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
Vvi18g480 . . Bda01g00901 . . . . . . . . . . . . . . Bhi04g00811 . . . . . Lcy13g1503 Cla08g01146 . . . . . . . . Cone17ag1191 . . . . Cme03g01826 . . Bda11g00788 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi08g01004 Csa02g02188 Chy03g01329 .
Vvi18g481 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone20ag0542 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g482 . . . . Bpe02g00134 . . Bma01g02591 . . . Cma09g00587 . . . Cpe06g00448 . . . . . . . . . . . . . . . Cone4ag1309 . . . . Csa03g04480 Chy04g00221 . . . Bda11g00790 . . . . . . Cmo01g01684 Cmo09g00572 . . . Car09g00516 . . Bhi09g02483 . . . Hepe01g2160 Mch11g0699 . . . . . . . . . . . Cme04g00248
Vvi18g483 . . . . Bpe02g00135 . . Bma01g02590 Cmo05g00557 . . . . . . . . . . . . . . . Cla08g01149 Cam08g1609 Cec08g1180 Cco08g1306 Clacu08g1308 . Cre08g1092 Cone4ag1308 Cone7ag0848 Cone17ag1189 Cone20ag0545 . . . Cme03g01823 Blo17g00102 . Bda11g00791 Bda13g01369 . Bpe14g00477 . Bma02g00120 . . . . Cma05g00530 Car05g00478 . Cpe11g00467 . . . . . . . . . . . . . . . Lsi08g01007 Csa02g02191 Chy03g01325 .
Vvi18g484 . . . . . . . . Cmo05g00558 . . . . . . . . . . . . . . . Cla08g01150 Cam08g1610 Cec08g1182 Cco08g1307 Clacu08g1309 . Cre08g1093 . . Cone17ag1188 Cone20ag0546 . . . Cme03g01822 Blo17g00101 . . Bda13g01368 . Bpe14g00478 . . . . . . Cma05g00531 Car05g00479 . Cpe11g00468 . . . . . . . . . . . . . . . Lsi08g01008 Csa02g02192 Chy03g01324 .
Vvi18g485 . . . Bda03g00463 . Bpe04g00424 Bma04g00438 . . . . . . Car12g00168 . . Cpe07g00156 . . . . . . . . . . . . . . . . . . Lsi04g02270 Csa03g04481 Chy04g00220 . . . . . . . . . . . . Cma12g00185 . . . . . . . . . . . . Cla11g01412 Cam11g1470 Cec11g1500 Cco11g1495 Clacu11g1631 Cmu11g1449 Cre11g1866 . . . Cme04g00247
Vvi18g486 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g487 . . . . . . . . . Cmo12g00144 Cma01g01638 . . Car12g00169 . . Cpe07g00157 . . . . . . . . . . . . . . . . . . Lsi04g02272 Csa03g04483 Chy04g00217 . . . . . . . . Bma02g00106 Sed13g1547 Cmo01g01685 . Cma12g00186 . . . . . Bhi09g02487 Tan01g3840 Cmetu04g2532 . Hepe01g2162 Mch11g0701 . Cla11g01415 Cam11g1472 Cec11g1502 Cco11g1497 Clacu11g1633 Cmu11g1451 Cre11g1869 . . . Cme04g00245
Vvi18g488 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g489 . . Bda01g00916 Bda03g00461 . Bpe04g00422 Bma04g00436 . . Cmo12g00145 . . . Car12g00170 . . Cpe07g00158 . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe02g01160 . . . . . . Cma12g00187 . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 41996970 41998424 + Bda003041.1 Bda01g00901 901
1 42298523 42324426 - Bda003061.2 Bda01g00916 916
3 3984819 3989770 - Bda016430.2 Bda03g00461 461
3 3995600 3997627 + Bda016432.1 Bda03g00463 463
11 7865024 7866366 - Bda005538.1 Bda11g00788 788
11 7871614 7882482 - Bda005540.1 Bda11g00790 790
11 7884683 7893176 - Bda005541.1 Bda11g00791 791
13 36245673 36248681 - Bda000187.1 Bda13g01368 1368
13 36271879 36273690 + Bda000188.1 Bda13g01369 1369
4 20443611 20445282 - XM_039028463.1 Bhi04g00811 811
9 67298673 67312822 - XM_039043475.1 Bhi09g02483 2483
9 67368277 67371171 - XM_039040757.1 Bhi09g02487 2487
17 848563 903749 - BLOR15922 Blo17g00101 101
17 913786 915549 + BLOR15923 Blo17g00102 102
1 83529174 83530939 + Bma003476.1 Bma01g02590 2590
1 83532568 83547384 + Bma003477.1 Bma01g02591 2591
2 969696 972054 - Bma014560.1 Bma02g00106 106
2 1139056 1140857 + Bma014575.3 Bma02g00120 120
4 3583750 3590047 - Bma031095 Bma04g00436 436
4 3595375 3597819 + Bma018905.1 Bma04g00438 438
2 915493 929613 - Bpe007984.1 Bpe02g00134 134
2 931022 932797 - Bpe007985.1 Bpe02g00135 135
2 15224751 15230871 - Bpe009022.1 Bpe02g01160 1160
4 2730405 2735556 - Bpe015108.1 Bpe04g00422 422
4 2741658 2743669 + Bpe015110.1 Bpe04g00424 424
14 4237740 4239533 - Bpe007126.1 Bpe14g00477 477
14 4243759 4246068 + Bpe007127.1 Bpe14g00478 478
8 22257233 22261119 - CaPI482276_08g016090.1 Cam08g1609 1609
8 22277477 22280745 + CaPI482276_08g016100.1 Cam08g1610 1610
11 27424338 27444139 - CaPI482276_11g014700.1 Cam11g1470 1470
11 27449928 27452066 - CaPI482276_11g014720.1 Cam11g1472 1472
5 2720856 2722449 - Carg08221-RA Car05g00478 478
5 2728128 2731535 + Carg08222-RA Car05g00479 479
9 2895819 2899874 - Carg02998-RA Car09g00516 516
12 1031087 1033632 - Carg22526-RA Car12g00168 168
12 1034918 1039950 - Carg22525-RA Car12g00169 169
12 1042492 1048947 + Carg22524-RA Car12g00170 170
8 24875559 24879481 - CcPI632755_08g013060.1 Cco08g1306 1306
8 24895583 24899404 + CcPI632755_08g013070.1 Cco08g1307 1307
11 27783990 27787826 - CcPI632755_11g014950.1 Cco11g1495 1495
11 27793207 27795747 - CcPI632755_11g014970.1 Cco11g1497 1497
8 23697968 23701862 - CePI673135_08g011800.1 Cec08g1180 1180
8 23718837 23722419 + CePI673135_08g011820.1 Cec08g1182 1182
11 29209278 29213045 - CePI673135_11g015000.1 Cec11g1500 1500
11 29218865 29221000 - CePI673135_11g015020.1 Cec11g1502 1502
3 16233874 16237591 - Chy3G063040.1 Chy03g01324 1324
3 16250589 16252482 + Chy3G063050.1 Chy03g01325 1325
3 16286431 16287912 + Chy3G063090.1 Chy03g01329 1329
4 1978907 1981932 + Chy4G069350.1 Chy04g00217 217
4 1986377 1989823 + Chy4G069380.1 Chy04g00220 220
4 1994985 2008311 + Chy4G069390.1 Chy04g00221 221
8 23029273 23033168 - ClG42_08g0130800.10 Clacu08g1308 1308
8 23049939 23053238 + ClG42_08g0130900.10 Clacu08g1309 1309
11 27454631 27474306 - ClG42_11g0163100.10 Clacu11g1631 1631
11 27479983 27482112 - ClG42_11g0163300.10 Clacu11g1633 1633
8 24215393 24218121 - ClCG08G011480.2 Cla08g01146 1146
8 24274694 24280436 - ClCG08G011510.2 Cla08g01149 1149
8 24297301 24300745 + ClCG08G011520.2 Cla08g01150 1150
11 27684693 27705081 - ClCG11G014440.2 Cla11g01412 1412
11 27708890 27712770 - ClCG11G014480.2 Cla11g01415 1415
1 11229337 11231513 - CmaCh01G016380.1 Cma01g01638 1638
5 2535606 2537595 - CmaCh05G005300.1 Cma05g00530 530
5 2542802 2546047 + CmaCh05G005310.1 Cma05g00531 531
9 2703158 2713566 - CmaCh09G005870.1 Cma09g00587 587
12 848110 852167 - CmaCh12G001850.1 Cma12g00185 185
12 853134 858211 - CmaCh12G001860.1 Cma12g00186 186
12 860516 866941 + CmaCh12G001870.1 Cma12g00187 187
3 26598495 26602251 - MELO3C011069.2.1 Cme03g01822 1822
3 26613276 26616410 + MELO3C011068.2.1 Cme03g01823 1823
3 26647838 26649568 + MELO3C011065.2.1 Cme03g01826 1826
4 1940694 1944170 + MELO3C003534.2.1 Cme04g00245 245
4 1948190 1952150 + MELO3C003536.2.1 Cme04g00247 247
4 1955264 1974764 + MELO3C003537.2.1 Cme04g00248 248
4 31412577 31415993 - PI0027132.1 Cmetu04g2532 2532
1 12686449 12699040 - CmoCh01G016840.1 Cmo01g01684 1684
1 12699067 12703928 - CmoCh01G016850.1 Cmo01g01685 1685
5 2692406 2694060 - CmoCh05G005570.1 Cmo05g00557 557
5 2699874 2702894 + CmoCh05G005580.1 Cmo05g00558 558
9 2783313 2794868 - CmoCh09G005720.1 Cmo09g00572 572
12 908622 917557 - CmoCh12G001440.1 Cmo12g00144 144
12 920511 927052 + CmoCh12G001450.1 Cmo12g00145 145
11 26706418 26726092 - CmPI595203_11g014490.1 Cmu11g1449 1449
11 26730018 26733898 - CmPI595203_11g014510.1 Cmu11g1451 1451
4 10767744 10770488 + Conep04aG0135400.1 Cone4ag1308 1308
4 10771320 10778814 + Conep04aG0135500.1 Cone4ag1309 1309
7 6444069 6446764 - Conep07aG0087700.1 Cone7ag0848 848
17 8704695 8706364 - Conep17aG0121800.1 Cone17ag1188 1188
17 8708758 8710540 + Conep17aG0121900.1 Cone17ag1189 1189
17 8729047 8730756 + Conep17aG0122100.1 Cone17ag1191 1191
20 3009426 3010670 - Conep20aG0055800.1 Cone20ag0542 542
20 3036345 3038138 - Conep20aG0056100.1 Cone20ag0545 545
20 3041509 3043303 + Conep20aG0056200.1 Cone20ag0546 546
6 2596156 2609129 - Cp4.1LG06g04180.1 Cpe06g00448 448
7 916270 919586 - Cp4.1LG07g01600.1 Cpe07g00156 156
7 923341 925912 - Cp4.1LG07g01630.1 Cpe07g00157 157
7 928089 934723 + Cp4.1LG07g01560.1 Cpe07g00158 158
11 2638096 2639932 - Cp4.1LG11g04660.1 Cpe11g00467 467
11 2646556 2650081 + Cp4.1LG11g04600.1 Cpe11g00468 468
8 24046681 24050544 - CrPI670011_08g010920.1 Cre08g1092 1092
8 24067483 24070751 + CrPI670011_08g010930.1 Cre08g1093 1093
11 30321977 30339946 - CrPI670011_11g018660.1 Cre11g1866 1866
11 30346870 30350410 - CrPI670011_11g018690.1 Cre11g1869 1869
2 19675209 19677195 - CsaV3_2G030070.1 Csa02g02188 2188
2 19704671 19708523 - CsaV3_2G030100.1 Csa02g02191 2191
2 19719951 19724440 + CsaV3_2G030110.1 Csa02g02192 2192
3 39036966 39051801 - CsaV3_3G047860.1 Csa03g04480 4480
3 39056155 39060207 - CsaV3_3G047870.1 Csa03g04481 4481
3 39064748 39068373 - CsaV3_3G047890.1 Csa03g04483 4483
1 86234987 86255035 - Hsped.01g21600.1 Hepe01g2160 2160
1 86265947 86268547 - Hsped.01g21620.1 Hepe01g2162 2162
13 33716892 33718391 + Maker00034209 Lcy13g1503 1503
4 29715150 29737463 - Lsi04G022700.1 Lsi04g02270 2270
4 29741498 29744610 - Lsi04G022720.1 Lsi04g02272 2272
8 18524456 18525970 - Lsi08G010040.1 Lsi08g01004 1004
8 18603898 18607099 - Lsi08G010070.1 Lsi08g01007 1007
8 18628536 18633541 + Lsi08G010080.1 Lsi08g01008 1008
11 4592383 4610342 - MC11g0588 Mch11g0699 699
11 4613534 4616232 - MC11g0590 Mch11g0701 701
13 20652808 20655990 + Sed0003078.1 Sed13g1547 1547
1 103185015 103188028 - Tan0018027.1 Tan01g3840 3840
18 5350193 5352136 - Vvi18g480 Vvi18g480 480
18 5354042 5361249 - Vvi18g481 Vvi18g481 481
18 5378722 5441999 - Vvi18g482 Vvi18g482 482
18 5462822 5465587 - Vvi18g483 Vvi18g483 483
18 5470373 5476297 + Vvi18g484 Vvi18g484 484
18 5477435 5481168 - Vvi18g485 Vvi18g485 485
18 5482253 5484157 - Vvi18g486 Vvi18g486 486
18 5485003 5490071 - Vvi18g487 Vvi18g487 487
18 5498179 5501829 - Vvi18g488 Vvi18g488 488
18 5505642 5516683 + Vvi18g489 Vvi18g489 489
       

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