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
Vvi3g446 . Blo15g00732 Bda06g01046 Bda08g00847 Bpe07g00394 Bpe12g00059 . Bma12g00468 Cmo19g00632 Cmo11g01351 . . . . Sed10g2042 Cpe04g00271 Cpe15g00497 Bhi05g01131 Tan02g0894 Cmetu01g2176 . Hepe02g0576 . . Cla02g00588 Cam02g0620 Cec02g0619 Cco02g0636 Clacu02g0618 Cmu02g0613 Cre02g0944 Cone12ag1104 Cone8ag1144 . . . Csa07g00771 . Cme01g00038 . Blo13g00571 Bda15g00032 . . . . Bma08g00797 . . . Cma11g01761 Cma19g00613 . Car19g00466 . . . . . . . . . . . . . . . . Lsi11g01019 . Chy01g00044 .
Vvi3g447 Blo02g00819 . Bda06g01045 . . . . Bma12g00469 . . Cma02g00443 Cma20g00892 Car02g00300 Car20g00769 . . . . . . . . . . . . . . . . . Cone6ag0064 Cone9ag0078 Cone14ag1139 Cone15ag1157 Lsi10g00304 . Chy11g00443 . . . . . . . . . . Cmo02g00452 Cmo20g00899 . . . . . Cpe05g01219 . . . . . . . Cla09g01707 Cam09g1803 Cec09g1863 Cco09g1956 . . Cre01g0704 . Csa02g01195 . Cme11g00517
Vvi3g448 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g449 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g450 . Blo15g00731 . . Bpe07g00395 . . Bma12g00470 . . . . . . . . . . . . . . . . . . . . . . . Cone12ag1106 Cone8ag1146 Cone3ag1111 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g451 . . . . . Bpe12g00060 . . Cmo19g00635 . . . . . Sed10g2044 . Cpe15g00499 Bhi05g01134 Tan02g0890 Cmetu01g0261 . Hepe02g0574 . . Cla02g00585 Cam02g0618 Cec02g0617 Cco02g0633 Clacu02g0615 Cmu02g0611 Cre02g0942 Cone12ag1107 Cone8ag1147 . . . Csa07g00774 . Cme01g00036 . Blo13g00570 Bda15g00031 . . . . Bma08g00796 . . . . Cma19g00616 . Car19g00469 . . . . . . . . . . . . . . . . Lsi11g01021 . Chy01g00042 .
Vvi3g452 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g453 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g454 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g455 Blo02g00818 . . Bda08g00845 . . . . Cmo19g00637 Cmo11g01349 . . . . . Cpe04g00269 Cpe15g00501 Bhi05g01138 . . . . . . Cla02g00583 Cam02g0616 Cec02g0615 Cco02g0631 Clacu02g0612 Cmu02g0609 Cre02g0940 . . . . . Csa07g00777 . Cme01g00034 . . . . . . . . . Cmo02g00580 . Cma11g01763 Cma19g00619 . Car19g00471 . . . . . . . . . . . . . . . . Lsi11g01023 . Chy01g00039 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 36790448 36796204 - Bda022796.1 Bda06g01045 1045
6 36798157 36800711 - Bda022797.1 Bda06g01046 1046
8 13917980 13920086 + Bda029412.1 Bda08g00845 845
8 13979288 13982464 - Bda034027 Bda08g00847 847
15 1746333 1747807 + Bda011787.2 Bda15g00031 31
15 1748877 1751373 - Bda011788.1 Bda15g00032 32
5 40712225 40717070 + XM_039032734.1 Bhi05g01131 1131
5 40760368 40766504 - XM_039032318.1 Bhi05g01134 1134
5 40809996 40816711 - XM_039032126.1 Bhi05g01138 1138
2 28988755 28994822 + BLOR10548 Blo02g00818 818
2 29104384 29113106 - BLOR10549 Blo02g00819 819
13 27818452 27819698 + BLOR19622 Blo13g00570 570
13 27821133 27823651 - BLOR19623 Blo13g00571 571
15 24247567 24248679 - BLOR07125 Blo15g00731 731
15 24275487 24302501 - BLOR07126 Blo15g00732 732
8 45599600 45601009 + Bma028184.1 Bma08g00796 796
8 45602661 45604722 - Bma028185.1 Bma08g00797 797
12 12494774 12497429 + Bma007486.2 Bma12g00468 468
12 12498613 12504315 + Bma007487.1 Bma12g00469 469
12 12558916 12560022 + Bma007490.1 Bma12g00470 470
7 3625639 3628240 + Bpe021212.1 Bpe07g00394 394
7 3642451 3643557 + Bpe021214.1 Bpe07g00395 395
12 442152 445113 + Bpe005298.1 Bpe12g00059 59
12 445585 447372 - Bpe024872 Bpe12g00060 60
2 7048510 7054871 + CaPI482276_02g006160.1 Cam02g0616 616
2 7070185 7074232 + CaPI482276_02g006180.1 Cam02g0618 618
2 7109665 7113761 - CaPI482276_02g006200.1 Cam02g0620 620
9 32361860 32371880 + CaPI482276_09g018030.1 Cam09g1803 1803
2 2013659 2016689 - Carg24057-RA Car02g00300 300
19 6344493 6346851 + Carg22058-RA Car19g00466 466
19 6354422 6358555 - Carg22055-RA Car19g00469 469
19 6362804 6368571 - Carg22053-RA Car19g00471 471
20 4526621 4535372 - Carg23614-RA Car20g00769 769
2 6231388 6237786 + CcPI632755_02g006310.1 Cco02g0631 631
2 6253180 6257093 + CcPI632755_02g006330.1 Cco02g0633 633
2 6292984 6297563 - CcPI632755_02g006360.1 Cco02g0636 636
9 33559879 33569970 + CcPI632755_09g019560.1 Cco09g1956 1956
2 6121627 6130699 + CePI673135_02g006150.1 Cec02g0615 615
2 6143455 6148004 + CePI673135_02g006170.1 Cec02g0617 617
2 6183179 6187243 - CePI673135_02g006190.1 Cec02g0619 619
9 35255250 35265281 + CePI673135_09g018630.1 Cec09g1863 1863
1 286934 292985 + Chy1G000390.1 Chy01g00039 39
1 299762 302697 + Chy1G000420.1 Chy01g00042 42
1 316963 320927 - Chy1G000440.1 Chy01g00044 44
11 4340936 4351811 - Chy11G190230.1 Chy11g00443 443
2 6040080 6046385 + ClG42_02g0061200.10 Clacu02g0612 612
2 6061706 6065648 + ClG42_02g0061500.10 Clacu02g0615 615
2 6100455 6104537 - ClG42_02g0061800.10 Clacu02g0618 618
2 6322773 6329713 + ClCG02G005760.1 Cla02g00583 583
2 6345013 6350252 + ClCG02G005780.2 Cla02g00585 585
2 6383900 6388618 - ClCG02G005800.2 Cla02g00588 588
9 34204193 34214269 + ClCG09G017440.2 Cla09g01707 1707
2 2254923 2269709 - CmaCh02G004430.1 Cma02g00443 443
11 11749711 11754453 + CmaCh11G017610.1 Cma11g01761 1761
11 11775814 11783065 - CmaCh11G017630.1 Cma11g01763 1763
19 6677721 6681351 + CmaCh19G006130.1 Cma19g00613 613
19 6688861 6693063 - CmaCh19G006160.1 Cma19g00616 616
19 6697473 6703557 - CmaCh19G006190.1 Cma19g00619 619
20 4287687 4295172 - CmaCh20G008920.1 Cma20g00892 892
1 279186 287692 + MELO3C018436.2.1 Cme01g00034 34
1 292732 296051 + MELO3C018438.2.1 Cme01g00036 36
1 309772 314522 - MELO3C018440.2.1 Cme01g00038 38
11 5297766 5307951 - MELO3C021906.2.1 Cme11g00517 517
1 345086 349090 + PI0000984.4 Cmetu01g0261 261
1 364923 369856 - PI0015947.1 Cmetu01g2176 2176
2 2362482 2366746 - CmoCh02G004520.1 Cmo02g00452 452
2 3425943 3430216 + CmoCh02G005800.1 Cmo02g00580 580
11 9362290 9369261 + CmoCh11G013490.1 Cmo11g01349 1349
11 9393075 9397600 - CmoCh11G013510.1 Cmo11g01351 1351
19 6882263 6885760 + CmoCh19G006320.1 Cmo19g00632 632
19 6894115 6898226 - CmoCh19G006350.1 Cmo19g00635 635
19 6902524 6908584 - CmoCh19G006370.1 Cmo19g00637 637
20 4559291 4567379 - CmoCh20G008990.1 Cmo20g00899 899
2 5946985 5953276 + CmPI595203_02g006090.1 Cmu02g0609 609
2 5968615 5973168 + CmPI595203_02g006110.1 Cmu02g0611 611
2 6007249 6011331 - CmPI595203_02g006130.1 Cmu02g0613 613
3 29683083 29684271 - Conep03aG0161500.1 Cone3ag1111 1111
6 343548 347268 + Conep06aG0006400.1 Cone6ag0064 64
8 10017921 10021085 + Conep08aG0117600.1 Cone8ag1144 1144
8 10026059 10027255 + Conep08aG0117800.1 Cone8ag1146 1146
8 10028778 10030471 - Conep08aG0117900.1 Cone8ag1147 1147
9 347050 351079 + Conep09aG0007800.1 Cone9ag0078 78
12 8975176 8978385 + Conep12aG0114000.1 Cone12ag1104 1104
12 8983211 8984663 + Conep12aG0114200.1 Cone12ag1106 1106
12 8985535 8988212 - Conep12aG0114300.1 Cone12ag1107 1107
14 9445105 9450570 + Conep14aG0116300.1 Cone14ag1139 1139
15 9359542 9363689 + Conep15aG0118600.1 Cone15ag1157 1157
4 3351058 3358306 + Cp4.1LG04g08190.1 Cpe04g00269 269
4 3375436 3380512 - Cp4.1LG04g08080.1 Cpe04g00271 271
5 8539375 8540730 + Cp4.1LG05g12120.1 Cpe05g01219 1219
15 5923675 5927792 + Cp4.1LG15g04920.1 Cpe15g00497 497
15 5934430 5939406 - Cp4.1LG15g04990.1 Cpe15g00499 499
15 5943747 5949877 - Cp4.1LG15g05000.1 Cpe15g00501 501
1 6706971 6717003 - CrPI670011_01g007040.1 Cre01g0704 704
2 6571113 6577463 + CrPI670011_02g009400.1 Cre02g0940 940
2 6595821 6600370 + CrPI670011_02g009420.1 Cre02g0942 942
2 6638699 6642781 - CrPI670011_02g009440.1 Cre02g0944 944
2 11747886 11760260 + CsaV3_2G014110.1 Csa02g01195 1195
7 5412330 5417391 + CsaV3_7G008700.1 Csa07g00771 771
7 5429231 5434710 - CsaV3_7G008730.1 Csa07g00774 774
7 5441131 5447807 - CsaV3_7G008760.1 Csa07g00777 777
2 5807118 5810386 + Hsped.02g05740.1 Hepe02g0574 574
2 5841661 5846031 - Hsped.02g05760.1 Hepe02g0576 576
10 4890733 4900434 + Lsi10G003040.1 Lsi10g00304 304
11 17277332 17282326 + Lsi11G010190.1 Lsi11g01019 1019
11 17357538 17362283 - Lsi11G010210.1 Lsi11g01021 1021
11 17391336 17398079 - Lsi11G010230.1 Lsi11g01023 1023
10 36925656 36932107 + Sed0019542.2 Sed10g2042 2042
10 36955625 36960452 - Sed0011670.1 Sed10g2044 2044
2 10130024 10140679 + Tan0021474.1 Tan02g0890 890
2 10209902 10214423 - Tan0018910.2 Tan02g0894 894
3 4299947 4306720 + Vvi3g446 Vvi3g446 446
3 4306719 4311753 + Vvi3g447 Vvi3g447 447
3 4315101 4317754 + Vvi3g448 Vvi3g448 448
3 4318214 4325277 + Vvi3g449 Vvi3g449 449
3 4327742 4329320 + Vvi3g450 Vvi3g450 450
3 4335010 4339814 - Vvi3g451 Vvi3g451 451
3 4346114 4351793 + Vvi3g452 Vvi3g452 452
3 4359738 4367121 - Vvi3g453 Vvi3g453 453
3 4367149 4367733 - Vvi3g454 Vvi3g454 454
3 4368309 4388395 - Vvi3g455 Vvi3g455 455
       

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