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
Vvi17g186 . . . Bda15g00557 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone2ag0774 . . . . . . . . . . Bda14g01105 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g187 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g188 . . . . . . . . Cmo13g01016 . . . . . . . . . . . . . . . . . . . . . . Cone2ag0772 . . . . . . . . . . . . . . Bma08g00104 . . . Cma13g00982 . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g189 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g190 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g191 . . . Bda15g00554 Bpe12g00654 . . . . . . Cma11g00318 . Car11g00293 Sed12g2124 . Cpe04g01364 Bhi02g00152 Tan09g1809 Cmetu02g1580 . Hepe09g0398 . . Cla06g01414 Cam06g1567 Cec06g1627 Cco06g1619 Clacu06g1529 Cmu06g1483 Cre06g2292 . . . Cone19ag0339 . . . . Blo13g00128 . . . . . . Bma08g00099 . . Cmo11g00323 . . . . . . . . . . . . . . . . . . . . Lsi06g01274 Csa01g00441 Chy02g02304 Cme02g01675
Vvi17g192 . . . . . . . . Cmo13g01020 . . . . . . Cpe20g00157 . . . . . . . . . . . . . . . Cone2ag0768 . . . Lsi02g00239 Csa01g00720 Chy12g01392 Cme12g01826 . . . . . Bpe15g00506 Bma03g00922 . . . . Cma13g00985 . Car13g00821 . . . . . . . . . . Cla04g01041 Cam04g1086 Cec01g1599 Cco01g1647 Clacu04g1112 Cmu04g1095 Cre01g1394 . . . .
Vvi17g193 . . Bda06g00823 . . . . Bma12g01247 Cmo13g01021 Cmo18g00058 . . . . . Cpe20g00156 . . . . . . . . . . . . . . . . . . Cone19ag0338 Lsi02g00238 Csa01g00719 Chy12g01393 Cme12g01827 . Blo15g00056 . . Bpe07g01051 . . . Sed08g2761 . . Cma13g00986 Cma18g00076 Car13g00822 Car18g00067 Cpe09g01111 . Bhi08g01299 Tan05g2186 Cmetu12g0492 . Hepe07g2351 . . Cla04g01042 Cam04g1087 Cec01g1600 Cco01g1648 Clacu04g1113 Cmu04g1096 Cre01g1395 . . . .
Vvi17g194 . . . . . . . . Cmo13g01025 Cmo18g00057 . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy12g01395 Cme12g01829 . . . . . . . . Sed08g2759 . . Cma13g00989 Cma18g00074 Car13g00824 Car18g00066 Cpe09g01112 . Bhi08g01295 Tan05g2189 Cmetu12g2098 Lac10g0291 Hepe07g2353 . . . . . . . . . . . . .
Vvi17g195 Blo04g00855 . . . . . . . . . . . . . . Cpe20g00155 . . . . . . . . . . . . . . . Cone2ag0767 . . . Lsi02g00236 Csa01g00718 . . . . . . . Bpe15g00507 Bma03g00921 . . . . . . . . . . . . . . . . . Cla04g01043 Cam04g1088 Cec01g1601 Cco01g1649 Clacu04g1114 Cmu04g1097 Cre01g1396 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 11467392 11471300 - Bda024154.2 Bda06g00823 823
14 9958040 9959478 + Bda027936.1 Bda14g01105 1105
15 8671578 8673999 + Bda012391.1 Bda15g00554 554
15 8687777 8691183 - Bda012394.2 Bda15g00557 557
2 2794371 2796713 - XM_039022481.1 Bhi02g00152 152
8 39537215 39540427 + XM_039039286.1 Bhi08g01295 1295
8 39611073 39615375 + XM_039039069.1 Bhi08g01299 1299
4 9364818 9381142 + BLOR13767 Blo04g00855 855
13 3737563 3744107 - BLOR05409 Blo13g00128 128
15 446758 450768 + BLOR06450 Blo15g00056 56
3 9533517 9539868 + Bma017244.1 Bma03g00921 921
3 9540378 9544179 + Bma017245.2 Bma03g00922 922
8 1208822 1211215 + Bma027099.1 Bma08g00099 99
8 1233037 1236014 - Bma027104.1 Bma08g00104 104
12 45467944 45471882 - Bma008612.1 Bma12g01247 1247
7 15985191 15989070 - Bpe021894.1 Bpe07g01051 1051
12 12189381 12191861 - Bpe005914.1 Bpe12g00654 654
15 16291321 16295168 - Bpe001439.1 Bpe15g00506 506
15 16295871 16301946 - Bpe001440.1 Bpe15g00507 507
4 25006821 25009704 - CaPI482276_04g010860.1 Cam04g1086 1086
4 25012402 25016415 + CaPI482276_04g010870.1 Cam04g1087 1087
4 25016528 25025113 - CaPI482276_04g010880.1 Cam04g1088 1088
6 27157478 27159519 + CaPI482276_06g015670.1 Cam06g1567 1567
11 1603919 1605957 - Carg09096-RA Car11g00293 293
13 8936268 8939492 - Carg04851-RA Car13g00821 821
13 8940494 8944214 + Carg04850-RA Car13g00822 822
13 8951867 8954666 - Carg04848-RA Car13g00824 824
18 340416 341611 + Carg06631-RA Car18g00066 66
18 343953 347349 - Carg06632-RA Car18g00067 67
1 29211119 29214005 - CcPI632755_01g016470.1 Cco01g1647 1647
1 29216683 29220695 + CcPI632755_01g016480.1 Cco01g1648 1648
1 29221967 29229614 - CcPI632755_01g016490.1 Cco01g1649 1649
6 26800438 26802426 + CcPI632755_06g016190.1 Cco06g1619 1619
1 30639001 30641876 - CePI673135_01g015990.1 Cec01g1599 1599
1 30644554 30648540 + CePI673135_01g016000.1 Cec01g1600 1600
1 30649788 30657292 - CePI673135_01g016010.1 Cec01g1601 1601
6 29874712 29876676 + CePI673135_06g016270.1 Cec06g1627 1627
2 27082192 27084174 + Chy2G045710.1 Chy02g02304 2304
12 18069356 18072299 - Chy12G219920.1 Chy12g01392 1392
12 18073363 18076806 + Chy12G219930.1 Chy12g01393 1393
12 18082373 18085050 - Chy12G219950.1 Chy12g01395 1395
4 25369057 25371936 - ClG42_04g0111200.10 Clacu04g1112 1112
4 25374616 25378637 + ClG42_04g0111300.10 Clacu04g1113 1113
4 25378693 25389861 - ClG42_04g0111400.10 Clacu04g1114 1114
6 26212638 26214631 + ClG42_06g0152900.10 Clacu06g1529 1529
4 25580813 25584079 - ClCG04G010590.2 Cla04g01041 1041
4 25586608 25591009 + ClCG04G010600.1 Cla04g01042 1042
4 25591550 25600782 - ClCG04G010610.2 Cla04g01043 1043
6 27699090 27703212 + ClCG06G014260.1 Cla06g01414 1414
11 1580923 1583533 - CmaCh11G003180.1 Cma11g00318 318
13 7631399 7634269 + CmaCh13G009820.1 Cma13g00982 982
13 7643955 7647198 - CmaCh13G009850.1 Cma13g00985 985
13 7648366 7651867 + CmaCh13G009860.1 Cma13g00986 986
13 7660727 7662216 - CmaCh13G009890.1 Cma13g00989 989
18 329922 331187 + CmaCh18G000740.1 Cma18g00074 74
18 332594 336106 - CmaCh18G000760.1 Cma18g00076 76
2 23902557 23904728 + MELO3C017363.2.1 Cme02g01675 1675
12 24660806 24664030 - MELO3C002137.2.1 Cme12g01826 1826
12 24664692 24668686 + MELO3C002135.2.1 Cme12g01827 1827
12 24675963 24677437 - MELO3C002133.2.1 Cme12g01829 1829
2 22319333 22322042 + PI0017987.1 Cmetu02g1580 1580
12 1577830 1581516 - PI0002268.2 Cmetu12g0492 492
12 1567708 1570409 + PI0010557.1 Cmetu12g2098 2098
11 1568837 1571760 - CmoCh11G003230.1 Cmo11g00323 323
13 8622441 8625286 + CmoCh13G010160.1 Cmo13g01016 1016
13 8635930 8639031 - CmoCh13G010200.1 Cmo13g01020 1020
13 8639956 8643432 + CmoCh13G010210.1 Cmo13g01021 1021
13 8651244 8652684 - CmoCh13G010250.1 Cmo13g01025 1025
18 373965 374917 + CmoCh18G000570.1 Cmo18g00057 57
18 376736 380272 - CmoCh18G000580.1 Cmo18g00058 58
4 25553548 25556427 - CmPI595203_04g010950.1 Cmu04g1095 1095
4 25559123 25563144 + CmPI595203_04g010960.1 Cmu04g1096 1096
4 25564350 25571485 - CmPI595203_04g010970.1 Cmu04g1097 1097
6 26116014 26117996 + CmPI595203_06g014830.1 Cmu06g1483 1483
2 33571595 33585620 - Conep02aG0179400.1 Cone2ag0767 767
2 33576400 33580790 + Conep02aG0179500.1 Cone2ag0768 768
2 33658196 33662568 + Conep02aG0179900.1 Cone2ag0772 772
2 33689598 33698705 - Conep02aG0180100.1 Cone2ag0774 774
19 2736443 2740481 - Conep19aG0034900.1 Cone19ag0338 338
19 2744253 2746444 - Conep19aG0035000.1 Cone19ag0339 339
4 11103297 11105664 + Cp4.1LG04g13620.1 Cpe04g01364 1364
9 9573145 9576561 + Cp4.1LG09g11120.1 Cpe09g01111 1111
9 9578261 9579620 - Cp4.1LG09g11190.1 Cpe09g01112 1112
20 874855 882549 + Cp4.1LG20g01410.1 Cpe20g00155 155
20 881822 886886 - Cp4.1LG20g01550.1 Cpe20g00156 156
20 887728 891106 + Cp4.1LG20g01620.1 Cpe20g00157 157
1 27203860 27206627 - CrPI670011_01g013940.1 Cre01g1394 1394
1 27209329 27213334 + CrPI670011_01g013950.1 Cre01g1395 1395
1 27214557 27221989 - CrPI670011_01g013960.1 Cre01g1396 1396
6 30879901 30881876 + CrPI670011_06g022920.1 Cre06g2292 2292
1 2769801 2772344 - CsaV3_1G004410.1 Csa01g00441 441
1 4555656 4563847 + CsaV3_1G007180.1 Csa01g00718 718
1 4559146 4564845 - CsaV3_1G007190.1 Csa01g00719 719
1 4565305 4568963 + CsaV3_1G007200.1 Csa01g00720 720
7 67863096 67868036 + Hsped.07g23510.1 Hepe07g2351 2351
7 67880684 67882505 - Hsped.07g23530.1 Hepe07g2353 2353
9 3565555 3568089 - Hsped.09g03980.1 Hepe09g0398 398
10 2220391 2221778 + Lag0024336.1 Lac10g0291 291
2 2015841 2023875 + Lsi02G002360.1 Lsi02g00236 236
2 2024774 2028937 - Lsi02G002380.1 Lsi02g00238 238
2 2029805 2030704 + Lsi02G002390.1 Lsi02g00239 239
6 23319362 23323196 + Lsi06G012740.1 Lsi06g01274 1274
8 39246157 39248491 + Sed0012839.1 Sed08g2759 2759
8 39249887 39254579 - Sed0018638.2 Sed08g2761 2761
12 31906929 31910337 - Sed0023736.1 Sed12g2124 2124
5 72768035 72772658 + Tan0009951.2 Tan05g2186 2186
5 72792891 72795765 - Tan0022767.1 Tan05g2189 2189
9 69547115 69549311 + Tan0005127.1 Tan09g1809 1809
17 1833036 1848019 - Vvi17g186 Vvi17g186 186
17 1848499 1853570 - Vvi17g187 Vvi17g187 187
17 1857306 1861479 - Vvi17g188 Vvi17g188 188
17 1867712 1882977 - Vvi17g189 Vvi17g189 189
17 1883949 1899856 - Vvi17g190 Vvi17g190 190
17 1900869 1903798 + Vvi17g191 Vvi17g191 191
17 1903891 1909337 - Vvi17g192 Vvi17g192 192
17 1919254 1930143 + Vvi17g193 Vvi17g193 193
17 1966512 1970126 - Vvi17g194 Vvi17g194 194
17 1971632 1993484 - Vvi17g195 Vvi17g195 195
       

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