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
Vvi3g76 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g77 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma03g00587 . . . . . Cma19g00712 . . . . . . . . . . . . . . . . . . . . . .
Vvi3g78 . . . . . . . . . Cmo11g01712 . . . . . . . Bhi05g01760 . . . . . . Cla02g00465 Cam02g0471 Cec02g0471 . Clacu02g0474 Cmu02g0469 Cre02g0802 . . . . . Csa07g00062 . . . . Bda15g01053 . . . . Bma08g00771 . . . Cma11g01408 . . . . . . . . . . . . . . . . . . . Lsi11g01164 Csa02g01335 . .
Vvi3g79 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g80 . . . . . . . . . . . . . . . . . . . . . . . . Cla02g00464 Cam02g0470 Cec02g0470 . Clacu02g0473 Cmu02g0467 Cre02g0801 . . . . Lsi10g00455 . Chy11g00309 Cme01g01296 . . . . . . Bma03g00588 Bma08g00770 . Cmo02g00338 Cmo20g00780 . . . . . . . . . . . . . . . . . . . . Lsi11g01165 Csa02g01336 Chy01g00714 .
Vvi3g81 . . . . . Bpe12g00104 . . Cmo19g00728 Cmo11g01713 . . . . . . . . . . . . . . Cla02g00458 Cam02g0466 Cec02g0465 . Clacu02g0468 Cmu02g0462 Cre02g0796 . . . . . Csa07g00063 . . . . Bda15g01052 . Bpe15g00833 . . . Sed01g0247 . . Cma11g01407 Cma19g00717 . . . . Bhi10g01907 Tan05g1206 Cmetu11g0253 . . . . . . . . . . . Lsi11g01166 Csa02g01342 . .
Vvi3g82 . . . . . Bpe12g00105 . . . Cmo11g01714 Cma02g00343 Cma20g00778 . . . . . . . . . . . . Cla02g00454 Cam02g0461 Cec02g0461 . Clacu02g0463 Cmu02g0457 Cre02g0791 . . . . . . Chy11g00307 Cme01g01295 . Blo13g00528 . . . . . Bma08g00769 Sed01g0241 Cmo02g00335 Cmo20g00777 . . . . . . Bhi10g01906 Tan05g1205 Cmetu11g2080 . . . . . . . . . . . Lsi11g01171 Csa02g01344 Chy01g00707 Cme11g00428
Vvi3g83 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g84 . . . . . Bpe12g00106 . . . Cmo11g01717 Cma02g00337 Cma20g00777 . . . . . . . . . . . . . . . . . . . . . . . Lsi10g00456 Csa07g00071 . . . . Bda15g01051 . . . . . Sed01g0233 . Cmo20g00776 Cma11g01404 . . . . . Bhi10g01905 Tan05g1204 . . . . . . . . . . . . Lsi11g01173 Csa02g01345 . Cme11g00426
Vvi3g85 . . . Bda08g00972 . . Bma05g00408 . . . Cma02g00333 Cma20g00774 Car02g00214 Car20g00677 . . . . . . . . . . . . . . . . . . . . . Lsi10g00458 . Chy11g00302 . . . . . . . . . Sed01g0228 Cmo02g00330 Cmo20g00774 . . . . Cpe16g00291 Cpe05g01307 Bhi10g01901 Tan05g1200 Cmetu11g2217 . Hepe08g0952 . . . . . . . . . . Csa02g01347 . Cme11g00424
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 19199733 19215523 - Bda029640.1 Bda08g00972 972
15 19554452 19554760 + Bda013041.1 Bda15g01051 1051
15 19555900 19556187 + Bda013042.1 Bda15g01052 1052
15 19558965 19559243 + Bda013043.1 Bda15g01053 1053
5 56230590 56231462 - XM_039031974.1 Bhi05g01760 1760
10 47704654 47715449 + XM_039045467.1 Bhi10g01901 1901
10 47737412 47737951 - XM_039045229.1 Bhi10g01905 1905
10 47740044 47740616 - XM_039045230.1 Bhi10g01906 1906
10 47743080 47743549 - XM_039045232.1 Bhi10g01907 1907
13 26903470 26903754 - BLOR05809 Blo13g00528 528
3 4906067 4906339 - Bma016879.1 Bma03g00587 587
3 4908453 4908737 + Bma016880.1 Bma03g00588 588
5 12866665 12877965 + Bma021242.1 Bma05g00408 408
8 44771927 44772214 - Bma028148.1 Bma08g00769 769
8 44849080 44849355 + Bma028149.1 Bma08g00770 770
8 44853609 44853914 + Bma028150.1 Bma08g00771 771
12 756660 756935 + Bpe005344.1 Bpe12g00104 104
12 766624 766905 - Bpe005345.1 Bpe12g00105 105
12 768548 768811 + Bpe005346.1 Bpe12g00106 106
15 18375352 18375603 + Bpe024583 Bpe15g00833 833
2 5291211 5291549 - CaPI482276_02g004610.1 Cam02g0461 461
2 5328513 5328767 - CaPI482276_02g004660.1 Cam02g0466 466
2 5354916 5355218 + CaPI482276_02g004700.1 Cam02g0470 470
2 5358397 5358699 + CaPI482276_02g004710.1 Cam02g0471 471
2 1307158 1317518 + Carg19804-RA Car02g00214 214
20 3807607 3817854 + Carg16198-RA Car20g00677 677
2 4333386 4333688 - CePI673135_02g004610.1 Cec02g0461 461
2 4350790 4351044 - CePI673135_02g004650.1 Cec02g0465 465
2 4377059 4377355 + CePI673135_02g004700.1 Cec02g0470 470
2 4379069 4379371 + CePI673135_02g004710.1 Cec02g0471 471
1 5169969 5170900 + Chy1G007070.1 Chy01g00707 707
1 5216813 5217331 + Chy1G007140.1 Chy01g00714 714
11 2759886 2770076 + Chy11G188820.1 Chy11g00302 302
11 2790257 2790751 - Chy11G188870.1 Chy11g00307 307
11 2794627 2795519 - Chy11G188890.1 Chy11g00309 309
2 4190972 4191274 - ClG42_02g0046300.10 Clacu02g0463 463
2 4208378 4208632 - ClG42_02g0046800.10 Clacu02g0468 468
2 4234547 4234849 + ClG42_02g0047300.10 Clacu02g0473 473
2 4236631 4238324 + ClG42_02g0047400.10 Clacu02g0474 474
2 4452312 4455411 - ClCG02G004387.1 Cla02g00454 454
2 4467446 4470201 - ClCG02G004400.1 Cla02g00458 458
2 4496433 4498704 + ClCG02G004412.1 Cla02g00464 464
2 4499530 4502179 + ClCG02G004413.1 Cla02g00465 465
2 1647891 1658400 + CmaCh02G003330.1 Cma02g00333 333
2 1668082 1669233 - CmaCh02G003370.1 Cma02g00337 337
2 1680819 1681112 - CmaCh02G003430.1 Cma02g00343 343
11 9226895 9227197 - CmaCh11G014040.1 Cma11g01404 1404
11 9254472 9254774 + CmaCh11G014070.1 Cma11g01407 1407
11 9256722 9257012 + CmaCh11G014080.1 Cma11g01408 1408
19 7257222 7257524 - CmaCh19G007120.1 Cma19g00712 712
19 7280039 7281529 + CmaCh19G007170.1 Cma19g00717 717
20 3662123 3672986 + CmaCh20G007740.1 Cma20g00774 774
20 3683719 3684012 - CmaCh20G007770.1 Cma20g00777 777
20 3686225 3686518 - CmaCh20G007780.1 Cma20g00778 778
1 16281512 16281977 - MELO3C013385.2.1 Cme01g01295 1295
1 16317414 16317986 - MELO3C013386.2.1 Cme01g01296 1296
11 4260878 4271784 + MELO3C020773.2.1 Cme11g00424 424
11 4280768 4281285 - MELO3C020771.2.1 Cme11g00426 426
11 4287806 4288326 - MELO3C034603.2.1 Cme11g00428 428
11 28156682 28158744 - PI0026343.1 Cmetu11g0253 253
11 28131542 28132147 + PI0026379.1 Cmetu11g2080 2080
11 28189393 28199707 - PI0005069.1 Cmetu11g2217 2217
2 1703925 1713815 + CmoCh02G003300.1 Cmo02g00330 330
2 1727300 1727593 - CmoCh02G003350.1 Cmo02g00335 335
2 1733363 1733656 - CmoCh02G003380.1 Cmo02g00338 338
11 12150597 12150899 - CmoCh11G017120.1 Cmo11g01712 1712
11 12153104 12153406 - CmoCh11G017130.1 Cmo11g01713 1713
11 12155447 12155743 - CmoCh11G017140.1 Cmo11g01714 1714
11 12172279 12172581 + CmoCh11G017170.1 Cmo11g01717 1717
19 7542842 7544360 + CmoCh19G007280.1 Cmo19g00728 728
20 3881106 3892650 + CmoCh20G007740.1 Cmo20g00774 774
20 3902900 3903193 - CmoCh20G007760.1 Cmo20g00776 776
20 3905373 3905666 - CmoCh20G007770.1 Cmo20g00777 777
20 3909381 3909674 - CmoCh20G007800.1 Cmo20g00780 780
2 4186990 4187292 - CmPI595203_02g004570.1 Cmu02g0457 457
2 4204383 4204637 - CmPI595203_02g004620.1 Cmu02g0462 462
2 4230536 4230838 + CmPI595203_02g004670.1 Cmu02g0467 467
2 4232620 4234313 + CmPI595203_02g004690.1 Cmu02g0469 469
5 9160289 9171814 - Cp4.1LG05g13160.1 Cpe05g01307 1307
16 4897112 4907296 - Cp4.1LG16g02900.1 Cpe16g00291 291
2 4745872 4746210 - CrPI670011_02g007910.1 Cre02g0791 791
2 4782931 4783185 - CrPI670011_02g007960.1 Cre02g0796 796
2 4805594 4805890 + CrPI670011_02g008010.1 Cre02g0801 801
2 4807607 4807909 + CrPI670011_02g008020.1 Cre02g0802 802
2 12932355 12933254 + CsaV3_2G015510.1 Csa02g01335 1335
2 12934603 12939336 + CsaV3_2G015520.1 Csa02g01336 1336
2 12952262 12952823 + CsaV3_2G015580.1 Csa02g01342 1342
2 12958005 12958298 + CsaV3_2G015600.1 Csa02g01344 1344
2 12960837 12961130 + CsaV3_2G015610.1 Csa02g01345 1345
2 12970585 12981803 - CsaV3_2G015630.1 Csa02g01347 1347
7 671113 671631 - CsaV3_7G000620.1 Csa07g00062 62
7 672970 673516 - CsaV3_7G000630.1 Csa07g00063 63
7 719059 720050 + CsaV3_7G000710.1 Csa07g00071 71
8 8794501 8805569 + Hsped.08g09520.1 Hepe08g0952 952
10 6630491 6630784 + Lsi10G004550.1 Lsi10g00455 455
10 6633304 6633597 + Lsi10G004560.1 Lsi10g00456 456
10 6648175 6660000 - Lsi10G004580.1 Lsi10g00458 458
11 20164832 20165134 - Lsi11G011640.1 Lsi11g01164 1164
11 20167073 20167369 - Lsi11G011650.1 Lsi11g01165 1165
11 20175811 20176113 - Lsi11G011660.1 Lsi11g01166 1166
11 20204770 20205051 + Lsi11G011710.1 Lsi11g01171 1171
11 20220217 20220567 + Lsi11G011730.1 Lsi11g01173 1173
1 1804049 1813951 + Sed0010933.1 Sed01g0228 228
1 1839242 1839706 + Sed0013275.1 Sed01g0233 233
1 1863371 1863907 - Sed0013861.1 Sed01g0241 241
1 1899837 1900395 + Sed0023803.1 Sed01g0247 247
5 11874321 11885602 + Tan0005782.1 Tan05g1200 1200
5 11909440 11912571 + Tan0011599.1 Tan05g1204 1204
5 11919975 11921758 - Tan0021835.1 Tan05g1205 1205
5 11925483 11925776 + Tan0000105.1 Tan05g1206 1206
3 888665 888953 + Vvi3g76 Vvi3g76 76
3 890778 895141 - Vvi3g77 Vvi3g77 77
3 897890 898178 + Vvi3g78 Vvi3g78 78
3 898285 903569 - Vvi3g79 Vvi3g79 79
3 905891 909162 + Vvi3g80 Vvi3g80 80
3 915229 915499 - Vvi3g81 Vvi3g81 81
3 915997 917711 - Vvi3g82 Vvi3g82 82
3 918670 922108 - Vvi3g83 Vvi3g83 83
3 922118 927953 + Vvi3g84 Vvi3g84 84
3 930889 960586 - Vvi3g85 Vvi3g85 85
       

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