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
Vvi5g369 . . . . . Bpe14g01151 . . . Cmo17g00295 . . . . . . . . . . . . . . Cla06g00507 Cam06g0547 Cec06g0547 Cco06g0555 Clacu06g0533 Cmu06g0532 Cre06g1301 Cone14ag0788 Cone15ag0789 Cone7ag0182 Cone4ag0177 . . Chy11g01467 . Blo02g00577 Blo07g00190 Bda11g00543 . . Bpe13g00646 . Bma06g01520 . . . Cma08g01200 Cma17g00305 Car08g01078 Car17g00281 Cpe12g00257 Cpe17g00097 Bhi12g01745 . . . . . . . . . . . . . Lsi09g01393 . . Cme11g01973
Vvi5g370 . . . . . Bpe14g01152 . . . . . Cma14g01648 . Car14g01481 . . Cpe03g01392 Bhi01g00926 . . . . . Lcy11g1459 . . . . . . . . . Cone7ag0183 Cone4ag0178 Lsi05g01496 . . Cme06g00683 Blo02g00576 . . . . . . . . . Cmo14g01692 . . . . . . . . . . . . . Cla05g00610 . . . . . . . Csa03g01408 Chy06g00651 .
Vvi5g371 . . . . . Bpe14g01153 . . . . Cma06g01457 Cma14g01649 Car06g01259 Car14g01483 Sed02g1676 Cpe08g00220 Cpe03g01393 Bhi01g00925 Tan10g0941 Cmetu06g0809 . Hepe05g1489 . Lcy11g1461 . . . . . . . Cone14ag0789 Cone15ag0790 . . Lsi05g01493 . . Cme06g00682 Blo02g00553 . . . . . Bma02g00714 . . Cmo06g01459 Cmo14g01693 . . . . . . . . . . . . . Cla05g00609 Cam05g0669 Cec05g0679 Cco05g0673 Clacu05g0664 Cmu05g0632 Cre05g0702 . Csa03g01407 Chy06g00650 .
Vvi5g372 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g373 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g374 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g375 . . . . Bpe04g01172 . . . Cmo08g01173 Cmo17g00292 . . . . . . . . . . . . . . Cla06g00511 Cam06g0550 Cec06g0550 Cco06g0557 Clacu06g0536 Cmu06g0536 Cre06g1304 . . . . . . Chy11g01464 . . . . . . . . . . . . Cma08g01199 Cma17g00302 Car08g01076 Car17g00278 Cpe12g00255 Cpe17g00099 Bhi12g01747 . . . . . . . . . . . . . Lsi09g01390 . . Cme11g01970
Vvi5g376 . Blo12g00044 Bda03g01216 . . . Bma04g01089 . Cmo08g01172 Cmo17g00291 . . . . . . . . . . . . . . . . . . . . . Cone14ag0793 Cone15ag0794 . . . . Chy11g01463 . . . . . . . . . . . . . . Car08g01075 Car17g00277 Cpe12g00254 Cpe17g00100 Bhi12g01748 . . . . . . . . . . . . . . . . Cme11g01969
Vvi5g377 . . . . . . . . Cmo08g01171 Cmo17g00289 . . . . . . . . . . . . . . Cla06g00513 Cam06g0551 Cec06g0551 Cco06g0558 Clacu06g0537 Cmu06g0537 Cre06g1305 Cone14ag0794 Cone15ag0795 . . . . Chy11g01462 . . . . . . . . . . . . Cma08g01198 Cma17g00301 Car08g01074 Car17g00276 Cpe12g00253 Cpe17g00101 Bhi12g01749 . . . . . . . . . . . . . Lsi09g01389 . . Cme11g01968
Vvi5g378 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 15151863 15162124 - Bda017307.1 Bda03g01216 1216
11 5667689 5668895 + Bda005278.1 Bda11g00543 543
1 17263790 17303363 - XM_039043072.1 Bhi01g00925 925
1 17327574 17334231 + XM_039022045.1 Bhi01g00926 926
12 56700650 56705187 + XM_039020163.1 Bhi12g01745 1745
12 56761426 56768641 + XM_039051187.1 Bhi12g01747 1747
12 56770182 56777505 + XM_039019705.1 Bhi12g01748 1748
12 56777793 56783111 - XM_039050529.1 Bhi12g01749 1749
2 9732994 9739437 - BLOR10283 Blo02g00553 553
2 10599294 10602645 + BLOR10306 Blo02g00576 576
2 10603424 10608005 - BLOR10307 Blo02g00577 577
7 2373907 2376319 + BLOR18122 Blo07g00190 190
12 2926677 2936727 - BLOR04063 Blo12g00044 44
2 29988319 30003742 + Bma015374.2 Bma02g00714 714
4 24490697 24499943 + Bma019769.1 Bma04g01089 1089
6 51625625 51626654 + Bma024633.1 Bma06g01520 1520
4 12966796 12969591 - Bpe015865.1 Bpe04g01172 1172
13 13310984 13311969 - Bpe010346.1 Bpe13g00646 646
14 8576897 8577595 + Bpe014526.1 Bpe14g01151 1151
14 8578504 8584885 - Bpe014527.1 Bpe14g01152 1152
14 8586680 8606400 + Bpe014528.2 Bpe14g01153 1153
5 5817076 5843390 - CaPI482276_05g006690.1 Cam05g0669 669
6 7551398 7555507 + CaPI482276_06g005470.1 Cam06g0547 547
6 7582122 7588392 + CaPI482276_06g005500.1 Cam06g0550 550
6 7589428 7594834 - CaPI482276_06g005510.1 Cam06g0551 551
6 9035279 9052958 - Carg17376-RA Car06g01259 1259
8 7315630 7321610 + Carg15953-RA Car08g01074 1074
8 7322121 7327550 - Carg15954-RA Car08g01075 1075
8 7329132 7331981 - Carg15955-RA Car08g01076 1076
8 7341198 7344763 - Carg15957-RA Car08g01078 1078
14 12284845 12291680 - Carg20145-RA Car14g01481 1481
14 12295121 12319516 + Carg20147-RA Car14g01483 1483
17 1704183 1710969 + Carg05482-RA Car17g00276 276
17 1711451 1716690 - Carg05483-RA Car17g00277 277
17 1718032 1720776 - Carg05484-RA Car17g00278 278
17 1732083 1735819 - Carg05487-RA Car17g00281 281
5 5514508 5540234 - CcPI632755_05g006730.1 Cco05g0673 673
6 5987975 5991949 + CcPI632755_06g005550.1 Cco06g0555 555
6 6015414 6028374 + CcPI632755_06g005570.1 Cco06g0557 557
6 6029840 6035453 - CcPI632755_06g005580.1 Cco06g0558 558
5 5532279 5557376 - CePI673135_05g006790.1 Cec05g0679 679
6 6089661 6092967 + CePI673135_06g005470.1 Cec06g0547 547
6 6120033 6126421 + CePI673135_06g005500.1 Cec06g0550 550
6 6127840 6133079 - CePI673135_06g005510.1 Cec06g0551 551
6 4418828 4446253 - Chy6G111780.1 Chy06g00650 650
6 4451975 4457811 + Chy6G111790.1 Chy06g00651 651
11 21380668 21385348 + Chy11G200420.1 Chy11g01462 1462
11 21386383 21393456 - Chy11G200430.1 Chy11g01463 1463
11 21394787 21397615 - Chy11G200440.1 Chy11g01464 1464
11 21414239 21417381 - Chy11G200470.1 Chy11g01467 1467
5 5546133 5571884 - ClG42_05g0066400.10 Clacu05g0664 664
6 6093481 6097530 + ClG42_06g0053300.10 Clacu06g0533 533
6 6122601 6129418 + ClG42_06g0053600.10 Clacu06g0536 536
6 6131705 6137385 - ClG42_06g0053700.10 Clacu06g0537 537
5 5610172 5636571 - ClCG05G005740.2 Cla05g00609 609
5 5635987 5646152 + ClCG05G005750.2 Cla05g00610 610
6 6159780 6164375 + ClCG06G005420.1 Cla06g00507 507
6 6184624 6197577 + ClCG06G005460.2 Cla06g00511 511
6 6198219 6204188 - ClCG06G005470.2 Cla06g00513 513
6 9308257 9321419 - CmaCh06G014570.1 Cma06g01457 1457
8 7353712 7359871 + CmaCh08G011980.1 Cma08g01198 1198
8 7360260 7369988 - CmaCh08G011990.1 Cma08g01199 1199
8 7380111 7383930 - CmaCh08G012000.1 Cma08g01200 1200
14 12324153 12331110 - CmaCh14G016480.1 Cma14g01648 1648
14 12332424 12360000 + CmaCh14G016490.1 Cma14g01649 1649
17 1607153 1614217 + CmaCh17G003010.1 Cma17g00301 301
17 1615159 1624768 - CmaCh17G003020.1 Cma17g00302 302
17 1635855 1639373 - CmaCh17G003050.1 Cma17g00305 305
6 4421398 4443537 - MELO3C006601.2.1 Cme06g00682 682
6 4446588 4453217 + MELO3C006602.2.1 Cme06g00683 683
11 27685119 27690753 + MELO3C021371.2.1 Cme11g01968 1968
11 27692427 27698376 - MELO3C021370.2.1 Cme11g01969 1969
11 27700433 27707397 - MELO3C021368.2.1 Cme11g01970 1970
11 27720372 27724313 - MELO3C021366.2.1 Cme11g01973 1973
6 4667570 4689574 - PI0026006.1 Cmetu06g0809 809
6 10512251 10532052 - CmoCh06G014590.1 Cmo06g01459 1459
8 7452009 7458724 + CmoCh08G011710.1 Cmo08g01171 1171
8 7458719 7464009 - CmoCh08G011720.1 Cmo08g01172 1172
8 7465091 7467931 - CmoCh08G011730.1 Cmo08g01173 1173
14 13276907 13284722 - CmoCh14G016920.1 Cmo14g01692 1692
14 13286293 13314280 + CmoCh14G016930.1 Cmo14g01693 1693
17 1744669 1751182 + CmoCh17G002890.1 Cmo17g00289 289
17 1752452 1757242 - CmoCh17G002910.1 Cmo17g00291 291
17 1758544 1761342 - CmoCh17G002920.1 Cmo17g00292 292
17 1773133 1776539 - CmoCh17G002950.1 Cmo17g00295 295
5 5389569 5409807 - CmPI595203_05g006320.1 Cmu05g0632 632
6 5900872 5904957 + CmPI595203_06g005320.1 Cmu06g0532 532
6 5931683 5937974 + CmPI595203_06g005360.1 Cmu06g0536 536
6 5939110 5948381 - CmPI595203_06g005370.1 Cmu06g0537 537
4 830013 831354 + Conep04aG0018500.1 Cone4ag0177 177
4 831592 836480 - Conep04aG0018600.1 Cone4ag0178 178
7 765480 766937 + Conep07aG0018600.1 Cone7ag0182 182
7 767243 772773 - Conep07aG0018700.1 Cone7ag0183 183
14 4612764 4615058 + Conep14aG0080500.1 Cone14ag0788 788
14 4625574 4645654 + Conep14aG0080600.1 Cone14ag0789 789
14 4673672 4679257 + Conep14aG0081000.1 Cone14ag0793 793
14 4679365 4684759 - Conep14aG0081100.1 Cone14ag0794 794
15 4806267 4808896 + Conep15aG0080400.1 Cone15ag0789 789
15 4820883 4847038 + Conep15aG0080500.1 Cone15ag0790 790
15 4866074 4867439 + Conep15aG0080900.1 Cone15ag0794 794
15 4868179 4874836 - Conep15aG0081000.1 Cone15ag0795 795
3 11203371 11210740 - Cp4.1LG03g11140.1 Cpe03g01392 1392
3 11212318 11238952 + Cp4.1LG03g11190.1 Cpe03g01393 1393
8 1463405 1481181 + Cp4.1LG08g04660.1 Cpe08g00220 220
12 1684845 1691843 + Cp4.1LG12g02580.1 Cpe12g00253 253
12 1692265 1697580 - Cp4.1LG12g02590.1 Cpe12g00254 254
12 1699027 1701825 - Cp4.1LG12g02620.1 Cpe12g00255 255
12 1717307 1721107 - Cp4.1LG12g02600.1 Cpe12g00257 257
17 597393 602131 + Cp4.1LG17g00930.1 Cpe17g00097 97
17 612964 615804 + Cp4.1LG17g00940.1 Cpe17g00099 99
17 617338 622513 + Cp4.1LG17g01010.1 Cpe17g00100 100
17 622564 629467 - Cp4.1LG17g01130.1 Cpe17g00101 101
5 6182705 6208590 - CrPI670011_05g007020.1 Cre05g0702 702
6 6952245 6956319 + CrPI670011_06g013010.1 Cre06g1301 1301
6 6983230 6989658 + CrPI670011_06g013040.1 Cre06g1304 1304
6 6990820 6996729 - CrPI670011_06g013050.1 Cre06g1305 1305
3 10542795 10564955 - CsaV3_3G014070.1 Csa03g01407 1407
3 10568545 10575249 + CsaV3_3G014080.1 Csa03g01408 1408
5 64344022 64375667 + Hsped.05g14890.1 Hepe05g1489 1489
11 38492822 38499816 - Maker00031997 Lcy11g1459 1459
11 38512723 38536429 + Maker00032093 Lcy11g1461 1461
5 22749197 22780368 - Lsi05G014930.1 Lsi05g01493 1493
5 22783776 22789934 + Lsi05G014960.1 Lsi05g01496 1496
9 21926685 21931434 + Lsi09G013890.1 Lsi09g01389 1389
9 21931932 21944680 - Lsi09G013900.1 Lsi09g01390 1390
9 21964057 21968314 - Lsi09G013930.1 Lsi09g01393 1393
2 51924358 51935780 - Sed0000619.1 Sed02g1676 1676
10 8154148 8187146 - Tan0018749.1 Tan10g0941 941
5 3702251 3705298 + Vvi5g369 Vvi5g369 369
5 3710368 3717780 - Vvi5g370 Vvi5g370 370
5 3724866 3754247 + Vvi5g371 Vvi5g371 371
5 3754732 3758829 + Vvi5g372 Vvi5g372 372
5 3759484 3791485 + Vvi5g373 Vvi5g373 373
5 3793981 3795853 + Vvi5g374 Vvi5g374 374
5 3803511 3809392 + Vvi5g375 Vvi5g375 375
5 3809767 3819769 + Vvi5g376 Vvi5g376 376
5 3820376 3827378 - Vvi5g377 Vvi5g377 377
5 3838327 3838420 + Vvi5g378 Vvi5g378 378
       

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