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
Vvi3g586 Blo02g00802 . . Bda08g00928 . . Bma05g00467 . Cmo19g00676 . Cma02g00403 . Car02g00263 Car20g00737 Sed04g3936 . Cpe15g00536 Bhi05g01226 Tan02g0805 Cmetu01g2256 . Hepe02g0512 . . Cla02g00526 Cam02g0544 Cec02g0545 Cco02g0551 Clacu02g0545 Cmu02g0540 Cre02g0871 . . Cone3ag1160 Cone10ag1168 Lsi10g00362 . Chy11g00386 Cme01g01427 . . . . . . . . Sed01g0307 Cmo02g00408 Cmo20g00863 . Cma19g00662 . Car19g00505 . Cpe05g01254 Bhi10g02018 Tan05g1316 Cmetu11g1598 . Hepe08g1021 . . . . . . . . . Lsi11g01099 Csa02g01251 Chy01g00792 .
Vvi3g587 . . . . . . . . Cmo19g00677 . . . . . . Cpe04g00123 Cpe15g00537 Bhi05g01227 . . . . . . Cla02g00525 . . . . . . Cone12ag1149 Cone8ag1197 Cone3ag1161 Cone10ag1169 . . . Cme01g01426 . Blo13g00554 . Bda14g01440 . . Bma03g01344 . . . . . Cma19g00663 . Car19g00506 . . . . . . . . . . . . . . . . Lsi11g01100 . Chy01g00791 .
Vvi3g588 . . . . . . . . Cmo19g00678 . . . . . Sed05g2319 Cpe04g00122 Cpe15g00538 Bhi05g01228 Tan02g0802 Cmetu01g1049 . Hepe02g0510 . . Cla02g00524 Cam02g0542 Cec02g0543 Cco02g0549 Clacu02g0543 Cmu02g0538 Cre02g0869 Cone12ag1150 Cone8ag1198 . . . . . Cme01g01424 Blo04g00510 . . Bda14g00551 Bpe15g00869 . Bma03g00550 . . . . . Cma19g00664 . Car19g00507 . . . . . . . . . . . . . . . . Lsi11g01101 . Chy01g00790 .
Vvi3g589 Blo02g00954 . Bda06g00942 Bda08g01289 . . Bma05g00463 . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag1199 . Cone10ag1170 . . . . . . . . . Bpe05g00497 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g590 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g591 . . . . . . . . Cmo19g00680 . . . . . Sed04g3932 Cpe04g00120 Cpe15g00540 Bhi05g01230 Tan02g0799 Cmetu01g2454 . Hepe02g0508 . . Cla02g00522 Cam02g0540 . Cco02g0547 Clacu02g0541 Cmu02g0536 Cre02g0867 Cone12ag1151 Cone8ag1201 . . . . . Cme01g01422 . . . . Bpe15g00868 . . . . . . . Cma19g00666 . Car19g00509 . . . . . . . . . . . . . . . . Lsi11g01103 . Chy01g00788 .
Vvi3g592 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma03g01396 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g593 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g594 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone10ag1172 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g595 . . . . . . . . . . . . . . . . Cpe15g00541 Bhi05g01232 . . . . . . Cla02g00521 Cam02g0538 Cec02g0541 Cco02g0546 Clacu02g0539 Cmu02g0534 Cre02g0866 Cone12ag1152 . . . . . . Cme01g01421 Blo04g00511 . . Bda14g00552 Bpe15g00867 . Bma03g00551 . . . . . Cma19g00667 . Car19g00510 . . . . . . . . . . . . . . . . Lsi11g01104 . Chy01g00786 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 25632113 25633092 + Bda022572.1 Bda06g00942 942
8 17101098 17104916 - Bda029561.2 Bda08g00928 928
8 52420639 52421945 + Bda030315.1 Bda08g01289 1289
14 4039311 4041935 + Bda027297.1 Bda14g00551 551
14 4049291 4052335 - Bda033939 Bda14g00552 552
14 18817693 18819965 + Bda011175.2 Bda14g01440 1440
5 43912665 43917226 - XM_039032679.1 Bhi05g01226 1226
5 43928455 43935023 - XM_039033140.1 Bhi05g01227 1227
5 43978002 43980950 + XM_039031875.1 Bhi05g01228 1228
5 43987495 43991429 + XM_039031847.1 Bhi05g01230 1230
5 43992365 43997145 - XM_039031845.1 Bhi05g01232 1232
10 50541002 50545791 + XM_039046093.1 Bhi10g02018 2018
2 27325824 27329913 - BLOR10532 Blo02g00802 802
2 36967719 36971530 - BLOR10684 Blo02g00954 954
4 4328789 4336181 + BLOR13422 Blo04g00510 510
4 4336074 4344483 - BLOR13423 Blo04g00511 511
13 27519862 27522067 + BLOR05835 Blo13g00554 554
3 4519033 4521661 + Bma016836.1 Bma03g00550 550
3 4526020 4533889 - Bma016837.3 Bma03g00551 551
3 28445738 28448014 - Bma017871.1 Bma03g01344 1344
3 35051588 35063087 - Bma017990.2 Bma03g01396 1396
5 15903408 15904869 + Bma021330.1 Bma05g00463 463
5 16437755 16442978 + Bma021342.1 Bma05g00467 467
5 19173312 19177095 - Bpe017917.1 Bpe05g00497 497
15 18632310 18640735 + Bpe001790.1 Bpe15g00867 867
15 18640631 18643577 - Bpe024585 Bpe15g00868 868
15 18645232 18647857 - Bpe001791.1 Bpe15g00869 869
2 6165808 6170374 + CaPI482276_02g005380.1 Cam02g0538 538
2 6172156 6175402 - CaPI482276_02g005400.1 Cam02g0540 540
2 6183243 6186070 - CaPI482276_02g005420.1 Cam02g0542 542
2 6212729 6216293 + CaPI482276_02g005440.1 Cam02g0544 544
2 1786885 1792414 + Carg22948-RA Car02g00263 263
19 6718521 6723581 - Carg19415-RA Car19g00505 505
19 6726105 6729664 - Carg19414-RA Car19g00506 506
19 6736137 6739538 + Carg19413-RA Car19g00507 507
19 6743172 6746717 + Carg19411-RA Car19g00509 509
19 6746795 6751361 - Carg19410-RA Car19g00510 510
20 4318115 4323353 + Carg27533-RA Car20g00737 737
2 5211573 5216487 + CcPI632755_02g005460.1 Cco02g0546 546
2 5218022 5222638 - CcPI632755_02g005470.1 Cco02g0547 547
2 5227069 5229673 - CcPI632755_02g005490.1 Cco02g0549 549
2 5262957 5266521 + CcPI632755_02g005510.1 Cco02g0551 551
2 5186130 5191989 + CePI673135_02g005410.1 Cec02g0541 541
2 5201318 5204144 - CePI673135_02g005430.1 Cec02g0543 543
2 5231000 5234572 + CePI673135_02g005450.1 Cec02g0545 545
1 6311761 6315944 + Chy1G007860.1 Chy01g00786 786
1 6318676 6321839 - Chy1G007880.1 Chy01g00788 788
1 6326721 6329173 - Chy1G007900.1 Chy01g00790 790
1 6342088 6345841 + Chy1G007910.1 Chy01g00791 791
1 6357407 6361417 + Chy1G007920.1 Chy01g00792 792
11 3652131 3656168 + Chy11G189660.1 Chy11g00386 386
2 5126598 5131455 + ClG42_02g0053900.10 Clacu02g0539 539
2 5132930 5136238 - ClG42_02g0054100.10 Clacu02g0541 541
2 5141885 5144710 - ClG42_02g0054300.10 Clacu02g0543 543
2 5173660 5177231 + ClG42_02g0054500.10 Clacu02g0545 545
2 5368052 5375604 + ClCG02G005000.1 Cla02g00521 521
2 5376459 5380176 - ClCG02G005010.1 Cla02g00522 522
2 5386712 5389869 - ClCG02G005030.1 Cla02g00524 524
2 5408472 5412485 + ClCG02G005040.1 Cla02g00525 525
2 5418688 5422614 + ClCG02G005050.2 Cla02g00526 526
2 2032625 2038552 + CmaCh02G004030.1 Cma02g00403 403
19 6963248 6966883 - CmaCh19G006620.1 Cma19g00662 662
19 6968966 6972916 - CmaCh19G006630.1 Cma19g00663 663
19 6979507 6982929 + CmaCh19G006640.1 Cma19g00664 664
19 6986629 6990172 + CmaCh19G006660.1 Cma19g00666 666
19 6990266 6994663 - CmaCh19G006670.1 Cma19g00667 667
1 18088954 18095204 + MELO3C012521.2.1 Cme01g01421 1421
1 18096298 18099939 - MELO3C012522.2.1 Cme01g01422 1422
1 18105116 18108126 - MELO3C012524.2.1 Cme01g01424 1424
1 18142257 18146922 + MELO3C012525.2.1 Cme01g01426 1426
1 18158366 18161737 + MELO3C012526.2.1 Cme01g01427 1427
1 6334601 6338250 - PI0004172.1 Cmetu01g1049 1049
1 6375469 6379671 + PI0007501.1 Cmetu01g2256 2256
1 6327202 6330410 - PI0015817.1 Cmetu01g2454 2454
11 27376528 27381435 - PI0015663.2 Cmetu11g1598 1598
2 2102040 2107529 + CmoCh02G004080.1 Cmo02g00408 408
19 7194325 7199275 - CmoCh19G006760.1 Cmo19g00676 676
19 7201711 7205623 - CmoCh19G006770.1 Cmo19g00677 677
19 7212772 7216149 + CmoCh19G006780.1 Cmo19g00678 678
19 7220019 7223458 + CmoCh19G006800.1 Cmo19g00680 680
20 4354772 4361194 + CmoCh20G008630.1 Cmo20g00863 863
2 5045282 5050170 + CmPI595203_02g005340.1 Cmu02g0534 534
2 5051645 5054970 - CmPI595203_02g005360.1 Cmu02g0536 536
2 5060624 5063451 - CmPI595203_02g005380.1 Cmu02g0538 538
2 5092445 5096016 + CmPI595203_02g005400.1 Cmu02g0540 540
3 30249593 30253634 - Conep03aG0166500.1 Cone3ag1160 1160
3 30254998 30257640 - Conep03aG0166600.1 Cone3ag1161 1161
8 10205338 10208006 - Conep08aG0123200.1 Cone8ag1197 1197
8 10209436 10211288 + Conep08aG0123300.1 Cone8ag1198 1198
8 10211443 10212615 - Conep08aG0123400.1 Cone8ag1199 1199
8 10215446 10217599 + Conep08aG0123600.1 Cone8ag1201 1201
10 8495131 8499661 - Conep10aG0120200.1 Cone10ag1168 1168
10 8511197 8514229 - Conep10aG0120300.1 Cone10ag1169 1169
10 8514707 8516470 - Conep10aG0120400.1 Cone10ag1170 1170
10 8526742 8528296 + Conep10aG0120600.1 Cone10ag1172 1172
12 9172547 9174874 - Conep12aG0118600.1 Cone12ag1149 1149
12 9176568 9178434 + Conep12aG0118700.1 Cone12ag1150 1150
12 9182512 9184554 + Conep12aG0118800.1 Cone12ag1151 1151
12 9185184 9187743 - Conep12aG0118900.1 Cone12ag1152 1152
4 1099728 1103153 - Cp4.1LG04g00920.1 Cpe04g00120 120
4 1105297 1108078 - Cp4.1LG04g00890.1 Cpe04g00122 122
4 1113601 1117623 + Cp4.1LG04g00970.1 Cpe04g00123 123
5 8777685 8783360 - Cp4.1LG05g12600.1 Cpe05g01254 1254
15 6241926 6246955 - Cp4.1LG15g05370.1 Cpe15g00536 536
15 6249056 6253099 - Cp4.1LG15g05380.1 Cpe15g00537 537
15 6259372 6263176 + Cp4.1LG15g05310.1 Cpe15g00538 538
15 6266582 6270795 + Cp4.1LG15g05410.1 Cpe15g00540 540
15 6269462 6274694 - Cp4.1LG15g05500.1 Cpe15g00541 541
2 5615452 5620799 + CrPI670011_02g008660.1 Cre02g0866 866
2 5621836 5625111 - CrPI670011_02g008670.1 Cre02g0867 867
2 5630929 5633758 - CrPI670011_02g008690.1 Cre02g0869 869
2 5662945 5666517 + CrPI670011_02g008710.1 Cre02g0871 871
2 12250349 12255563 - CsaV3_2G014670.1 Csa02g01251 1251
2 5097348 5101462 - Hsped.02g05080.1 Hepe02g0508 508
2 5105638 5109028 - Hsped.02g05100.1 Hepe02g0510 510
2 5129712 5134597 + Hsped.02g05120.1 Hepe02g0512 512
8 9795474 9800561 + Hsped.08g10210.1 Hepe08g1021 1021
10 5613569 5617611 - Lsi10G003620.1 Lsi10g00362 362
11 19120698 19125104 - Lsi11G010990.1 Lsi11g01099 1099
11 19137663 19141825 - Lsi11G011000.1 Lsi11g01100 1100
11 19164874 19168130 + Lsi11G011010.1 Lsi11g01101 1101
11 19176932 19182112 + Lsi11G011030.1 Lsi11g01103 1103
11 19182980 19188327 - Lsi11G011040.1 Lsi11g01104 1104
1 2343396 2349922 + Sed0023087.1 Sed01g0307 307
4 47404074 47408290 - Sed0011539.2 Sed04g3932 3932
4 47443638 47447403 + Sed0027089.1 Sed04g3936 3936
5 35660581 35663303 - Sed0022084.1 Sed05g2319 2319
2 8106405 8109976 - Tan0013771.1 Tan02g0799 799
2 8116654 8119803 - Tan0018947.1 Tan02g0802 802
2 8171862 8176550 + Tan0017515.1 Tan02g0805 805
5 16348837 16353371 + Tan0014223.1 Tan05g1316 1316
3 5725985 5735086 - Vvi3g586 Vvi3g586 586
3 5738844 5760758 - Vvi3g587 Vvi3g587 587
3 5760787 5767481 + Vvi3g588 Vvi3g588 588
3 5768048 5770485 - Vvi3g589 Vvi3g589 589
3 5779676 5782836 - Vvi3g590 Vvi3g590 590
3 5783039 5789875 + Vvi3g591 Vvi3g591 591
3 5790696 5798203 + Vvi3g592 Vvi3g592 592
3 5798733 5801287 + Vvi3g593 Vvi3g593 593
3 5801292 5802070 + Vvi3g594 Vvi3g594 594
3 5802833 5807050 - Vvi3g595 Vvi3g595 595
       

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