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
Vvi3g786 . . . . . . . . . . . . . . . . . . . . . . . . Cla10g00953 Cam10g0978 Cec10g1008 Cco10g0972 Clacu10g1000 Cmu10g1782 Cre10g1156 . . . . . . . . . . . . . . . . Sed07g1152 Cmo04g00456 Cmo16g00318 . . . . Cpe14g00248 Cpe01g00382 Bhi11g01094 Tan01g0598 Cmetu07g1054 . . Mch10g0402 . . . . . . . . Lsi03g01000 . . Cme07g02217
Vvi3g787 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1052 Cone10ag1070 . . . . . . . . . . . . Sed07g1153 . Cmo16g00317 . . . . Cpe14g00247 Cpe01g00381 Bhi11g01093 Tan01g0597 Cmetu07g1866 . Hepe07g0387 Mch10g0400 . . . . . . . . . . . Cme07g02218
Vvi3g788 . Blo03g00055 Bda06g01151 . Bpe07g00296 . . Bma12g00307 . . . . . . . . . . . . . . . . Cla10g00951 Cam10g0976 Cec10g1006 Cco10g0970 Clacu10g0998 Cmu10g1780 Cre10g1154 . Cone8ag1062 . . . . . . . . . . . . . . Sed07g1154 . Cmo16g00316 . . . . Cpe14g00246 . Bhi11g01092 Tan01g0595 Cmetu07g0762 . . Mch10g0399 . . . . . . . . Lsi03g00998 . . Cme07g02220
Vvi3g789 . . . . Bpe07g00297 . . Bma12g00308 . . . . . . . . . . . . . . . . . . . . . . . Cone12ag1027 Cone8ag1061 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g790 . Blo03g00054 Bda06g01150 . . . Bma05g00637 . Cmo19g00544 Cmo11g01430 . . . . Sed10g1935 . . Bhi05g01000 Tan02g1067 Cmetu01g2331 Lac12g0135 . . . Cla02g00703 Cam02g0736 Cec02g0750 Cco02g0776 Clacu02g0746 Cmu02g0741 Cre02g1054 . . . . Lsi03g00608 Csa07g00665 . Cme01g00137 . . . . . . . . . . . . Cma19g00535 . . . . . . . . . . . . . . . . . . . . Chy01g00149 .
Vvi3g791 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g792 . Blo03g00053 Bda06g01149 . Bpe07g00298 . Bma05g00636 Bma12g00310 Cmo19g00543 . . . . . . Cpe04g00336 Cpe15g00425 . . . . . . . Cla02g00705 Cam02g0738 Cec02g0752 Cco02g0778 Clacu02g0748 Cmu02g0742 Cre02g1056 . . . . Lsi03g00618 Csa07g00664 . Cme01g00139 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy01g00150 Cme07g02221
Vvi3g793 . . Bda06g01148 . . . . . . . . . . . . . . . . . . . . . Cla02g00706 Cam02g0740 Cec02g0754 Cco02g0780 Clacu02g0749 Cmu02g0743 Cre02g1057 . . . . Lsi03g00622 Csa07g00663 . Cme01g00140 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy01g00151 .
Vvi3g794 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g795 . . Bda06g01147 . Bpe07g00299 . . Bma12g00311 Cmo19g00542 . . . . . . Cpe04g00337 Cpe15g00421 . . . . . . . Cla02g00708 Cam02g0744 Cec02g0756 Cco02g0783 Clacu02g0751 Cmu02g0745 Cre02g1060 Cone12ag1024 Cone8ag1057 . . Lsi03g00624 Csa07g00662 . Cme01g00141 . . . . . . . . . . . . Cma19g00533 . . . . . . . . . . . . . . . . . . . . Chy01g00152 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 40527291 40527770 + Bda022948.1 Bda06g01147 1147
6 40557791 40558273 + Bda022950.1 Bda06g01148 1148
6 40577781 40578260 + Bda022951.1 Bda06g01149 1149
6 40583785 40584342 + Bda022952.1 Bda06g01150 1150
6 40597037 40598367 - Bda022953.1 Bda06g01151 1151
5 35317737 35318389 + XM_039032920.1 Bhi05g01000 1000
11 32089717 32092151 - XM_039049474.1 Bhi11g01092 1092
11 32097598 32101453 + XM_039048864.1 Bhi11g01093 1093
11 32112925 32114899 - XM_039050284.1 Bhi11g01094 1094
3 2021369 2028670 + BLOR11234 Blo03g00053 53
3 2086575 2087042 + BLOR11235 Blo03g00054 54
3 2138676 2144192 - BLOR11236 Blo03g00055 55
5 37346105 37346593 + Bma021668.1 Bma05g00636 636
5 37349998 37350477 + Bma021669.1 Bma05g00637 637
12 4339555 4340962 + Bma007214.1 Bma12g00307 307
12 4342597 4343951 + Bma007215.1 Bma12g00308 308
12 4402042 4402518 - Bma007218.1 Bma12g00310 310
12 4416014 4416481 - Bma007219.1 Bma12g00311 311
7 2150889 2152289 + Bpe021106.1 Bpe07g00296 296
7 2154219 2155031 + Bpe021107.1 Bpe07g00297 297
7 2161089 2161556 - Bpe021108.1 Bpe07g00298 298
7 2166138 2166605 - Bpe021109.1 Bpe07g00299 299
2 8974834 8975325 - CaPI482276_02g007360.1 Cam02g0736 736
2 9002954 9003454 + CaPI482276_02g007380.1 Cam02g0738 738
2 9007795 9008295 + CaPI482276_02g007400.1 Cam02g0740 740
2 9017482 9017982 + CaPI482276_02g007440.1 Cam02g0744 744
10 21838072 21840037 - CaPI482276_10g009760.1 Cam10g0976 976
10 21851177 21852691 - CaPI482276_10g009780.1 Cam10g0978 978
2 8325596 8326084 - CcPI632755_02g007760.1 Cco02g0776 776
2 8379587 8383315 + CcPI632755_02g007780.1 Cco02g0778 778
2 8410083 8410505 - CcPI632755_02g007800.1 Cco02g0780 780
2 8438490 8438978 - CcPI632755_02g007830.1 Cco02g0783 783
10 21010914 21013357 - CcPI632755_10g009700.1 Cco10g0970 970
10 21024753 21026267 - CcPI632755_10g009720.1 Cco10g0972 972
2 8252355 8252846 - CePI673135_02g007500.1 Cec02g0750 750
2 8308119 8308850 + CePI673135_02g007520.1 Cec02g0752 752
2 8321960 8322448 - CePI673135_02g007540.1 Cec02g0754 754
2 8357603 8358214 - CePI673135_02g007560.1 Cec02g0756 756
10 22701180 22703617 - CePI673135_10g010060.1 Cec10g1006 1006
10 22714723 22716232 - CePI673135_10g010080.1 Cec10g1008 1008
1 1030655 1032527 - Chy1G001490.1 Chy01g00149 149
1 1035597 1042130 - Chy1G001500.1 Chy01g00150 150
1 1042178 1044131 + Chy1G001510.1 Chy01g00151 151
1 1045498 1048769 - Chy1G001520.1 Chy01g00152 152
2 7941757 7942248 - ClG42_02g0074600.10 Clacu02g0746 746
2 7971687 7972178 - ClG42_02g0074800.10 Clacu02g0748 748
2 7991807 7992538 + ClG42_02g0074900.10 Clacu02g0749 749
2 8009253 8009741 - ClG42_02g0075100.10 Clacu02g0751 751
10 21472488 21474445 - ClG42_10g0099800.10 Clacu10g0998 998
10 21485376 21486890 - ClG42_10g0100000.10 Clacu10g1000 1000
2 8309794 8310285 - ClCG02G007190.1 Cla02g00703 703
2 8340033 8340524 - ClCG02G007210.1 Cla02g00705 705
2 8362468 8363279 + ClCG02G007220.2 Cla02g00706 706
2 8393294 8393782 - ClCG02G007240.1 Cla02g00708 708
10 22457685 22459642 - ClCG10G009910.1 Cla10g00951 951
10 22471343 22472857 - ClCG10G009930.1 Cla10g00953 953
19 6152535 6153026 + CmaCh19G005330.1 Cma19g00533 533
19 6163481 6163999 + CmaCh19G005350.1 Cma19g00535 535
1 1010602 1011238 - MELO3C018536.2.1 Cme01g00137 137
1 1020103 1020594 - MELO3C018538.2.1 Cme01g00139 139
1 1023454 1024330 - MELO3C018539.2.1 Cme01g00140 140
1 1030810 1031348 + MELO3C018540.2.1 Cme01g00141 141
7 26373892 26375993 + MELO3C018031.2.1 Cme07g02217 2217
7 26376713 26380464 - MELO3C018032.2.1 Cme07g02218 2218
7 26383224 26385502 + MELO3C018033.2.1 Cme07g02220 2220
7 26387904 26388407 - MELO3C018034.2.1 Cme07g02221 2221
1 1188126 1189026 + PI0024341.1 Cmetu01g2331 2331
7 205632 208033 - PI0006724.1 Cmetu07g0762 762
7 216881 218738 - PI0000183.1 Cmetu07g1054 1054
7 212209 216177 + PI0018011.1 Cmetu07g1866 1866
4 2263415 2265377 - CmoCh04G004560.1 Cmo04g00456 456
11 10067116 10067553 - CmoCh11G014300.1 Cmo11g01430 1430
16 1445361 1447969 - CmoCh16G003160.1 Cmo16g00316 316
16 1451152 1453314 + CmoCh16G003170.1 Cmo16g00317 317
16 1453793 1455681 - CmoCh16G003180.1 Cmo16g00318 318
19 6281534 6282025 + CmoCh19G005420.1 Cmo19g00542 542
19 6286146 6286583 + CmoCh19G005430.1 Cmo19g00543 543
19 6289444 6289911 + CmoCh19G005440.1 Cmo19g00544 544
2 7850010 7850501 - CmPI595203_02g007410.1 Cmu02g0741 741
2 7879948 7880439 - CmPI595203_02g007420.1 Cmu02g0742 742
2 7900075 7900806 + CmPI595203_02g007430.1 Cmu02g0743 743
2 7917505 7917993 - CmPI595203_02g007450.1 Cmu02g0745 745
10 22080442 22082399 - CmPI595203_10g017800.1 Cmu10g1780 1780
10 22093348 22094862 - CmPI595203_10g017820.1 Cmu10g1782 1782
3 29260597 29262291 - Conep03aG0155300.1 Cone3ag1052 1052
8 9646801 9647444 - Conep08aG0108600.1 Cone8ag1057 1057
8 9659636 9661523 - Conep08aG0109000.1 Cone8ag1061 1061
8 9662367 9663514 - Conep08aG0109100.1 Cone8ag1062 1062
10 7427975 7430613 - Conep10aG0109700.1 Cone10ag1070 1070
12 8597656 8598287 - Conep12aG0105300.1 Cone12ag1024 1024
12 8606330 8608271 - Conep12aG0105600.1 Cone12ag1027 1027
1 2201972 2203693 + Cp4.1LG01g02830.1 Cpe01g00381 381
1 2204100 2206135 - Cp4.1LG01g02720.1 Cpe01g00382 382
4 4095712 4096149 - Cp4.1LG04g07420.1 Cpe04g00336 336
4 4106885 4107373 + Cp4.1LG04g07480.1 Cpe04g00337 337
14 1429142 1431792 - Cp4.1LG14g04690.1 Cpe14g00246 246
14 1434932 1436572 + Cp4.1LG14g04810.1 Cpe14g00247 247
14 1434985 1439268 - Cp4.1LG14g04680.1 Cpe14g00248 248
15 5351516 5352004 + Cp4.1LG15g04130.1 Cpe15g00421 421
15 5386033 5386521 + Cp4.1LG15g04250.1 Cpe15g00425 425
2 8481477 8481968 - CrPI670011_02g010540.1 Cre02g1054 1054
2 8522890 8523360 + CrPI670011_02g010560.1 Cre02g1056 1056
2 8530419 8530841 - CrPI670011_02g010570.1 Cre02g1057 1057
2 8555876 8556364 - CrPI670011_02g010600.1 Cre02g1060 1060
10 23757132 23759589 - CrPI670011_10g011540.1 Cre10g1154 1154
10 23770982 23772492 - CrPI670011_10g011560.1 Cre10g1156 1156
7 4730797 4731911 + CsaV3_7G007610.1 Csa07g00662 662
7 4733920 4734764 - CsaV3_7G007620.1 Csa07g00663 663
7 4737383 4739312 + CsaV3_7G007630.1 Csa07g00664 664
7 4743514 4744161 + CsaV3_7G007640.1 Csa07g00665 665
7 3950298 3953958 + Hsped.07g03870.1 Hepe07g0387 387
12 1511571 1512065 + Lag0014507.1 Lac12g0135 135
3 7613253 7613714 + Lsi03G006080.1 Lsi03g00608 608
3 7703271 7703741 - Lsi03G006180.1 Lsi03g00618 618
3 7757407 7757904 - Lsi03G006220.1 Lsi03g00622 622
3 7766711 7767208 - Lsi03G006240.1 Lsi03g00624 624
3 19244181 19247091 - Lsi03G009980.1 Lsi03g00998 998
3 19261650 19263556 - Lsi03G010000.1 Lsi03g01000 1000
10 2644164 2646274 - MC10g0327 Mch10g0399 399
10 2650862 2652496 + MC10g0328 Mch10g0400 400
10 2655198 2656641 - MC10g0329 Mch10g0402 402
7 8641055 8642884 + Sed0010221.1 Sed07g1152 1152
7 8644404 8648313 - Sed0027893.1 Sed07g1153 1153
7 8653948 8655989 + Sed0004861.1 Sed07g1154 1154
10 36003696 36004202 + Sed0009825.1 Sed10g1935 1935
1 5466583 5469096 - Tan0002520.1 Tan01g0595 595
1 5472861 5476912 + Tan0021136.2 Tan01g0597 597
1 5478383 5480281 - Tan0009193.1 Tan01g0598 598
2 17434664 17435143 - Tan0014919.1 Tan02g1067 1067
3 8825458 8827504 + Vvi3g786 Vvi3g786 786
3 8828256 8831730 - Vvi3g787 Vvi3g787 787
3 8842960 8844343 + Vvi3g788 Vvi3g788 788
3 8864716 8881628 + Vvi3g789 Vvi3g789 789
3 8895285 8912074 - Vvi3g790 Vvi3g790 790
3 8915654 8927983 - Vvi3g791 Vvi3g791 791
3 8949484 8950329 - Vvi3g792 Vvi3g792 792
3 8986183 8986955 - Vvi3g793 Vvi3g793 793
3 8995954 9000573 + Vvi3g794 Vvi3g794 794
3 9044692 9045211 - Vvi3g795 Vvi3g795 795
       

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