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
Vvi17g296 . . . . . . . . . . Cma10g00306 . Car10g00291 . . Cpe20g00129 . . . . . . . . . . . . . . . . . Cone13ag0308 . Lsi02g00190 Csa01g00672 Chy12g01429 Cme12g01867 . . . . . . . . Sed08g2189 Cmo10g00327 . . . Car13g00850 . . . Bhi08g01242 Tan05g2258 Cmetu12g1703 Lac10g0246 Hepe07g2381 . . . . . . . . . . . . .
Vvi17g297 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy12g01430 Cme12g01868 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa01g00397 . .
Vvi17g298 . Blo16g00133 . . . Bpe13g00358 Bma06g00048 . Cmo13g01058 . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00189 Csa01g00671 Chy12g01431 Cme12g01869 . . Bda11g01772 . . . . . Sed08g2188 . . . Cma18g00047 Car13g00851 Car18g00041 Cpe09g01133 . Bhi08g01241 Tan05g2259 Cmetu12g1441 Lac10g0245 Hepe07g2382 . . Cla04g01083 Cam04g1135 Cec01g1645 Cco01g1694 Clacu04g1163 Cmu04g1144 Cre01g1440 . . . .
Vvi17g299 Blo04g00831 . Bda06g00810 Bda15g00514 Bpe12g00694 . . Bma12g01234 . . Cma10g00305 Cma11g00284 Car10g00290 Car11g00258 . . Cpe04g01394 . . . . . . . Cla06g01457 Cam06g1609 Cec06g1671 Cco06g1665 . . . . . Cone13ag0306 . . . . . Blo13g00170 Blo15g00066 . . Bpe07g01039 Bpe15g00528 Bma03g00898 Bma08g00059 . Cmo10g00326 Cmo11g00287 . . . . . Cpe18g00810 . . . . . . . . . . . . . . Lsi06g01320 Csa01g00206 Chy02g02353 Cme02g01729
Vvi17g300 . . . . . Bpe13g00357 . . . . Cma10g00304 Cma11g00283 Car10g00289 Car11g00257 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo10g00325 Cmo11g00286 . . . . . . . . . . . . . . . . . . . . Lsi06g01321 . . Cme02g01730
Vvi17g301 . . Bda06g00809 . . . . Bma12g01233 Cmo13g01060 . . . . . . Cpe20g00127 . . . . . . . . Cla06g01459 Cam06g1611 Cec06g1673 Cco06g1667 Clacu06g1575 Cmu06g1527 Cre06g2338 . . Cone2ag0431 Cone16ag0569 Lsi02g00187 Csa01g00670 . Cme12g01871 . Blo15g00067 . . Bpe07g01038 . . . Sed08g2187 . . Cma13g01019 . Car13g00853 Car18g00040 Cpe09g01134 . Bhi08g01240 Tan05g2261 Cmetu03g1280 Lac10g0243 Hepe07g2387 . . Cla04g01085 Cam04g1138 Cec01g1648 Cco01g1697 Clacu04g1166 Cmu04g1147 Cre01g1442 Lsi06g01322 . . .
Vvi17g302 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g303 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g304 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g305 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 11323189 11323827 + Bda024138.1 Bda06g00809 809
6 11326123 11338357 - Bda024139.1 Bda06g00810 810
11 52560513 52563437 + Bda008692.1 Bda11g01772 1772
15 8211756 8220255 + Bda012344.1 Bda15g00514 514
8 38329775 38331126 + XM_039039658.1 Bhi08g01240 1240
8 38365572 38369013 + XM_039038580.1 Bhi08g01241 1241
8 38369158 38371948 + XM_039038581.1 Bhi08g01242 1242
4 8806497 8821707 - BLOR13743 Blo04g00831 831
13 6011704 6020273 - BLOR05451 Blo13g00170 170
15 557250 565975 + BLOR06460 Blo15g00066 66
15 568520 569167 - BLOR06461 Blo15g00067 67
16 3023539 3026463 - BLOR07381 Blo16g00133 133
3 8870137 8878308 - Bma017223.1 Bma03g00898 898
6 817159 820080 + Bma022658.1 Bma06g00048 48
8 750624 759133 + Bma027055.1 Bma08g00059 59
12 45288517 45289149 + Bma008599.1 Bma12g01233 1233
12 45293119 45302102 - Bma008600.1 Bma12g01234 1234
7 15892787 15893425 + Bpe021882.1 Bpe07g01038 1038
7 15895945 15904982 - Bpe021883.1 Bpe07g01039 1039
12 12513117 12521553 - Bpe005954.1 Bpe12g00694 694
13 11353868 11354625 - Bpe006484.1 Bpe13g00357 357
13 11355168 11358092 + Bpe006485.1 Bpe13g00358 358
15 16437261 16445524 - Bpe001463.1 Bpe15g00528 528
4 25440495 25443413 - CaPI482276_04g011350.1 Cam04g1135 1135
4 25455800 25456531 - CaPI482276_04g011380.1 Cam04g1138 1138
6 27562789 27572602 + CaPI482276_06g016090.1 Cam06g1609 1609
6 27582306 27583076 - CaPI482276_06g016110.1 Cam06g1611 1611
10 1390003 1390770 - Carg15156-RA Car10g00289 289
10 1392582 1401596 - Carg15157-RA Car10g00290 290
10 1405147 1407609 + Carg15158-RA Car10g00291 291
11 1422055 1422689 - Carg09132-RA Car11g00257 257
11 1423895 1431529 - Carg09131-RA Car11g00258 258
13 9102797 9104136 - Carg04822-RA Car13g00850 850
13 9104995 9107820 - Carg04821-RA Car13g00851 851
13 9110089 9110829 - Carg04819-RA Car13g00853 853
18 178497 179231 + Carg22746-RA Car18g00040 40
18 180323 183259 + Carg22745-RA Car18g00041 41
1 29677256 29680174 - CcPI632755_01g016940.1 Cco01g1694 1694
1 29695223 29695954 - CcPI632755_01g016970.1 Cco01g1697 1697
6 27234205 27244649 + CcPI632755_06g016650.1 Cco06g1665 1665
6 27253696 27254466 - CcPI632755_06g016670.1 Cco06g1667 1667
1 31116130 31119048 - CePI673135_01g016450.1 Cec01g1645 1645
1 31131583 31132314 - CePI673135_01g016480.1 Cec01g1648 1648
6 30305957 30315795 + CePI673135_06g016710.1 Cec06g1671 1671
6 30325631 30326401 - CePI673135_06g016730.1 Cec06g1673 1673
2 27414126 27426859 + Chy2G046200.1 Chy02g02353 2353
12 18333955 18336396 - Chy12G220290.1 Chy12g01429 1429
12 18338285 18339708 - Chy12G220300.1 Chy12g01430 1430
12 18340646 18343579 - Chy12G220310.1 Chy12g01431 1431
4 25828754 25831672 - ClG42_04g0116300.10 Clacu04g1163 1163
4 25844132 25844863 - ClG42_04g0116600.10 Clacu04g1166 1166
6 26639192 26639962 - ClG42_06g0157500.10 Clacu06g1575 1575
4 26018509 26024016 - ClCG04G011000.2 Cla04g01083 1083
4 26032426 26034551 - ClCG04G011030.2 Cla04g01085 1085
6 28129883 28140526 + ClCG06G014680.2 Cla06g01457 1457
6 28149785 28150555 - ClCG06G014700.2 Cla06g01459 1459
10 1375377 1376854 - CmaCh10G003040.1 Cma10g00304 304
10 1377743 1387802 - CmaCh10G003050.1 Cma10g00305 305
10 1390730 1393191 + CmaCh10G003060.1 Cma10g00306 306
11 1407135 1408048 - CmaCh11G002830.1 Cma11g00283 283
11 1408956 1418976 - CmaCh11G002840.1 Cma11g00284 284
13 7817245 7817967 - CmaCh13G010190.1 Cma13g01019 1019
18 191123 194059 + CmaCh18G000470.1 Cma18g00047 47
2 24301944 24311228 + MELO3C017320.2.1 Cme02g01729 1729
2 24313843 24315479 + MELO3C017319.2.1 Cme02g01730 1730
12 24901650 24904536 - MELO3C002098.2.1 Cme12g01867 1867
12 24906240 24908178 - MELO3C002097.2.1 Cme12g01868 1868
12 24908785 24911987 - MELO3C002096.2.1 Cme12g01869 1869
12 24914815 24915714 - MELO3C002094.2.1 Cme12g01871 1871
3 15576045 15576902 - PI0021634.1 Cmetu03g1280 1280
12 1310551 1313483 + PI0018948.1 Cmetu12g1441 1441
12 1314451 1316121 + PI0017535.1 Cmetu12g1703 1703
10 1464973 1466319 - CmoCh10G003250.1 Cmo10g00325 325
10 1467626 1477012 - CmoCh10G003260.1 Cmo10g00326 326
10 1480381 1482916 + CmoCh10G003270.1 Cmo10g00327 327
11 1388736 1389479 - CmoCh11G002860.1 Cmo11g00286 286
11 1390582 1400439 - CmoCh11G002870.1 Cmo11g00287 287
13 8813036 8815861 - CmoCh13G010580.1 Cmo13g01058 1058
13 8818099 8818929 - CmoCh13G010600.1 Cmo13g01060 1060
4 26010759 26013677 - CmPI595203_04g011440.1 Cmu04g1144 1144
4 26026138 26026869 - CmPI595203_04g011470.1 Cmu04g1147 1147
6 26542139 26542909 - CmPI595203_06g015270.1 Cmu06g1527 1527
2 2327101 2327915 + Conep02aG0044200.1 Cone2ag0431 431
13 2395636 2404077 - Conep13aG0032400.1 Cone13ag0306 306
13 2429995 2432374 + Conep13aG0032600.1 Cone13ag0308 308
16 7555821 7557150 - Conep16aG0293000.1 Cone16ag0569 569
4 11273317 11283609 + Cp4.1LG04g14000.1 Cpe04g01394 1394
9 9715537 9718473 - Cp4.1LG09g11300.1 Cpe09g01133 1133
9 9719579 9720313 - Cp4.1LG09g11310.1 Cpe09g01134 1134
18 7551304 7558541 - Cp4.1LG18g08120.1 Cpe18g00810 810
20 707612 708349 + Cp4.1LG20g01310.1 Cpe20g00127 127
20 710524 715819 + Cp4.1LG20g01280.1 Cpe20g00129 129
1 27660396 27663314 - CrPI670011_01g014400.1 Cre01g1440 1440
1 27671356 27672087 - CrPI670011_01g014420.1 Cre01g1442 1442
6 31329197 31329967 - CrPI670011_06g023380.1 Cre06g2338 2338
1 1326160 1333097 + CsaV3_1G002060.1 Csa01g00206 206
1 2479842 2484920 + CsaV3_1G003970.1 Csa01g00397 397
1 4310545 4313593 + CsaV3_1G006700.1 Csa01g00670 670
1 4314343 4318053 + CsaV3_1G006710.1 Csa01g00671 671
1 4318571 4320365 + CsaV3_1G006720.1 Csa01g00672 672
7 68189361 68192646 - Hsped.07g23810.1 Hepe07g2381 2381
7 68192692 68195586 - Hsped.07g23820.1 Hepe07g2382 2382
7 68209383 68210619 - Hsped.07g23870.1 Hepe07g2387 2387
10 1902158 1902889 + Lag0024288.1 Lac10g0243 243
10 1907907 1910837 + Lag0024290.1 Lac10g0245 245
10 1911986 1914107 + Lag0024291.1 Lac10g0246 246
2 1604418 1605137 + Lsi02G001870.1 Lsi02g00187 187
2 1609515 1612409 + Lsi02G001890.1 Lsi02g00189 189
2 1612454 1620917 + Lsi02G001900.1 Lsi02g00190 190
6 23789810 23800065 + Lsi06G013200.1 Lsi06g01320 1320
6 23803475 23805195 + Lsi06G013210.1 Lsi06g01321 1321
6 23809173 23809943 - Lsi06G013220.1 Lsi06g01322 1322
8 35782640 35783308 + Sed0020630.1 Sed08g2187 2187
8 35785663 35788297 + Sed0024950.1 Sed08g2188 2188
8 35789354 35791134 + Sed0025513.1 Sed08g2189 2189
5 73499709 73501367 - Tan0015636.1 Tan05g2258 2258
5 73502522 73505940 - Tan0001249.1 Tan05g2259 2259
5 73516303 73517854 - Tan0007161.1 Tan05g2261 2261
17 3280282 3282567 - Vvi17g296 Vvi17g296 296
17 3284711 3285848 - Vvi17g297 Vvi17g297 297
17 3301317 3304411 - Vvi17g298 Vvi17g298 298
17 3316244 3333781 + Vvi17g299 Vvi17g299 299
17 3334899 3336318 + Vvi17g300 Vvi17g300 300
17 3340205 3341555 - Vvi17g301 Vvi17g301 301
17 3349145 3349561 - Vvi17g302 Vvi17g302 302
17 3351113 3351628 - Vvi17g303 Vvi17g303 303
17 3359777 3359966 - Vvi17g304 Vvi17g304 304
17 3359967 3361323 - Vvi17g305 Vvi17g305 305
       

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