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
Vvi19g194 . . . . . . . . Cmo16g00435 . . . . . . . . . . . . . . . . . . . . . . Cone6ag0156 Cone9ag0180 . . . . . . Blo07g00953 . Bda05g00773 . . Bpe03g00841 . . . . . . Cma16g00401 . Car16g00367 Cpe14g00337 . . . . . . . . Cla05g01004 Cam05g1093 Cec05g1103 Cco05g1096 Clacu05g1088 Cmu05g1038 Cre05g1113 . . Chy06g01162 .
Vvi19g195 . . . . . . . . . . . Cma09g00855 . Car09g00769 . . . Bhi09g03441 . . . Hepe01g1394 Mch11g1059 . Cla11g01753 Cam11g1820 Cec11g1840 Cco11g1847 Clacu11g1980 Cmu11g1790 Cre11g2197 . . . . . . . . Blo07g00952 Blo10g00756 . Bda12g00836 . . . . . . Cmo09g00848 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g196 . . . . Bpe09g00238 . . Bma13g00945 Cmo16g00434 . . . . . . Cpe06g00682 . . . . . . . . . . . . . . . . Cone9ag0179 . . Lsi04g02064 Csa04g02334 Chy07g00066 . . Blo10g00758 . . . . . . . . . . Cma16g00400 . Car16g00366 . . . . . . . . . Cla05g01005 Cam05g1094 Cec05g1104 Cco05g1097 Clacu05g1090 Cmu05g1041 Cre05g1114 . . . .
Vvi19g197 . . . . . . Bma10g00496 Bma13g00946 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo10g00759 . . . Bpe03g00840 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g198 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g199 . . . Bda09g00514 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0153 Cone9ag0178 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g200 . . . . . . . . . . . Cma09g00858 . Car09g00773 Sed04g2404 Cpe06g00684 . Bhi09g03437 Tan01g4387 Cmetu07g0477 . . Mch11g1063 . Cla11g01756 Cam11g1823 Cec11g1843 Cco11g1850 Clacu11g1983 Cmu11g1793 Cre11g2200 . . Cone14ag1059 Cone15ag1051 Lsi04g02066 Csa04g02337 Chy07g00068 . . . . . . . . . . . Cmo09g00850 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g201 . . . . Bpe09g00237 . . Bma13g00947 Cmo16g00433 . Cma01g01212 . Car01g01036 . Sed04g2403 . Cpe02g00698 Bhi09g03436 Tan01g0815 . . Hepe01g1391 . . Cla11g01757 Cam11g1824 Cec11g1844 Cco11g1851 Clacu11g1984 Cmu11g1794 Cre11g2201 Cone6ag0152 Cone9ag0177 . Cone15ag1052 Lsi04g02067 Csa04g02338 Chy07g00069 . . Blo10g00760 . Bda12g00837 . . . . . Cmo01g01266 . . Cma16g00399 . Car16g00364 Cpe14g00336 . . . . . . . . . . . . . . . . . Chy06g01160 .
Vvi19g202 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g203 . . . . . . . . . . Cma01g01210 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo01g01264 . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 56194971 56197127 - Bda021923.1 Bda05g00773 773
9 6802308 6803099 - Bda031114.1 Bda09g00514 514
12 38003173 38006070 + Bda009354.1 Bda12g00836 836
12 38012738 38014093 + Bda009355.1 Bda12g00837 837
9 86762692 86770295 - XM_039042972.1 Bhi09g03436 3436
9 86780825 86796993 + XM_039042586.1 Bhi09g03437 3437
9 86960047 86964311 - XM_039043764.1 Bhi09g03441 3441
7 28808369 28811220 - BLOR18884 Blo07g00952 952
7 28812459 28815019 - BLOR18885 Blo07g00953 953
10 23756077 23759801 + BLOR02546 Blo10g00756 756
10 23779979 23781897 + BLOR02548 Blo10g00758 758
10 23782455 23783906 + BLOR02549 Blo10g00759 759
10 23786427 23791417 + BLOR02550 Blo10g00760 760
10 5859651 5866336 + Bma004187.1 Bma10g00496 496
13 40394837 40398355 + Bma010035.1 Bma13g00945 945
13 40417009 40419343 + Bma010036.1 Bma13g00946 946
13 40420733 40427136 + Bma010037.1 Bma13g00947 947
3 28261735 28264387 - Bpe012749.1 Bpe03g00840 840
3 28265612 28267908 - Bpe025397 Bpe03g00841 841
9 1708407 1714524 - Bpe023907.1 Bpe09g00237 237
9 1715729 1719465 - Bpe023908.1 Bpe09g00238 238
5 9988544 9991407 + CaPI482276_05g010930.1 Cam05g1093 1093
5 10005690 10017873 + CaPI482276_05g010940.1 Cam05g1094 1094
11 30725046 30727684 + CaPI482276_11g018200.1 Cam11g1820 1820
11 30751613 30761257 - CaPI482276_11g018230.1 Cam11g1823 1823
11 30765201 30772245 + CaPI482276_11g018240.1 Cam11g1824 1824
1 9819275 9825675 - Carg14700-RA Car01g01036 1036
9 4537904 4541364 + Carg17091-RA Car09g00769 769
9 4551297 4559430 - Carg17095-RA Car09g00773 773
16 2254682 2258761 - Carg11331-RA Car16g00364 364
16 2260505 2268301 - Carg11333-RA Car16g00366 366
16 2269222 2272751 - Carg11334-RA Car16g00367 367
5 9757735 9760400 + CcPI632755_05g010960.1 Cco05g1096 1096
5 9775169 9787046 + CcPI632755_05g010970.1 Cco05g1097 1097
11 31150363 31152990 + CcPI632755_11g018470.1 Cco11g1847 1847
11 31177000 31186755 - CcPI632755_11g018500.1 Cco11g1850 1850
11 31190740 31197804 + CcPI632755_11g018510.1 Cco11g1851 1851
5 9745279 9748129 + CePI673135_05g011030.1 Cec05g1103 1103
5 9762471 9774980 + CePI673135_05g011040.1 Cec05g1104 1104
11 32591146 32593777 + CePI673135_11g018400.1 Cec11g1840 1840
11 32618041 32627426 - CePI673135_11g018430.1 Cec11g1843 1843
11 32631331 32638180 + CePI673135_11g018440.1 Cec11g1844 1844
6 10267555 10273160 - Chy6G116880.1 Chy06g01160 1160
6 10281463 10285688 - Chy6G116900.1 Chy06g01162 1162
7 604738 609436 + Chy7G128960.1 Chy07g00066 66
7 640555 648465 - Chy7G128980.1 Chy07g00068 68
7 653156 659641 + Chy7G128990.1 Chy07g00069 69
5 9723440 9726298 + ClG42_05g0108800.10 Clacu05g1088 1088
5 9752943 9757448 + ClG42_05g0109000.10 Clacu05g1090 1090
11 30764492 30767128 + ClG42_11g0198000.10 Clacu11g1980 1980
11 30790912 30800213 - ClG42_11g0198300.10 Clacu11g1983 1983
11 30804168 30811145 + ClG42_11g0198400.10 Clacu11g1984 1984
5 10095213 10098348 + ClCG05G009290.2 Cla05g01004 1004
5 10117450 10130360 + ClCG05G009300.2 Cla05g01005 1005
11 31134803 31137801 + ClCG11G017980.1 Cla11g01753 1753
11 31163194 31173435 - ClCG11G018010.2 Cla11g01756 1756
11 31177081 31184589 + ClCG11G018020.1 Cla11g01757 1757
1 8767247 8771451 + CmaCh01G012100.1 Cma01g01210 1210
1 8779239 8785725 - CmaCh01G012120.1 Cma01g01212 1212
9 4194180 4199015 + CmaCh09G008550.1 Cma09g00855 855
9 4207230 4217021 - CmaCh09G008580.1 Cma09g00858 858
16 1983033 1987548 - CmaCh16G003990.1 Cma16g00399 399
16 1988139 1991192 - CmaCh16G004000.1 Cma16g00400 400
16 1992877 2001326 - CmaCh16G004010.1 Cma16g00401 401
7 21971901 21980268 - PI0015590.1 Cmetu07g0477 477
1 10120784 10124969 + CmoCh01G012640.1 Cmo01g01264 1264
1 10132216 10138666 - CmoCh01G012660.1 Cmo01g01266 1266
9 4353374 4357375 + CmoCh09G008480.1 Cmo09g00848 848
9 4366839 4377539 - CmoCh09G008500.1 Cmo09g00850 850
16 2054272 2058682 - CmoCh16G004330.1 Cmo16g00433 433
16 2059234 2062270 - CmoCh16G004340.1 Cmo16g00434 434
16 2063625 2071851 - CmoCh16G004350.1 Cmo16g00435 435
5 9563943 9566801 + CmPI595203_05g010380.1 Cmu05g1038 1038
5 9593394 9597899 + CmPI595203_05g010410.1 Cmu05g1041 1041
11 30020098 30022734 + CmPI595203_11g017900.1 Cmu11g1790 1790
11 30046519 30055840 - CmPI595203_11g017930.1 Cmu11g1793 1793
11 30059798 30066770 + CmPI595203_11g017940.1 Cmu11g1794 1794
6 763080 766367 - Conep06aG0015300.1 Cone6ag0152 152
6 768003 770049 - Conep06aG0015400.1 Cone6ag0153 153
6 775395 776834 - Conep06aG0015700.1 Cone6ag0156 156
9 783737 786953 - Conep09aG0017900.1 Cone9ag0177 177
9 788605 790792 - Conep09aG0018000.1 Cone9ag0178 178
9 791541 793541 + Conep09aG0018100.1 Cone9ag0179 179
9 794994 795411 - Conep09aG0018200.1 Cone9ag0180 180
14 8932296 8935329 - Conep14aG0108000.1 Cone14ag1059 1059
15 8709245 8712591 - Conep15aG0107300.1 Cone15ag1051 1051
15 8713311 8717815 + Conep15aG0107400.1 Cone15ag1052 1052
2 4407872 4414092 + Cp4.1LG02g01800.1 Cpe02g00698 698
6 4234428 4241607 + Cp4.1LG06g06800.1 Cpe06g00682 682
6 4250826 4260351 - Cp4.1LG06g06850.1 Cpe06g00684 684
14 2038798 2053482 - Cp4.1LG14g03820.1 Cpe14g00336 336
14 2054313 2057751 - Cp4.1LG14g03810.1 Cpe14g00337 337
5 10447294 10450148 + CrPI670011_05g011130.1 Cre05g1113 1113
5 10471084 10483595 + CrPI670011_05g011140.1 Cre05g1114 1114
11 33687241 33689871 + CrPI670011_11g021970.1 Cre11g2197 2197
11 33713916 33723653 - CrPI670011_11g022000.1 Cre11g2200 2200
11 33727738 33734793 + CrPI670011_11g022010.1 Cre11g2201 2201
4 23805843 23808666 + CsaV3_4G033600.1 Csa04g02334 2334
4 23826244 23834598 - CsaV3_4G033630.1 Csa04g02337 2337
4 23836221 23844070 + CsaV3_4G033640.1 Csa04g02338 2338
1 79120701 79128773 - Hsped.01g13910.1 Hepe01g1391 1391
1 79160551 79164319 - Hsped.01g13940.1 Hepe01g1394 1394
4 27763832 27767498 + Lsi04G020640.1 Lsi04g02064 2064
4 27787420 27807445 - Lsi04G020660.1 Lsi04g02066 2066
4 27809903 27817347 + Lsi04G020670.1 Lsi04g02067 2067
11 7368429 7370960 + MC11g0868 Mch11g1059 1059
11 7386149 7396261 - MC11g0870 Mch11g1063 1063
4 37324462 37332418 - Sed0013988.2 Sed04g2403 2403
4 37333840 37343007 + Sed0008037.1 Sed04g2404 2404
1 7898461 7904145 - Tan0004946.2 Tan01g0815 815
1 108926316 108941497 - Tan0006453.1 Tan01g4387 4387
19 2504139 2508208 + Vvi19g194 Vvi19g194 194
19 2528397 2530537 + Vvi19g195 Vvi19g195 195
19 2532217 2534678 + Vvi19g196 Vvi19g196 196
19 2535018 2537063 + Vvi19g197 Vvi19g197 197
19 2537067 2537838 + Vvi19g198 Vvi19g198 198
19 2541539 2543028 + Vvi19g199 Vvi19g199 199
19 2550311 2573720 - Vvi19g200 Vvi19g200 200
19 2576355 2588557 + Vvi19g201 Vvi19g201 201
19 2589234 2590393 + Vvi19g202 Vvi19g202 202
19 2599265 2600477 - Vvi19g203 Vvi19g203 203
       

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