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
Vvi3g556 . Blo15g00688 Bda06g00948 . Bpe07g00459 . . Bma12g00546 . . Cma02g00425 . Car02g00281 . . . . . . . . . . . . . . . . . . . . Cone3ag1142 . Lsi10g00335 . Chy11g00416 . . . . . . . . . . Cmo02g00426 . . . . . . Cpe05g01236 . . . . . . . Cla09g01743 Cam09g1834 Cec09g1895 Cco09g1987 . . Cre01g0676 . Csa02g01222 . Cme11g00475
Vvi3g557 . . . Bda08g01294 . Bpe12g00075 . . . Cmo11g01316 Cma02g00424 . Car02g00280 . Sed01g4040 Cpe04g00245 . Bhi05g01197 Tan02g1941 Cmetu09g0736 . . . . Cla02g00545 Cam02g0568 Cec02g0571 Cco02g0582 Clacu02g0569 Cmu02g0565 Cre02g0896 Cone12ag1137 Cone8ag1184 . . Lsi10g00336 . Chy11g00415 Cme01g01471 . . Bda15g00851 Bda14g00540 Bpe15g00876 . Bma03g00542 . . Cmo02g00425 . . . Car11g01060 . . Cpe05g01237 . . . . . . . Cla09g01744 Cam09g1835 Cec09g1896 Cco09g1988 . . Cre01g0675 Lsi11g01070 Csa02g01223 Chy01g00822 Cme11g00474
Vvi3g558 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g559 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g560 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g561 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g562 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g563 . . . . . . . . Cmo19g00661 . . . . . . . Cpe15g00525 Bhi05g01201 . . . . . . Cla02g00543 . . . . . . . . . . . Csa07g00783 . Cme01g01469 . . . Bda14g00541 . . . . . . Cmo16g00372 . Cma19g00651 . Car19g00495 . . . . . . . . . . . . . . . . Lsi11g01072 . Chy01g00820 .
Vvi3g564 . . . Bda08g00779 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo04g00513 . . . . . Cpe14g00287 . . . . . . . . . . . . . . . . . . .
Vvi3g565 . . Bda06g00947 . . . . Bma12g00524 Cmo19g00663 Cmo11g01315 Cma02g00413 . Car02g00271 . . Cpe04g00244 Cpe15g00527 Bhi05g01211 Tan02g1972 . . . . . Cla02g00539 Cam02g0559 Cec02g0561 Cco02g0572 Clacu02g0560 Cmu02g0557 Cre02g0892 Cone12ag1139 Cone8ag1188 Cone3ag1149 Cone10ag1160 Lsi10g00350 . Chy11g00399 Cme01g01449 . . . Bda14g00542 Bpe15g00874 . . Bma08g00575 Sed14g1103 Cmo02g00417 . . Cma19g00653 Car11g01059 Car19g00496 . Cpe05g01246 Bhi10g02034 Tan05g1329 Cmetu01g1244 . Hepe08g1031 . . . . . . . . . Lsi11g01084 Csa02g01238 Chy01g00806 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 26018850 26020632 - Bda022578.1 Bda06g00947 947
6 26139457 26140780 + Bda022580.1 Bda06g00948 948
8 10499587 10501020 + Bda029290.1 Bda08g00779 779
8 52613966 52616314 + Bda030327.1 Bda08g01294 1294
14 3947382 3948270 - Bda027286.1 Bda14g00540 540
14 3953503 3958150 - Bda027287.2 Bda14g00541 541
14 3961315 3963160 + Bda027288.1 Bda14g00542 542
15 13267818 13268952 - Bda012732.1 Bda15g00851 851
5 42389883 42393518 - XM_039032558.1 Bhi05g01197 1197
5 42595815 42605422 - XM_039031224.1 Bhi05g01201 1201
5 43188064 43193386 + XM_039031777.1 Bhi05g01211 1211
10 50839367 50841493 - XM_039046125.1 Bhi10g02034 2034
15 21317889 21319227 - BLOR07082 Blo15g00688 688
3 4402289 4403177 - Bma016828.1 Bma03g00542 542
8 34100714 34102161 + Bma027846.1 Bma08g00575 575
12 18911743 18913534 - Bma007629.1 Bma12g00524 524
12 22488224 22489467 + Bma007680.1 Bma12g00546 546
7 6711947 6713272 - Bpe021292.1 Bpe07g00459 459
12 522721 523792 - Bpe005314.1 Bpe12g00075 75
15 18712503 18714368 - Bpe001796.1 Bpe15g00874 874
15 18727760 18728658 + Bpe001798.1 Bpe15g00876 876
2 6400851 6402975 - CaPI482276_02g005590.1 Cam02g0559 559
2 6484259 6485758 + CaPI482276_02g005680.1 Cam02g0568 568
9 32861500 32863147 - CaPI482276_09g018340.1 Cam09g1834 1834
9 32865415 32866739 - CaPI482276_09g018350.1 Cam09g1835 1835
2 1843195 1844939 - Carg22956-RA Car02g00271 271
2 1900419 1902800 + Carg22965-RA Car02g00280 280
2 1903515 1905421 + Carg22966-RA Car02g00281 281
11 8174800 8176523 - Carg26493-RA Car11g01059 1059
11 8187205 8189149 + Carg26492-RA Car11g01060 1060
19 6543542 6551368 - Carg22028-RA Car19g00495 495
19 6553252 6554988 + Carg22027-RA Car19g00496 496
2 5519540 5521651 - CcPI632755_02g005720.1 Cco02g0572 572
2 5638222 5641757 + CcPI632755_02g005820.1 Cco02g0582 582
9 34098970 34100558 - CcPI632755_09g019870.1 Cco09g1987 1987
9 34102820 34104142 - CcPI632755_09g019880.1 Cco09g1988 1988
2 5440304 5442424 - CePI673135_02g005610.1 Cec02g0561 561
2 5526946 5528385 + CePI673135_02g005710.1 Cec02g0571 571
9 35803931 35805550 - CePI673135_09g018950.1 Cec09g1895 1895
9 35807820 35809144 - CePI673135_09g018960.1 Cec09g1896 1896
1 6644435 6646147 - Chy1G008060.1 Chy01g00806 806
1 6833748 6835694 + Chy1G008200.1 Chy01g00820 820
1 6847975 6849849 + Chy1G008220.1 Chy01g00822 822
11 3795190 3796880 - Chy11G189790.1 Chy11g00399 399
11 3977235 3978470 + Chy11G189950.1 Chy11g00415 415
11 3980703 3982718 + Chy11G189960.1 Chy11g00416 416
2 5383203 5384921 - ClG42_02g0056000.10 Clacu02g0560 560
2 5452663 5460315 + ClG42_02g0056900.10 Clacu02g0569 569
2 5623686 5632579 - ClCG02G005200.2 Cla02g00539 539
2 5711402 5713423 + ClCG02G005230.1 Cla02g00543 543
2 5722620 5724122 + ClCG02G005250.1 Cla02g00545 545
9 34768740 34772016 - ClCG09G017790.1 Cla09g01743 1743
9 34773833 34775157 - ClCG09G017800.2 Cla09g01744 1744
2 2091817 2093860 - CmaCh02G004130.1 Cma02g00413 413
2 2146935 2148176 + CmaCh02G004240.1 Cma02g00424 424
2 2149367 2150962 + CmaCh02G004250.1 Cma02g00425 425
19 6871014 6876851 - CmaCh19G006510.1 Cma19g00651 651
19 6888361 6890230 + CmaCh19G006530.1 Cma19g00653 653
1 18707288 18709533 - MELO3C012550.2.1 Cme01g01449 1449
1 19079537 19081570 + MELO3C012561.2.1 Cme01g01469 1469
1 19086908 19091596 + MELO3C012563.2.1 Cme01g01471 1471
11 4625336 4627864 + MELO3C021945.2.1 Cme11g00474 474
11 4628628 4630524 + MELO3C021944.2.1 Cme11g00475 475
1 6725298 6729991 - PI0005159.1 Cmetu01g1244 1244
9 3384272 3388091 - PI0016941.1 Cmetu09g0736 736
2 2165307 2167288 - CmoCh02G004170.1 Cmo02g00417 417
2 2220531 2225364 + CmoCh02G004250.1 Cmo02g00425 425
2 2226842 2228910 + CmoCh02G004260.1 Cmo02g00426 426
4 2544714 2547148 + CmoCh04G005130.1 Cmo04g00513 513
11 9088130 9089912 - CmoCh11G013150.1 Cmo11g01315 1315
11 9105399 9107033 + CmoCh11G013160.1 Cmo11g01316 1316
16 1708200 1710934 + CmoCh16G003720.1 Cmo16g00372 372
19 7102099 7108101 - CmoCh19G006610.1 Cmo19g00661 661
19 7116083 7118040 + CmoCh19G006630.1 Cmo19g00663 663
2 5301393 5303111 - CmPI595203_02g005570.1 Cmu02g0557 557
2 5370892 5378549 + CmPI595203_02g005650.1 Cmu02g0565 565
3 29991921 29993347 - Conep03aG0164700.1 Cone3ag1142 1142
3 30119793 30122386 + Conep03aG0165400.1 Cone3ag1149 1149
8 10156323 10157312 - Conep08aG0121800.1 Cone8ag1184 1184
8 10164185 10165967 + Conep08aG0122200.1 Cone8ag1188 1188
10 8412467 8414313 + Conep10aG0119400.1 Cone10ag1160 1160
12 9117853 9119146 - Conep12aG0117300.1 Cone12ag1137 1137
12 9122875 9125017 + Conep12aG0117500.1 Cone12ag1139 1139
4 3048187 3049906 - Cp4.1LG04g08390.1 Cpe04g00244 244
4 3067201 3070056 + Cp4.1LG04g08440.1 Cpe04g00245 245
5 8660123 8662029 - Cp4.1LG05g12470.1 Cpe05g01236 1236
5 8663388 8666809 - Cp4.1LG05g12440.1 Cpe05g01237 1237
5 8722239 8724272 + Cp4.1LG05g12370.1 Cpe05g01246 1246
14 1681202 1687366 + Cp4.1LG14g04300.1 Cpe14g00287 287
15 6156331 6158225 - Cp4.1LG15g05270.1 Cpe15g00525 525
15 6165843 6167705 + Cp4.1LG15g05150.1 Cpe15g00527 527
1 6209579 6210903 + CrPI670011_01g006750.1 Cre01g0675 675
1 6213172 6214821 + CrPI670011_01g006760.1 Cre01g0676 676
2 5930758 5939024 - CrPI670011_02g008920.1 Cre02g0892 892
2 5969119 5976727 + CrPI670011_02g008960.1 Cre02g0896 896
2 12007262 12009886 - CsaV3_2G014380.1 Csa02g01222 1222
2 12010900 12015251 - CsaV3_2G014390.1 Csa02g01223 1223
2 12128642 12130681 + CsaV3_2G014540.1 Csa02g01238 1238
7 5499742 5503239 - CsaV3_7G008820.1 Csa07g00783 783
8 9923791 9925448 - Hsped.08g10310.1 Hepe08g1031 1031
10 5308577 5313479 - Lsi10G003350.1 Lsi10g00335 335
10 5314846 5318535 - Lsi10G003360.1 Lsi10g00336 336
10 5475652 5477901 + Lsi10G003500.1 Lsi10g00350 350
11 18685615 18689274 - Lsi11G010700.1 Lsi11g01070 1070
11 18696136 18698157 - Lsi11G010720.1 Lsi11g01072 1072
11 18917937 18921643 + Lsi11G010840.1 Lsi11g01084 1084
1 69411667 69416451 - Sed0003589.3 Sed01g4040 4040
14 20515451 20517653 + Sed0022643.1 Sed14g1103 1103
2 87993150 87998192 - Tan0006400.1 Tan02g1941 1941
2 88438543 88445211 - Tan0018783.3 Tan02g1972 1972
5 17007201 17009547 - Tan0019842.1 Tan05g1329 1329
3 5411011 5414145 - Vvi3g556 Vvi3g556 556
3 5419478 5421579 - Vvi3g557 Vvi3g557 557
3 5429004 5431152 + Vvi3g558 Vvi3g558 558
3 5433669 5437872 - Vvi3g559 Vvi3g559 559
3 5438362 5441985 + Vvi3g560 Vvi3g560 560
3 5445685 5454159 - Vvi3g561 Vvi3g561 561
3 5454208 5461137 - Vvi3g562 Vvi3g562 562
3 5462189 5464132 - Vvi3g563 Vvi3g563 563
3 5469493 5470726 - Vvi3g564 Vvi3g564 564
3 5487804 5489892 + Vvi3g565 Vvi3g565 565
       

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