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
Vvi1g291 . . Bda01g01858 . . . Bma14g01704 . . Cmo18g01042 . Cma18g01030 . Car18g00952 Sed14g1516 Cpe09g00291 . Bhi07g01339 Tan04g0874 Cmetu10g1483 Lac13g0482 Hepe01g1204 . . Cla05g02311 Cam05g2484 . . Clacu05g2479 Cmu05g2340 . . . Cone6ag0456 Cone9ag0467 Lsi04g00266 Csa05g02600 Chy10g01135 Cme10g00272 . Blo11g00836 . . Bpe11g01696 . . . . . . . Cma15g01400 . Car15g01262 Cpe13g00051 . . . . . . . . Cla01g00533 Cam01g0553 Cec01g0545 Cco01g0569 Clacu01g0551 Cmu01g0524 Cre09g1986 Lsi09g00576 . Chy09g00937 Cme09g01465
Vvi1g292 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g293 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0454 Cone9ag0466 . . . . . . . . . . Bma01g00164 . . . . . . . . Cpe13g00412 . . . . . . . . . . . . . . . . . . .
Vvi1g294 Blo01g00495 Blo16g01057 Bda01g02081 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe02g02274 . . . . . . . . Car15g00849 . . . . . . . . . . . . . . . . . . . .
Vvi1g295 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g296 . . . . . . Bma14g01705 . . Cmo18g01040 . . . Car18g00950 Sed07g2078 Cpe09g00293 . Bhi07g01336 Tan04g0870 Cmetu10g0862 Lac13g0484 Hepe01g1202 . . Cla05g02309 Cam05g2482 Cec05g2505 Cco05g2547 Clacu05g2477 Cmu05g2338 Cre05g2456 . . . . Lsi04g00264 Csa05g02602 Chy10g01137 Cme10g00270 Blo06g00965 Blo11g00837 Bda07g01532 . Bpe11g01697 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g297 Blo01g00496 . Bda01g02080 Bda11g00204 Bpe13g01118 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0837 Cone19ag0844 . . . . . . . . . Bda11g00204 . Bpe02g02273 Bma01g00165 . . . Cmo15g00907 . . . Car15g00848 Cpe13g00413 . . . . . . . . . . . . . . . . . . .
Vvi1g298 . . . . . Bpe10g00939 Bma14g01707 Bma15g00085 . Cmo18g01038 . Cma18g01028 . Car18g00948 Sed06g1882 Cpe09g00295 . Bhi07g01334 Tan04g0868 Cmetu10g1073 Lac13g0486 Hepe01g1200 . . Cla05g02307 . Cec05g2503 Cco05g2545 . . Cre05g2454 Cone13ag0836 Cone19ag0843 . . Lsi04g00262 Csa05g02604 Chy10g01139 Cme10g00268 . Blo11g00839 Bda07g01534 . Bpe11g01698 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g299 Blo01g00497 Blo16g01059 Bda01g02079 Bda11g01142 Bpe13g01342 . . . Cmo04g01586 Cmo18g01037 . Cma18g01027 Car04g01566 Car18g00947 Sed06g1883 Cpe09g00296 . Bhi07g01332 Tan04g0866 Cmetu10g1799 Lac13g0487 Hepe01g1199 . . Cla05g02306 Cam05g2480 Cec05g2502 Cco05g2544 Clacu05g2475 Cmu05g2336 Cre05g2453 . . . . . Csa05g02605 Chy10g01140 Cme10g00267 Blo06g00964 . . Bda11g01142 . Bpe02g02272 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g300 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 54697844 54698927 + Bda004152.1 Bda01g01858 1858
1 57009981 57010550 + Bda004407.1 Bda01g02079 2079
1 57016457 57019848 + Bda004408.1 Bda01g02080 2080
1 57022383 57025915 + Bda004409.1 Bda01g02081 2081
7 28450271 28453355 + Bda028385.1 Bda07g01532 1532
7 28458650 28465293 - Bda028386.1 Bda07g01534 1534
11 2595737 2598468 + Bda004924.1 Bda11g00204 204
11 11631665 11632234 - Bda007629.1 Bda11g01142 1142
7 40689973 40690865 + XM_039035626.1 Bhi07g01332 1332
7 40803739 40811114 + XM_039036796.1 Bhi07g01334 1334
7 40814546 40818346 - XM_039036754.1 Bhi07g01336 1336
7 40925472 40933108 + XM_039036249.1 Bhi07g01339 1339
1 5424527 5431408 - BLOR00495 Blo01g00495 495
1 5449462 5452459 - BLOR00496 Blo01g00496 496
1 5462852 5463421 - BLOR00497 Blo01g00497 497
6 32874096 32874581 - BLOR17547 Blo06g00964 964
6 32918926 32920658 - BLOR17548 Blo06g00965 965
11 14305364 14313420 - BLOR03712 Blo11g00836 836
11 14346138 14349003 + BLOR03713 Blo11g00837 837
11 14353545 14364164 - BLOR03715 Blo11g00839 839
16 39107614 39111092 - BLOR21844 Blo16g01057 1057
16 39122885 39123427 - BLOR21846 Blo16g01059 1059
1 1532913 1536419 - Bma000330.1 Bma01g00164 164
1 1540837 1544067 - Bma000331.2 Bma01g00165 165
14 36173496 36178440 - Bma012452.1 Bma14g01704 1704
14 36184354 36187210 + Bma012453.1 Bma14g01705 1705
14 36193700 36200275 - Bma012454.1 Bma14g01707 1707
15 948331 956353 - Bma013060.1 Bma15g00085 85
2 23569279 23569848 + Bpe010090.1 Bpe02g02272 2272
2 23574640 23577984 + Bpe010091.1 Bpe02g02273 2273
2 23580842 23584338 + Bpe010092.1 Bpe02g02274 2274
10 14953382 14961288 + Bpe003244.1 Bpe10g00939 939
11 13239890 13246175 - Bpe005010.1 Bpe11g01696 1696
11 13247735 13250825 + Bpe005011.1 Bpe11g01697 1697
11 13252847 13260750 - Bpe005012.1 Bpe11g01698 1698
13 16772969 16777275 - Bpe010795.1 Bpe13g01118 1118
13 18648379 18648948 - Bpe011005.1 Bpe13g01342 1342
1 5897944 5917517 + CaPI482276_01g005530.1 Cam01g0553 553
5 32651783 32652319 + CaPI482276_05g024800.1 Cam05g2480 2480
5 32672015 32675433 - CaPI482276_05g024820.1 Cam05g2482 2482
5 32685211 32696646 + CaPI482276_05g024840.1 Cam05g2484 2484
4 9078559 9079122 + Carg01834-RA Car04g01566 1566
15 4931122 4932796 + Carg26875-RA Car15g00848 848
15 4937778 4943536 + Carg26876-RA Car15g00849 849
15 9852653 9866704 + Carg20780-RA Car15g01262 1262
18 10118030 10118602 + Carg21583-RA Car18g00947 947
18 10121494 10128674 + Carg21582-RA Car18g00948 948
18 10132114 10135835 - Carg21580-RA Car18g00950 950
18 10140177 10150458 + Carg21578-RA Car18g00952 952
1 5620830 5640438 + CcPI632755_01g005690.1 Cco01g0569 569
5 33732705 33733241 + CcPI632755_05g025440.1 Cco05g2544 2544
5 33742728 33750558 + CcPI632755_05g025450.1 Cco05g2545 2545
5 33754845 33758263 - CcPI632755_05g025470.1 Cco05g2547 2547
1 5657560 5677110 + CePI673135_01g005450.1 Cec01g0545 545
5 36066765 36067301 + CePI673135_05g025020.1 Cec05g2502 2502
5 36078446 36086775 + CePI673135_05g025030.1 Cec05g2503 2503
5 36090622 36094041 - CePI673135_05g025050.1 Cec05g2505 2505
9 12126112 12140537 - Chy9G166530.1 Chy09g00937 937
10 16306056 16312607 - Chy10G183290.1 Chy10g01135 1135
10 16320661 16323838 + Chy10G183310.1 Chy10g01137 1137
10 16327658 16333467 - Chy10G183330.1 Chy10g01139 1139
10 16336817 16337350 - Chy10G183340.1 Chy10g01140 1140
1 5532342 5551425 + ClG42_01g0055100.10 Clacu01g0551 551
5 32868102 32868638 + ClG42_05g0247500.10 Clacu05g2475 2475
5 32888118 32891535 - ClG42_05g0247700.10 Clacu05g2477 2477
5 32901186 32912577 + ClG42_05g0247900.10 Clacu05g2479 2479
1 5805010 5827705 + ClCG01G005430.1 Cla01g00533 533
5 34667977 34668513 + ClCG05G022790.1 Cla05g02306 2306
5 34675892 34684038 + ClCG05G022800.2 Cla05g02307 2307
5 34687651 34691606 - ClCG05G022820.1 Cla05g02309 2309
5 34701090 34712794 + ClCG05G022840.2 Cla05g02311 2311
15 8826657 8840911 + CmaCh15G014000.1 Cma15g01400 1400
18 8559109 8559681 + CmaCh18G010270.1 Cma18g01027 1027
18 8562492 8569422 + CmaCh18G010280.1 Cma18g01028 1028
18 8576049 8586519 + CmaCh18G010300.1 Cma18g01030 1030
9 19849599 19860872 - MELO3C005386.2.1 Cme09g01465 1465
10 1750415 1751305 + MELO3C012239.2.1 Cme10g00267 267
10 1754265 1760573 + MELO3C012238.2.1 Cme10g00268 268
10 1763673 1767375 - MELO3C012235.2.1 Cme10g00270 270
10 1774235 1781537 + MELO3C012233.2.1 Cme10g00272 272
10 20323500 20326718 + PI0000096.1 Cmetu10g0862 862
10 20330357 20336670 - PI0004888.1 Cmetu10g1073 1073
10 20307242 20312833 - PI0009789.1 Cmetu10g1483 1483
10 20340093 20340889 - PI0018627.1 Cmetu10g1799 1799
4 8093977 8094540 + CmoCh04G015860.1 Cmo04g01586 1586
15 4587759 4592805 - CmoCh15G009070.1 Cmo15g00907 907
18 11117949 11118521 + CmoCh18G010370.1 Cmo18g01037 1037
18 11121436 11128573 + CmoCh18G010380.1 Cmo18g01038 1038
18 11130440 11135917 - CmoCh18G010400.1 Cmo18g01040 1040
18 11140095 11149089 + CmoCh18G010420.1 Cmo18g01042 1042
1 5492085 5508061 + CmPI595203_01g005240.1 Cmu01g0524 524
5 32606282 32606818 + CmPI595203_05g023360.1 Cmu05g2336 2336
5 32626290 32629707 - CmPI595203_05g023380.1 Cmu05g2338 2338
5 32639373 32650764 + CmPI595203_05g023400.1 Cmu05g2340 2340
6 2232050 2236249 + Conep06aG0046400.1 Cone6ag0454 454
6 2237611 2250173 + Conep06aG0046600.1 Cone6ag0456 456
9 2217182 2220608 + Conep09aG0047600.1 Cone9ag0466 466
9 2222296 2231230 + Conep09aG0047700.1 Cone9ag0467 467
13 7561861 7567054 + Conep13aG0086200.1 Cone13ag0836 836
13 7570436 7573856 + Conep13aG0086300.1 Cone13ag0837 837
19 6645581 6651329 + Conep19aG0086700.1 Cone19ag0843 843
19 6655341 6659386 + Conep19aG0086800.1 Cone19ag0844 844
9 1718419 1726688 - Cp4.1LG09g02970.1 Cpe09g00291 291
9 1731320 1736776 + Cp4.1LG09g02880.1 Cpe09g00293 293
9 1739143 1745848 - Cp4.1LG09g03000.1 Cpe09g00295 295
9 1748774 1749346 - Cp4.1LG09g02930.1 Cpe09g00296 296
13 381166 395374 - Cp4.1LG13g00610.1 Cpe13g00051 51
13 4457646 4462936 - Cp4.1LG13g06650.1 Cpe13g00412 412
13 4470339 4473154 - Cp4.1LG13g06630.1 Cpe13g00413 413
5 35938343 35938879 + CrPI670011_05g024530.1 Cre05g2453 2453
5 35946511 35954329 + CrPI670011_05g024540.1 Cre05g2454 2454
5 35958554 35961975 - CrPI670011_05g024560.1 Cre05g2456 2456
9 38825816 38845089 - CrPI670011_09g019860.1 Cre09g1986 1986
5 27227096 27237383 - CsaV3_5G034190.1 Csa05g02600 2600
5 27244049 27247771 + CsaV3_5G034210.1 Csa05g02602 2602
5 27250343 27257589 - CsaV3_5G034230.1 Csa05g02604 2604
5 27258768 27261726 - CsaV3_5G034240.1 Csa05g02605 2605
1 77185049 77188522 + Hsped.01g11990.1 Hepe01g1199 1199
1 77191247 77203153 + Hsped.01g12000.1 Hepe01g1200 1200
1 77206122 77213131 - Hsped.01g12020.1 Hepe01g1202 1202
1 77232656 77242737 + Hsped.01g12040.1 Hepe01g1204 1204
13 3501511 3503397 - Lag0040278.1 Lac13g0482 482
13 3510832 3514152 + Lag0040280.1 Lac13g0484 484
13 3518534 3530841 - Lag0040282.1 Lac13g0486 486
13 3535104 3535679 - Lag0040283.1 Lac13g0487 487
4 2709806 2718017 + Lsi04G002620.1 Lsi04g00262 262
4 2723456 2727514 - Lsi04G002640.1 Lsi04g00264 264
4 2738810 2750231 + Lsi04G002660.1 Lsi04g00266 266
9 6196172 6209083 + Lsi09G005760.1 Lsi09g00576 576
6 43158665 43166698 - Sed0024821.2 Sed06g1882 1882
6 43176255 43177766 - Sed0025092.1 Sed06g1883 1883
7 36162388 36166314 + Sed0023484.1 Sed07g2078 2078
14 23465468 23469813 + Sed0020791.2 Sed14g1516 1516
4 7447748 7449321 + Tan0021885.1 Tan04g0866 866
4 7458821 7469037 + Tan0010031.2 Tan04g0868 868
4 7473618 7476936 - Tan0002246.1 Tan04g0870 870
4 7494532 7504825 + Tan0001679.2 Tan04g0874 874
1 3030504 3040686 - Vvi1g291 Vvi1g291 291
1 3044554 3045863 - Vvi1g292 Vvi1g292 292
1 3046872 3048873 - Vvi1g293 Vvi1g293 293
1 3048921 3049971 - Vvi1g294 Vvi1g294 294
1 3049999 3051482 - Vvi1g295 Vvi1g295 295
1 3061305 3065537 + Vvi1g296 Vvi1g296 296
1 3065974 3080363 - Vvi1g297 Vvi1g297 297
1 3084063 3093046 - Vvi1g298 Vvi1g298 298
1 3100681 3101924 - Vvi1g299 Vvi1g299 299
1 3112076 3117575 - Vvi1g300 Vvi1g300 300
       

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