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
Vvi19g74 . . . . . . . . . . Cma01g01260 . . . . . . Bhi09g03540 . . . . Mch11g0991 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g75 . . . . . . Bma10g00458 . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0206 Cone9ag0235 . . . . . . . . . . . . . . . . Cmo09g00656 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g76 . . . . . Bpe08g00985 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma07g01144 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g77 Blo03g00705 Blo03g01564 . . . . . . . . Cma01g01258 Cma09g00825 Car01g01081 Car09g00595 Sed04g2477 Cpe06g00524 Cpe02g00657 Bhi09g03538 Tan01g4292 Cmetu07g2287 . Hepe01g1456 Mch11g0993 . Cla11g01694 Cam11g1761 . Cco11g1785 Clacu11g1920 Cmu11g1731 . Cone6ag0205 . . . Lsi04g01992 Csa04g02265 Chy07g00007 Cme07g00515 . . . . Bpe11g00440 . . Bma14g00273 . Cmo01g01315 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g78 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g79 . . . . Bpe09g00267 . . Bma13g00924 Cmo16g00479 Cmo04g00712 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo10g00726 Bda05g00812 . . Bpe03g00874 . . . . . Cma04g00664 Cma16g00445 . . Cpe14g00374 Cpe01g00599 . . . . . . . Cla07g00969 Cam07g1042 Cec07g1113 Cco07g1090 Clacu07g1014 Cmu07g1007 Cre07g1384 . . Chy07g00983 Cme07g01358
Vvi19g80 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g81 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g82 . . . . . . Bma10g00457 . Cmo16g00463 . . . . . . . . . . . . . . . . . . . . . . Cone6ag0204 . . . . . . . . . . Bda12g00814 . . . . . . . . Cma16g00431 . . Cpe14g00363 . . . . . . . . . . . . . . . . Csa04g00815 . .
Vvi19g83 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 56614124 56617277 - Bda021969.1 Bda05g00812 812
12 37547736 37550395 - Bda009325.1 Bda12g00814 814
9 89087915 89093179 + XM_039042500.1 Bhi09g03538 3538
9 89108686 89120873 - XM_039043007.1 Bhi09g03540 3540
3 29856842 29860186 + BLOR11886 Blo03g00705 705
3 43442377 43446913 + BLOR12745 Blo03g01564 1564
10 22920767 22923616 - BLOR02516 Blo10g00726 726
7 45637910 45639225 + Bma026373.1 Bma07g01144 1144
10 5150979 5154187 + Bma004128.1 Bma10g00457 457
10 5156089 5160466 - Bma004129.1 Bma10g00458 458
13 39682631 39685301 - Bma010002.1 Bma13g00924 924
14 3255871 3259194 + Bma030649 Bma14g00273 273
3 28501935 28505062 - Bpe025399 Bpe03g00874 874
8 12227341 12228653 + Bpe023109.1 Bpe08g00985 985
9 1962330 1964940 + Bpe023938.1 Bpe09g00267 267
11 3331369 3334685 - Bpe003812.1 Bpe11g00440 440
7 24740667 24746260 - CaPI482276_07g010420.1 Cam07g1042 1042
11 30170706 30174991 - CaPI482276_11g017610.1 Cam11g1761 1761
1 10084974 10090578 + Carg14745-RA Car01g01081 1081
9 3359702 3365179 + Carg03078-RA Car09g00595 595
7 24443012 24445745 - CcPI632755_07g010900.1 Cco07g1090 1090
11 30577123 30582651 - CcPI632755_11g017850.1 Cco11g1785 1785
7 26331372 26334138 - CePI673135_07g011130.1 Cec07g1113 1113
7 97241 101066 - Chy7G128370.1 Chy07g00007 7
7 14482967 14485779 - Chy7G138130.1 Chy07g00983 983
7 24570088 24572819 - ClG42_07g0101400.10 Clacu07g1014 1014
11 30209435 30213708 - ClG42_11g0192000.10 Clacu11g1920 1920
7 25883743 25886446 - ClCG07G010170.2 Cla07g00969 969
11 30548224 30553218 - ClCG11G017260.1 Cla11g01694 1694
1 9048829 9053415 + CmaCh01G012580.1 Cma01g01258 1258
1 9059597 9082078 - CmaCh01G012600.1 Cma01g01260 1260
4 3386282 3389087 - CmaCh04G006640.1 Cma04g00664 664
9 4047428 4052379 + CmaCh09G008250.1 Cma09g00825 825
16 2148810 2151414 - CmaCh16G004310.1 Cma16g00431 431
16 2216001 2217848 - CmaCh16G004450.1 Cma16g00445 445
7 4334885 4339947 - MELO3C025660.2.1 Cme07g00515 515
7 19092023 19096019 - MELO3C016121.2.1 Cme07g01358 1358
7 21435968 21440456 - PI0028246.2 Cmetu07g2287 2287
1 10417106 10421685 + CmoCh01G013150.1 Cmo01g01315 1315
4 3530555 3533287 - CmoCh04G007120.1 Cmo04g00712 712
9 3288325 3296648 + CmoCh09G006560.1 Cmo09g00656 656
16 2222424 2225580 - CmoCh16G004630.1 Cmo16g00463 463
16 2292896 2294212 + CmoCh16G004790.1 Cmo16g00479 479
7 24814404 24819976 - CmPI595203_07g010070.1 Cmu07g1007 1007
11 29462467 29466740 - CmPI595203_11g017310.1 Cmu11g1731 1731
6 962545 966338 + Conep06aG0020600.1 Cone6ag0204 204
6 966674 969745 + Conep06aG0020700.1 Cone6ag0205 205
6 969913 975997 - Conep06aG0020800.1 Cone6ag0206 206
9 991865 998065 - Conep09aG0023800.1 Cone9ag0235 235
1 3456674 3460038 - Cp4.1LG01g00620.1 Cpe01g00599 599
2 4135770 4140903 - Cp4.1LG02g02160.1 Cpe02g00657 657
6 3128566 3133818 + Cp4.1LG06g05190.1 Cpe06g00524 524
14 2208805 2212919 - Cp4.1LG14g03490.1 Cpe14g00363 363
14 2291980 2293818 - Cp4.1LG14g03340.1 Cpe14g00374 374
7 28736847 28739575 - CrPI670011_07g013840.1 Cre07g1384 1384
4 5720049 5724301 + CsaV3_4G008150.1 Csa04g00815 815
4 23289774 23293602 - CsaV3_4G032910.1 Csa04g02265 2265
1 79784751 79790442 + Hsped.01g14560.1 Hepe01g1456 1456
4 27024989 27030096 - Lsi04G019920.1 Lsi04g01992 1992
11 6854818 6861092 + MC11g0810 Mch11g0991 991
11 6901234 6906958 - MC11g0812 Mch11g0993 993
4 37885401 37890911 + Sed0003063.3 Sed04g2477 2477
1 107796111 107802288 - Tan0003383.3 Tan01g4292 4292
19 836782 845543 + Vvi19g74 Vvi19g74 74
19 846311 864401 + Vvi19g75 Vvi19g75 75
19 865988 867580 + Vvi19g76 Vvi19g76 76
19 869586 883359 - Vvi19g77 Vvi19g77 77
19 884761 893703 + Vvi19g78 Vvi19g78 78
19 897657 902185 - Vvi19g79 Vvi19g79 79
19 905893 909343 - Vvi19g80 Vvi19g80 80
19 909762 916258 - Vvi19g81 Vvi19g81 81
19 917966 921705 - Vvi19g82 Vvi19g82 82
19 921704 942345 - Vvi19g83 Vvi19g83 83
       

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