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
Vvi3g56 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g57 . . . . . Bpe12g00099 . . Cmo19g00713 . . . . . . Cpe04g00094 Cpe15g00569 Bhi05g01774 . . . Hepe02g0459 . . Cla02g00475 Cam02g0482 Cec02g0484 Cco02g0489 Clacu02g0485 Cmu02g0480 Cre02g0815 Cone12ag1197 Cone8ag1245 . . . Csa07g00052 . Cme01g01319 Blo04g00544 Blo13g00530 Bda15g01060 Bda14g00583 Bpe15g00837 . Bma03g00577 Bma08g00776 . . . . Cma19g00704 . . . . . . . . . . . . . . . . . . Lsi11g01151 . Chy01g00730 .
Vvi3g58 . . . . . . . . Cmo19g00714 . . . . . Sed05g2278 . Cpe15g00570 Bhi05g01772 Tan02g0739 Cmetu01g1464 . Hepe02g0458 . . Cla02g00473 Cam02g0479 Cec02g0481 Cco02g0486 Clacu02g0483 Cmu02g0478 Cre02g0813 Cone12ag1198 . . . . Csa07g00053 . Cme01g01317 Blo04g00545 . . Bda14g00584 Bpe15g00836 . Bma03g00578 . . . . . Cma19g00705 . Car19g00544 . . . . . . . . . . . . . . . . Lsi11g01152 . Chy01g00729 .
Vvi3g59 Blo02g00658 . . Bda08g00971 . . Bma05g00406 . . . Cma02g00358 Cma20g00802 Car02g00225 Car20g00687 . . . . . . . . . . . . . . . . . Cone12ag1199 Cone8ag1246 Cone3ag1203 . Lsi10g00425 . Chy11g00327 . . . . . . . . . Sed01g0252 Cmo02g00360 Cmo20g00810 . . . . Cpe16g00281 Cpe05g01298 Bhi10g01929 Tan05g1228 Cmetu11g1361 . Hepe08g0964 . . . . . . . . . . Csa02g01318 . Cme11g00452
Vvi3g60 . . . . . . . . . . Cma02g00357 . Car02g00224 . . . . . . . . . . . . . . . . . . . . . . Lsi10g00426 . Chy11g00326 . . . . . . . . . Sed01g0251 Cmo02g00359 . . . . . . Cpe05g01299 Bhi10g01928 Tan05g1227 Cmetu11g1309 . Hepe08g0963 . . . . . . . . . . Csa02g01320 . Cme11g00451
Vvi3g61 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g62 . . . . . Bpe12g00100 . . Cmo19g00716 . Cma02g00356 Cma20g00800 Car02g00223 Car20g00684 Sed05g2274 . . Bhi05g01769 Tan02g0737 Cmetu01g1255 . Hepe02g0456 . . Cla02g00471 Cam02g0478 Cec02g0479 Cco02g0485 Clacu02g0482 Cmu02g0477 Cre02g0810 . . . . Lsi10g00427 Csa07g00056 Chy11g00325 Cme01g01314 . . Bda15g01059 Bda14g00585 Bpe15g00835 . Bma03g00579 Bma08g00775 Sed01g0250 Cmo02g00358 Cmo20g00808 . Cma19g00707 . Car19g00545 Cpe16g00283 Cpe05g01300 Bhi10g01927 Tan05g1225 Cmetu11g1460 . Hepe08g0962 . . . . . . . . . Lsi11g01154 Csa02g01321 Chy01g00725 Cme11g00450
Vvi3g63 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g64 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g65 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 19194029 19195600 + Bda029638.1 Bda08g00971 971
14 4466701 4468825 + Bda027335.1 Bda14g00583 583
14 4469707 4474243 + Bda027336.1 Bda14g00584 584
14 4479893 4480342 + Bda027337.1 Bda14g00585 585
15 19706294 19706743 - Bda013050.1 Bda15g01059 1059
15 19727057 19729228 - Bda013052.1 Bda15g01060 1060
5 56464128 56465100 - XM_039032482.1 Bhi05g01769 1769
5 56528248 56532280 - XM_039032736.1 Bhi05g01772 1772
5 56537548 56541372 - XM_039032219.1 Bhi05g01774 1774
10 47964149 47965081 - XM_039046109.1 Bhi10g01927 1927
10 48030079 48035107 + XM_039044614.1 Bhi10g01928 1928
10 48149806 48151858 + XM_039046241.1 Bhi10g01929 1929
2 16665004 16666584 + BLOR10388 Blo02g00658 658
4 4689415 4691378 + BLOR13456 Blo04g00544 544
4 4692209 4697399 + BLOR13457 Blo04g00545 545
13 27072180 27082852 - BLOR05811 Blo13g00530 530
3 4824891 4826990 + Bma016867.1 Bma03g00577 577
3 4829279 4834080 + Bma016868.1 Bma03g00578 578
3 4835449 4835907 + Bma016869.1 Bma03g00579 579
5 12793507 12795261 + Bma021239.1 Bma05g00406 406
8 45079638 45080087 - Bma028156.1 Bma08g00775 775
8 45085860 45087433 - Bma028157.1 Bma08g00776 776
12 711243 713412 + Bpe005339.2 Bpe12g00099 99
12 722603 723052 + Bpe005340.1 Bpe12g00100 100
15 18410126 18410578 - Bpe001759.1 Bpe15g00835 835
15 18412153 18416881 - Bpe001760.1 Bpe15g00836 836
15 18417720 18419826 - Bpe001761.1 Bpe15g00837 837
2 5418765 5419223 - CaPI482276_02g004780.1 Cam02g0478 478
2 5449989 5455588 - CaPI482276_02g004790.1 Cam02g0479 479
2 5474120 5477932 - CaPI482276_02g004820.1 Cam02g0482 482
2 1451573 1452031 - Carg27204-RA Car02g00223 223
2 1455141 1458512 + Carg27203-RA Car02g00224 224
2 1466293 1468020 + Carg27202-RA Car02g00225 225
19 6984124 6989713 + Carg19376-RA Car19g00544 544
19 7003587 7004039 + Carg19375-RA Car19g00545 545
20 3920385 3920831 - Carg25962-RA Car20g00684 684
20 3930199 3930999 + Carg25959-RA Car20g00687 687
2 4452922 4453380 - CcPI632755_02g004850.1 Cco02g0485 485
2 4480721 4486319 - CcPI632755_02g004860.1 Cco02g0486 486
2 4504526 4508326 - CcPI632755_02g004890.1 Cco02g0489 489
2 4449222 4449680 - CePI673135_02g004790.1 Cec02g0479 479
2 4476454 4481972 - CePI673135_02g004810.1 Cec02g0481 481
2 4505122 4508941 - CePI673135_02g004840.1 Cec02g0484 484
1 5277764 5278219 - Chy1G007250.1 Chy01g00725 725
1 5305411 5310575 - Chy1G007290.1 Chy01g00729 729
1 5316807 5332218 - Chy1G007300.1 Chy01g00730 730
11 2886823 2887476 - Chy11G189050.1 Chy11g00325 325
11 2896403 2898937 + Chy11G189060.1 Chy11g00326 326
11 2911218 2912951 + Chy11G189070.1 Chy11g00327 327
2 4295464 4295922 - ClG42_02g0048200.10 Clacu02g0482 482
2 4322830 4328424 - ClG42_02g0048300.10 Clacu02g0483 483
2 4346630 4350434 - ClG42_02g0048500.10 Clacu02g0485 485
2 4562111 4562615 - ClCG02G004420.1 Cla02g00471 471
2 4589126 4595127 - ClCG02G004440.1 Cla02g00473 473
2 4615232 4619655 - ClCG02G004460.1 Cla02g00475 475
2 1739187 1739645 - CmaCh02G003560.1 Cma02g00356 356
2 1743194 1746708 + CmaCh02G003570.1 Cma02g00357 357
2 1757120 1758841 + CmaCh02G003580.1 Cma02g00358 358
19 7204892 7208271 + CmaCh19G007040.1 Cma19g00704 704
19 7209539 7214983 + CmaCh19G007050.1 Cma19g00705 705
19 7228844 7229296 + CmaCh19G007070.1 Cma19g00707 707
20 3759823 3760269 - CmaCh20G008000.1 Cma20g00800 800
20 3768516 3770261 + CmaCh20G008020.1 Cma20g00802 802
1 16480066 16480867 - MELO3C013403.2.1 Cme01g01314 1314
1 16517920 16529284 - MELO3C013406.2.1 Cme01g01317 1317
1 16542908 16547543 - MELO3C013408.2.1 Cme01g01319 1319
11 4392377 4393242 + MELO3C020751.2.1 Cme11g00450 450
11 4404543 4408505 + MELO3C020750.2.1 Cme11g00451 451
11 4421323 4423332 + MELO3C020749.2.1 Cme11g00452 452
1 5583033 5583755 - PI0005568.1 Cmetu01g1255 1255
1 5613743 5619829 - PI0008652.1 Cmetu01g1464 1464
11 28054103 28056822 - PI0001663.1 Cmetu11g1309 1309
11 28037508 28039769 - PI0009733.1 Cmetu11g1361 1361
11 28069583 28070658 + PI0025553.1 Cmetu11g1460 1460
2 1804316 1804774 - CmoCh02G003580.1 Cmo02g00358 358
2 1807861 1812160 + CmoCh02G003590.1 Cmo02g00359 359
2 1816130 1817857 + CmoCh02G003600.1 Cmo02g00360 360
19 7466810 7470189 + CmoCh19G007130.1 Cmo19g00713 713
19 7471605 7477236 + CmoCh19G007140.1 Cmo19g00714 714
19 7493864 7494316 + CmoCh19G007160.1 Cmo19g00716 716
20 3991241 3991687 - CmoCh20G008080.1 Cmo20g00808 808
20 4003731 4005467 + CmoCh20G008100.1 Cmo20g00810 810
2 4291282 4291740 - CmPI595203_02g004770.1 Cmu02g0477 477
2 4318667 4324262 - CmPI595203_02g004780.1 Cmu02g0478 478
2 4342490 4346294 - CmPI595203_02g004800.1 Cmu02g0480 480
3 30752029 30755275 + Conep03aG0171000.1 Cone3ag1203 1203
8 10426305 10429297 + Conep08aG0128300.1 Cone8ag1245 1245
8 10429512 10431469 - Conep08aG0128400.1 Cone8ag1246 1246
12 9407322 9410375 + Conep12aG0123700.1 Cone12ag1197 1197
12 9410983 9414533 + Conep12aG0123800.1 Cone12ag1198 1198
12 9414783 9416783 - Conep12aG0123900.1 Cone12ag1199 1199
4 857097 867646 - Cp4.1LG04g01140.1 Cpe04g00094 94
5 9060532 9062259 - Cp4.1LG05g13010.1 Cpe05g01298 1298
5 9067083 9070368 - Cp4.1LG05g13030.1 Cpe05g01299 1299
5 9073617 9074075 + Cp4.1LG05g12980.1 Cpe05g01300 1300
15 6498133 6509599 + Cp4.1LG15g05670.1 Cpe15g00569 569
15 6510901 6516630 + Cp4.1LG15g05660.1 Cpe15g00570 570
16 4804185 4805930 - Cp4.1LG16g02790.1 Cpe16g00281 281
16 4814742 4815188 + Cp4.1LG16g02710.1 Cpe16g00283 283
2 4872610 4873068 - CrPI670011_02g008100.1 Cre02g0810 810
2 4909505 4915094 - CrPI670011_02g008130.1 Cre02g0813 813
2 4933479 4937259 - CrPI670011_02g008150.1 Cre02g0815 815
2 12806892 12809868 - CsaV3_2G015340.1 Csa02g01318 1318
2 12835919 12838502 - CsaV3_2G015360.1 Csa02g01320 1320
2 12856450 12857096 + CsaV3_2G015370.1 Csa02g01321 1321
7 584738 588713 + CsaV3_7G000520.1 Csa07g00052 52
7 592559 598379 + CsaV3_7G000530.1 Csa07g00053 53
7 620914 622093 + CsaV3_7G000560.1 Csa07g00056 56
2 4472477 4472935 - Hsped.02g04560.1 Hepe02g0456 456
2 4493346 4498961 - Hsped.02g04580.1 Hepe02g0458 458
2 4502107 4506008 - Hsped.02g04590.1 Hepe02g0459 459
8 8989817 8990623 - Hsped.08g09620.1 Hepe08g0962 962
8 9002257 9005229 + Hsped.08g09630.1 Hepe08g0963 963
8 9022249 9024492 + Hsped.08g09640.1 Hepe08g0964 964
10 6445421 6447145 - Lsi10G004250.1 Lsi10g00425 425
10 6466865 6472469 - Lsi10G004260.1 Lsi10g00426 426
10 6487662 6488366 + Lsi10G004270.1 Lsi10g00427 427
11 20041618 20044762 + Lsi11G011510.1 Lsi11g01151 1151
11 20048558 20054892 + Lsi11G011520.1 Lsi11g01152 1152
11 20083224 20083682 + Lsi11G011540.1 Lsi11g01154 1154
1 1946938 1947895 - Sed0008108.1 Sed01g0250 250
1 1956261 1959531 + Sed0014045.1 Sed01g0251 251
1 1970613 1972551 + Sed0025344.1 Sed01g0252 252
5 35337147 35337923 - Sed0006369.1 Sed05g2274 2274
5 35354288 35358544 - Sed0001411.1 Sed05g2278 2278
2 6895292 6895967 - Tan0015592.1 Tan02g0737 737
2 6941952 6947465 - Tan0010392.1 Tan02g0739 739
5 12188271 12189047 - Tan0014696.1 Tan05g1225 1225
5 12323878 12327876 + Tan0018642.2 Tan05g1227 1227
5 12393589 12395841 + Tan0022853.1 Tan05g1228 1228
3 689246 690081 + Vvi3g56 Vvi3g56 56
3 690084 693321 + Vvi3g57 Vvi3g57 57
3 694533 700837 + Vvi3g58 Vvi3g58 58
3 702192 704571 - Vvi3g59 Vvi3g59 59
3 714368 721528 - Vvi3g60 Vvi3g60 60
3 722302 732978 - Vvi3g61 Vvi3g61 61
3 736292 738636 + Vvi3g62 Vvi3g62 62
3 755205 760330 - Vvi3g63 Vvi3g63 63
3 799107 799188 + Vvi3g64 Vvi3g64 64
3 815277 815673 - Vvi3g65 Vvi3g65 65
       

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