g09980.1 Hepe08g0998 998
8 9507756 9514646 + Hsped.08g09990.1 Hepe08g0999 999
8 9517621 9521762 - Hsped.08g10000.1 Hepe08g1000 1000
10 5886872 5903751 - Lsi10G003870.1 Lsi10g00386 386
10 5912209 5917125 - Lsi10G003890.1 Lsi10g00389 389
10 5923363 5929131 + Lsi10G003900.1 Lsi10g00390 390
10 5931431 5942596 - Lsi10G003910.1 Lsi10g00391 391
10 5982268 5982744 + Lsi10G003920.1 Lsi10g00392 392
10 6009478 6013154 + Lsi10G003940.1 Lsi10g00394 394
1 2203344 2210068 + Sed0025967.1 Sed01g0288 288
1 2214312 2219598 - Sed0020449.1 Sed01g0289 289
1 2224116 2229604 + Sed0019329.1 Sed01g0290 290
1 2233674 2240888 + Sed0015701.1 Sed01g0291 291
5 43912719 43913927 + Sed0016710.1 Sed05g3527 3527
5 13985443 13990028 - Tan0010846.4 Tan05g1273 1273
5 14214402 14215997 - Tan0022804.1 Tan05g1278 1278
5 14319154 14326262 + Tan0020233.2 Tan05g1280 1280
5 14326990 14332774 - Tan0017837.1 Tan05g1281 1281
5 14417919 14422970 + Tan0016838.1 Tan05g1282 1282
5 14450381 14456631 + Tan0005443.1 Tan05g1284 1284
3 3205358 3214057 - Vvi3g346 Vvi3g346 346
3 3219635 3221351 + Vvi3g347 Vvi3g347 347
3 3227133 3234563 - Vvi3g348 Vvi3g348 348
3 3239809 3255189 + Vvi3g349 Vvi3g349 349
3 3260715 3270012 + Vvi3g350 Vvi3g350 350
3 3270356 3273742 - Vvi3g351 Vvi3g351 351
3 3277621 3287627 + Vvi3g352 Vvi3g352 352
3 3293149 3300416 + Vvi3g353 Vvi3g353 353
3 3303132 3306036 - Vvi3g354 Vvi3g354 354
3 3308723 3310004 - Vvi3g355 Vvi3g355 355
       

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