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
Vvi19g654 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g655 . . Bda07g00407 . . . . . . . . . . Car09g00917 Sed07g2745 Cpe06g00815 . Bhi09g01756 Tan01g3186 Cmetu01g2159 . . Mch11g1263 . . . . . . . . Cone6ag0011 Cone9ag0010 . . Lsi02g01839 . . . . . . . Bpe11g00584 . . Bma14g00686 . . Cmo09g01007 . . . . . . . . . . . . . Cla09g02067 Cam09g2156 Cec09g2221 . . . . . . Chy01g01152 Cme01g00921
Vvi19g656 . . . . . . . . . . Cma01g01078 Cma09g01006 Car01g00953 Car09g00918 Sed07g2746 Cpe06g00816 Cpe02g00820 Bhi09g01757 Tan01g3187 Cmetu01g0523 . . Mch11g1264 . . . . . . . . . . . . Lsi02g01838 Csa07g00915 . . . . . . Bpe11g00585 . . Bma14g00685 . Cmo01g01124 Cmo09g01009 . . . . . . . . . . . . . Cla09g02068 Cam09g2157 Cec09g2222 . . . . . . Chy01g01151 Cme01g00920
Vvi19g657 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g658 . . . . . . . Bma13g01112 . Cmo06g00688 . . . . . . . . . . . . . . Cla10g00437 Cam10g0436 Cec10g0458 Cco10g0447 Clacu10g0444 Cmu10g1275 Cre10g0691 . . Cone14ag1216 Cone15ag1237 . . . . . Blo10g00863 . Bda12g00961 . . . . . . . . . . . Cpe14g00791 . . . . . . . . . . . . . . . Lsi05g00493 . . .
Vvi19g659 . . Bda07g00410 . Bpe09g00129 . Bma10g00590 Bma13g01113 . Cmo06g00687 . . . . . . . . . . . . . . . . . . . . . . . Cone8ag1366 Cone12ag1312 . Csa03g00427 . . . Blo10g00864 . Bda12g00962 Bpe11g00587 . . Bma14g00682 . . . . . . . . . Bhi11g00479 . . . . . . . . . . . . . Lsi05g00494 . Chy06g01888 .
Vvi19g660 . Blo03g01482 Bda07g00411 Bda09g00437 . Bpe08g01092 . . . . Cma01g01076 Cma09g01007 Car01g00952 Car09g00919 . Cpe06g00817 Cpe02g00822 Bhi09g01762 . . . . Mch11g1266 . . . . . . . . . . . . Lsi02g01829 Csa07g00874 . . . . . . Bpe11g00588 . Bma07g01247 Bma14g00681 . Cmo01g01121 Cmo09g01010 . . . . . . . . . . . . . Cla09g02076 Cam09g2161 Cec09g2227 . . . . . . Chy01g01147 Cme01g00911
Vvi19g661 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda05g00688 . . Bpe03g00750 . Bma14g00130 . . . . . . . . . . . . . . . . . . . . . . . . . Chy01g01118 .
Vvi19g662 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g663 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 55183225 55199592 + Bda021823.1 Bda05g00688 688
7 5193886 5196626 - Bda033842 Bda07g00407 407
7 5279521 5280117 + Bda025502.1 Bda07g00410 410
7 5282654 5284810 - Bda025503.1 Bda07g00411 411
9 5789747 5791003 - Bda031025.1 Bda09g00437 437
12 40817134 40822421 + Bda009509.1 Bda12g00961 961
12 40824349 40824936 + Bda009510.1 Bda12g00962 962
9 47827180 47836005 + XM_039042192.1 Bhi09g01756 1756
9 47835982 47839868 - XM_039042193.1 Bhi09g01757 1757
9 47931462 47936319 - XM_039041410.1 Bhi09g01762 1762
11 11348114 11352430 + XM_039049891.1 Bhi11g00479 479
3 41599859 41601961 - BLOR12663 Blo03g01482 1482
10 27329760 27335021 + BLOR02653 Blo10g00863 863
10 27339437 27340021 + BLOR02654 Blo10g00864 864
7 47459777 47462937 + Bma026501.2 Bma07g01247 1247
10 7262662 7263198 + Bma004297.1 Bma10g00590 590
13 44255095 44260325 + Bma010242.1 Bma13g01112 1112
13 44263196 44263792 + Bma010243.1 Bma13g01113 1113
14 1899583 1909370 - Bma010533.1 Bma14g00130 130
14 7362259 7364484 + Bma011132.1 Bma14g00681 681
14 7366950 7367540 - Bma011133.1 Bma14g00682 682
14 7502803 7503323 + Bma011137.1 Bma14g00685 685
14 7503947 7506644 - Bma011138.1 Bma14g00686 686
3 27566162 27569115 + Bpe012659.1 Bpe03g00750 750
8 13003754 13005913 + Bpe023217.1 Bpe08g01092 1092
9 873594 874181 - Bpe023804.1 Bpe09g00129 129
11 4447023 4449714 + Bpe003949.1 Bpe11g00584 584
11 4450321 4451555 - Bpe003950.1 Bpe11g00585 585
11 4466290 4466886 + Bpe003952.1 Bpe11g00587 587
11 4469352 4471490 - Bpe003953.1 Bpe11g00588 588
9 36086162 36091472 + CaPI482276_09g021560.1 Cam09g2156 2156
9 36091953 36095263 - CaPI482276_09g021570.1 Cam09g2157 2157
9 36127651 36129837 - CaPI482276_09g021610.1 Cam09g2161 2161
10 6726187 6732100 + CaPI482276_10g004360.1 Cam10g0436 436
1 9135745 9138077 + Carg22411-RA Car01g00952 952
1 9149125 9152039 + Carg22410-RA Car01g00953 953
9 5644294 5647141 + Carg12872-RA Car09g00917 917
9 5647640 5650260 - Carg12873-RA Car09g00918 918
9 5652920 5664662 - Carg12874-RA Car09g00919 919
10 5277351 5283294 + CcPI632755_10g004470.1 Cco10g0447 447
9 39113720 39119022 + CePI673135_09g022210.1 Cec09g2221 2221
9 39119501 39122502 - CePI673135_09g022220.1 Cec09g2222 2222
9 39154482 39156647 - CePI673135_09g022270.1 Cec09g2227 2227
10 5470014 5475887 + CePI673135_10g004580.1 Cec10g0458 458
1 12783598 12789230 - Chy1G011180.1 Chy01g01118 1118
1 13396243 13398186 + Chy1G011470.1 Chy01g01147 1147
1 13462347 13465794 + Chy1G011510.1 Chy01g01151 1151
1 13466239 13469272 - Chy1G011520.1 Chy01g01152 1152
6 22731154 22734043 - Chy6G124160.1 Chy06g01888 1888
10 5522848 5528783 + ClG42_10g0044400.10 Clacu10g0444 444
9 38241205 38245003 + ClCG09G021240.1 Cla09g02067 2067
9 38245484 38248798 - ClCG09G021250.2 Cla09g02068 2068
9 38281012 38283480 - ClCG09G021320.2 Cla09g02076 2076
10 5879448 5886639 + ClCG10G004650.2 Cla10g00437 437
1 7940672 7942786 + CmaCh01G010760.1 Cma01g01076 1076
1 7954941 7957971 + CmaCh01G010780.1 Cma01g01078 1078
9 5133774 5136761 - CmaCh09G010060.1 Cma09g01006 1006
9 5138818 5144294 - CmaCh09G010070.1 Cma09g01007 1007
1 10550727 10555920 + MELO3C024936.2.1 Cme01g00911 911
1 10654486 10658597 + MELO3C024930.2.1 Cme01g00920 920
1 10657448 10661311 - MELO3C024929.2.1 Cme01g00921 921
1 13266394 13269483 - PI0019540.1 Cmetu01g0523 523
1 13262890 13265950 + PI0003406.1 Cmetu01g2159 2159
1 9260259 9262364 + CmoCh01G011210.1 Cmo01g01121 1121
1 9273907 9276959 + CmoCh01G011240.1 Cmo01g01124 1124
6 3488191 3488727 - CmoCh06G006870.1 Cmo06g00687 687
6 3490881 3498823 - CmoCh06G006880.1 Cmo06g00688 688
9 5356811 5359486 + CmoCh09G010070.1 Cmo09g01007 1007
9 5359833 5365767 - CmoCh09G010090.1 Cmo09g01009 1009
9 5366570 5368642 - CmoCh09G010100.1 Cmo09g01010 1010
10 5659645 5665592 + CmPI595203_10g012750.1 Cmu10g1275 1275
6 91683 92129 - Conep06aG0001100.1 Cone6ag0011 11
8 10907603 10909516 - Conep08aG0140500.1 Cone8ag1366 1366
9 56727 58793 - Conep09aG0001000.1 Cone9ag0010 10
12 9924263 9927221 - Conep12aG0135300.1 Cone12ag1312 1312
14 9898688 9903568 + Conep14aG0124800.1 Cone14ag1216 1216
15 9784110 9789085 + Conep15aG0126600.1 Cone15ag1237 1237
2 5250977 5254104 - Cp4.1LG02g00400.1 Cpe02g00820 820
2 5266104 5268224 - Cp4.1LG02g00460.1 Cpe02g00822 822
6 5210830 5214117 + Cp4.1LG06g08400.1 Cpe06g00815 815
6 5213960 5217659 - Cp4.1LG06g08310.1 Cpe06g00816 816
6 5221209 5223281 - Cp4.1LG06g08360.1 Cpe06g00817 817
14 6219348 6229167 - Cp4.1LG14g07910.1 Cpe14g00791 791
10 6580513 6586451 + CrPI670011_10g006910.1 Cre10g0691 691
3 3622009 3625576 + CsaV3_3G004270.1 Csa03g00427 427
7 6682448 6687382 + CsaV3_7G012700.1 Csa07g00874 874
7 7786713 7794229 - CsaV3_7G015090.1 Csa07g00915 915
2 24111816 24113948 + Lsi02G018290.1 Lsi02g01829 1829
2 24154195 24158444 + Lsi02G018380.1 Lsi02g01838 1838
2 24158184 24162836 - Lsi02G018390.1 Lsi02g01839 1839
5 6229566 6238751 + Lsi05G004930.1 Lsi05g00493 493
5 6245182 6245718 + Lsi05G004940.1 Lsi05g00494 494
11 8968833 8975769 + MC11g1044 Mch11g1263 1263
11 8971469 8972637 - MC11g1045 Mch11g1264 1264
11 8984518 8988409 - MC11g1047 Mch11g1266 1266
7 42542947 42546741 + Sed0020019.1 Sed07g2745 2745
7 42547012 42549748 - Sed0006731.1 Sed07g2746 2746
1 85597770 85601317 + Tan0003373.1 Tan01g3186 3186
1 85601581 85604932 - Tan0000770.1 Tan01g3187 3187
19 8340946 8343320 - Vvi19g654 Vvi19g654 654
19 8363687 8368560 + Vvi19g655 Vvi19g655 655
19 8370485 8373796 - Vvi19g656 Vvi19g656 656
19 8407034 8408225 - Vvi19g657 Vvi19g657 657
19 8443446 8455090 + Vvi19g658 Vvi19g658 658
19 8458281 8459992 + Vvi19g659 Vvi19g659 659
19 8464490 8466738 - Vvi19g660 Vvi19g660 660
19 8484221 8488496 - Vvi19g661 Vvi19g661 661
19 8489460 8494866 - Vvi19g662 Vvi19g662 662
19 8497126 8523598 - Vvi19g663 Vvi19g663 663
       

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