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
Vvi19g674 . . . . Bpe09g00125 . . Bma13g01117 . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1223 Cone15ag1244 . Csa03g00424 . Cme06g02770 . . . Bda12g00966 . . . . . . . . . . . Cpe14g00786 . Bhi11g00477 . . . . . . . . . . . . . . . Chy06g01889 .
Vvi19g675 . . . . . . . Bma13g01118 . . Cma01g01073 Cma09g01015 Car01g00949 . Sed07g2762 Cpe06g00823 Cpe02g00825 Bhi09g01779 Tan01g3197 Cmetu01g1493 . . Mch11g1282 . . . . . . . . . . Cone14ag1224 Cone15ag1245 Lsi02g01822 . . . . Blo10g00866 . Bda12g00967 . . . . . Cmo01g01117 Cmo09g01018 . . . . . . . . . . . . . Cla09g02082 Cam09g2170 Cec09g2235 . . . . . . Chy01g01141 Cme01g00895
Vvi19g676 . . . . Bpe09g00124 . Bma10g00593 Bma13g01119 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g00423 . Cme06g02769 . . . Bda12g00968 . . . . . . . . . . . Cpe14g00785 . Bhi11g00476 . . . . Mch10g1448 . . . . . . . . . . Chy06g01890 .
Vvi19g677 . . . . Bpe09g00121 . . Bma13g01121 . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1229 Cone15ag1253 . Csa03g00422 . Cme06g02768 . . . Bda12g00970 . . . . . . . . . . . Cpe14g00784 . Bhi11g00474 . . . . . . . . . . . . . . . Chy06g01891 .
Vvi19g678 Blo03g00505 . Bda07g00413 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0007 . . . . Csa07g00858 . . . . . . Bpe11g00590 . . Bma14g00679 . . . . . . . . . . . . . . . . . . . . . . . . . Chy01g01039 Cme01g01121
Vvi19g679 . . Bda07g00414 . . . . . . . Cma01g01071 . Car01g00947 . . . Cpe02g00827 Bhi09g01781 . . . . . . . . . . . . . Cone6ag0006 . . . Lsi02g01820 . . . . . . . Bpe11g00591 . . Bma14g00678 . Cmo01g01114 . . . . . . . . . . . . . . Cla09g02083 Cam09g2171 Cec09g2236 . . . . . . Chy01g01138 .
Vvi19g680 . . . . Bpe09g00120 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g00420 . . . . . . . . . . . . . . . . . Cpe14g00783 . Bhi11g00472 . . . . . . . . . . . . . . . . .
Vvi19g681 . . . . . . . Bma13g01122 . Cmo06g00681 . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1250 Cone15ag1274 . . . . . Blo10g00871 . Bda12g00971 . . . . . . . . . . . . . Bhi11g00471 . . . . . . . . . . . . . . . Chy06g01892 .
Vvi19g682 . . . . . . . . . . . . . . Sed07g2758 . . Bhi09g01783 Tan01g3200 Cmetu06g0507 . . . . . . . . . . . . . . Cone15ag1275 . Csa03g00419 . . . . . . . . . . . . . . . . . . . Bhi11g00469 . . . . . . . . . . . . . . . Chy01g01137 Cme01g00893
Vvi19g683 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo07g00860 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 5296630 5301104 - Bda025505.1 Bda07g00413 413
7 5312911 5314482 + Bda025507.1 Bda07g00414 414
12 40840293 40842542 - Bda009514.1 Bda12g00966 966
12 40854186 40857008 + Bda009515.1 Bda12g00967 967
12 40858567 40860595 + Bda009516.1 Bda12g00968 968
12 40864764 40868440 - Bda009517.1 Bda12g00970 970
12 40871709 40886287 + Bda009518.2 Bda12g00971 971
9 48308429 48318358 + XM_039042873.1 Bhi09g01779 1779
9 48370671 48373979 + XM_039043228.1 Bhi09g01781 1781
9 48406058 48408269 + XM_039041899.1 Bhi09g01783 1783
11 11168405 11171066 - XM_039049997.1 Bhi11g00469 469
11 11192973 11209509 - XM_039047328.1 Bhi11g00471 471
11 11192973 11209491 - XM_039047329.1 Bhi11g00472 472
11 11318850 11322810 + XM_039048617.1 Bhi11g00474 474
11 11322972 11325148 - XM_039048619.1 Bhi11g00476 476
11 11336078 11343112 + XM_039047087.1 Bhi11g00477 477
3 18793170 18809144 - BLOR11686 Blo03g00505 505
7 27032089 27052434 - BLOR18792 Blo07g00860 860
10 27391602 27402275 + BLOR02656 Blo10g00866 866
10 27469448 27487738 + BLOR02661 Blo10g00871 871
10 7271495 7273474 + Bma004300.1 Bma10g00593 593
13 44284882 44285538 - Bma010247.1 Bma13g01117 1117
13 44293793 44300229 + Bma010248.1 Bma13g01118 1118
13 44301359 44303392 + Bma010249.1 Bma13g01119 1119
13 44309334 44312990 - Bma010250.1 Bma13g01121 1121
13 44317846 44331551 + Bma010251.1 Bma13g01122 1122
14 7323531 7325019 - Bma011129.1 Bma14g00678 678
14 7339793 7344634 + Bma011130.2 Bma14g00679 679
9 806869 821482 - Bpe023794.1 Bpe09g00120 120
9 824764 828419 + Bpe023795.1 Bpe09g00121 121
9 836252 838276 - Bpe023798.1 Bpe09g00124 124
9 852335 854644 + Bpe023800.3 Bpe09g00125 125
11 4484421 4488853 - Bpe003955.1 Bpe11g00590 590
11 4496336 4497912 + Bpe003956.1 Bpe11g00591 591
9 36200641 36212712 + CaPI482276_09g021700.1 Cam09g2170 2170
9 36217792 36225875 + CaPI482276_09g021710.1 Cam09g2171 2171
1 9109052 9111531 - Carg22416-RA Car01g00947 947
1 9117121 9126592 - Carg22414-RA Car01g00949 949
9 39230500 39239906 + CePI673135_09g022350.1 Cec09g2235 2235
9 39247578 39254171 + CePI673135_09g022360.1 Cec09g2236 2236
1 11245562 11248231 - Chy1G010390.1 Chy01g01039 1039
1 13174108 13175723 - Chy1G011370.1 Chy01g01137 1137
1 13185137 13187789 - Chy1G011380.1 Chy01g01138 1138
1 13216992 13228730 - Chy1G011410.1 Chy01g01141 1141
6 22739227 22742852 - Chy6G124170.1 Chy06g01889 1889
6 22748430 22750445 + Chy6G124180.1 Chy06g01890 1890
6 22750732 22754424 - Chy6G124190.1 Chy06g01891 1891
6 22772035 22787273 + Chy6G124200.1 Chy06g01892 1892
9 38358450 38368127 + ClCG09G021380.2 Cla09g02082 2082
9 38375953 38384323 + ClCG09G021390.2 Cla09g02083 2083
1 7912403 7915368 - CmaCh01G010710.1 Cma01g01071 1071
1 7920979 7930776 - CmaCh01G010730.1 Cma01g01073 1073
9 5191318 5201383 + CmaCh09G010150.1 Cma09g01015 1015
1 10257553 10259864 - MELO3C024949.2.1 Cme01g00893 893
1 10278513 10288511 - MELO3C024947.2.1 Cme01g00895 895
1 14320817 14324368 - MELO3C013227.2.1 Cme01g01121 1121
6 34937663 34941759 + MELO3C014116.2.1 Cme06g02768 2768
6 34941554 34943764 - MELO3C014117.2.1 Cme06g02769 2769
6 34964810 34968996 + MELO3C014119.2.1 Cme06g02770 2770
1 13926784 13936113 + PI0020670.1 Cmetu01g1493 1493
6 27060492 27063930 + PI0022825.1 Cmetu06g0507 507
1 9232461 9235171 - CmoCh01G011140.1 Cmo01g01114 1114
1 9240784 9250287 - CmoCh01G011170.1 Cmo01g01117 1117
6 3443640 3460205 - CmoCh06G006810.1 Cmo06g00681 681
9 5417914 5429112 + CmoCh09G010180.1 Cmo09g01018 1018
6 55262 57183 - Conep06aG0000600.1 Cone6ag0006 6
6 57730 68578 + Conep06aG0000700.1 Cone6ag0007 7
14 9928343 9929860 - Conep14aG0125500.1 Cone14ag1223 1223
14 9930339 9937219 + Conep14aG0125600.1 Cone14ag1224 1224
14 9993588 9996430 - Conep14aG0126100.1 Cone14ag1229 1229
14 10074312 10089522 + Conep14aG0128200.1 Cone14ag1250 1250
15 9813442 9815164 - Conep15aG0127300.1 Cone15ag1244 1244
15 9815328 9822192 + Conep15aG0127400.1 Cone15ag1245 1245
15 9879057 9879713 - Conep15aG0128200.1 Cone15ag1253 1253
15 10012671 10027678 + Conep15aG0130300.1 Cone15ag1274 1274
15 10028381 10029798 + Conep15aG0130400.1 Cone15ag1275 1275
2 5279294 5290895 + Cp4.1LG02g00480.1 Cpe02g00825 825
2 5294045 5297099 + Cp4.1LG02g00530.1 Cpe02g00827 827
6 5275328 5285653 + Cp4.1LG06g08410.1 Cpe06g00823 823
14 6167347 6184370 - Cp4.1LG14g07820.1 Cpe14g00783 783
14 6186213 6192623 + Cp4.1LG14g07840.1 Cpe14g00784 784
14 6191249 6192239 - Cp4.1LG14g07950.1 Cpe14g00785 785
14 6195569 6197982 + Cp4.1LG14g07880.1 Cpe14g00786 786
3 3541208 3544719 - CsaV3_3G004190.1 Csa03g00419 419
3 3559773 3575088 - CsaV3_3G004200.1 Csa03g00420 420
3 3584298 3590719 + CsaV3_3G004220.1 Csa03g00422 422
3 3588410 3590425 - CsaV3_3G004230.1 Csa03g00423 423
3 3593562 3598952 + CsaV3_3G004240.1 Csa03g00424 424
7 6380384 6385935 - CsaV3_7G011550.1 Csa07g00858 858
2 24011061 24014152 - Lsi02G018200.1 Lsi02g01820 1820
2 24027496 24036891 - Lsi02G018220.1 Lsi02g01822 1822
10 14161913 14163805 + MC10g1143 Mch10g1448 1448
11 9073913 9081573 + MC11g1062 Mch11g1282 1282
7 42638882 42642092 - Sed0005274.1 Sed07g2758 2758
7 42651929 42660469 - Sed0003689.3 Sed07g2762 2762
1 85903641 85913839 + Tan0017673.1 Tan01g3197 3197
1 86019309 86021067 + Tan0014392.1 Tan01g3200 3200
19 8679587 8686228 - Vvi19g674 Vvi19g674 674
19 8691934 8704283 + Vvi19g675 Vvi19g675 675
19 8704991 8712705 + Vvi19g676 Vvi19g676 676
19 8712743 8718835 - Vvi19g677 Vvi19g677 677
19 8721936 8728041 - Vvi19g678 Vvi19g678 678
19 8728276 8730857 + Vvi19g679 Vvi19g679 679
19 8734444 8743698 + Vvi19g680 Vvi19g680 680
19 8744182 8752009 + Vvi19g681 Vvi19g681 681
19 8775196 8778689 + Vvi19g682 Vvi19g682 682
19 8779484 8786078 - Vvi19g683 Vvi19g683 683
       

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