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
Vvi17g316 Blo04g00823 . Bda06g00806 . . . . . Cmo13g01065 Cmo18g00035 . Cma11g00273 Car10g00217 Car11g00249 . Cpe20g00121 . . . . . . . . . . . . . . . . . Cone13ag0280 . Lsi02g00181 Csa01g00664 Chy12g01439 Cme12g01877 . Blo15g00070 . Bda14g00929 . Bpe15g00523 Bma03g00894 . Sed08g2181 Cmo10g00245 Cmo11g00278 Cma13g01024 Cma18g00042 Car13g00859 Car18g00036 Cpe09g01138 . Bhi08g01232 Tan05g2269 Cmetu12g1130 Lac10g0236 Hepe07g2393 . . Cla04g01093 Cam04g1144 Cec01g1654 Cco01g1703 Clacu04g1172 Cmu04g1153 Cre01g1448 . Csa01g00387 . Cme02g01738
Vvi17g317 . Blo16g00136 . . . Bpe13g00351 . . . . Cma10g00232 Cma11g00271 Car10g00218 Car11g00248 . . Cpe04g01403 . . . . . . . Cla06g01466 Cam06g1619 Cec06g1682 Cco06g1674 Clacu06g1584 Cmu06g1535 Cre06g2346 . . Cone13ag0281 . . . . . . . . . . . . . . Cmo10g00246 Cmo11g00277 . . . . . Cpe18g00760 . . . . . . . . . . . . . . Lsi06g01329 Csa01g00386 Chy02g02360 Cme02g01739
Vvi17g318 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g319 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo13g00165 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g320 . . . Bda15g00516 Bpe12g00691 . . . Cmo13g01066 Cmo18g00034 . . . . . Cpe20g00120 . . . . . . . . . . . . . . . . . . . Lsi02g00180 Csa01g00663 Chy12g01440 Cme12g01878 . . . . . . . Bma08g00062 Sed08g2180 . . Cma13g01025 Cma18g00041 Car13g00860 Car18g00035 Cpe09g01139 . Bhi08g01231 Tan05g2270 Cmetu12g1774 Lac10g0235 Hepe07g2394 . . Cla04g01094 Cam04g1145 Cec01g1655 Cco01g1704 Clacu04g1173 Cmu04g1154 Cre01g1449 . . . .
Vvi17g321 Blo04g00775 . . . . . . Bma12g01231 . . Cma10g00233 Cma11g00270 Car10g00219 . . . . . . . . . . . Cla06g01467 . . . . . . . . Cone13ag0282 Cone19ag0281 . . . . . Blo15g00071 . . Bpe07g01035 . . . . Cmo10g00248 Cmo11g00276 . . . . . . . . . . . . . . . . . . . . . Csa01g00247 Chy02g02362 Cme02g01740
Vvi17g322 . . . Bda15g00517 Bpe12g00690 . . . . . Cma10g00234 Cma11g00269 Car10g00220 Car11g00246 . . Cpe04g01405 . . . . . . . Cla06g01468 Cam06g1621 Cec06g1684 Cco06g1676 Clacu06g1586 Cmu06g1537 Cre06g2348 . . Cone13ag0283 . . . . . Blo13g00164 . . . . . . Bma08g00063 . Cmo10g00249 Cmo11g00275 . . . . . Cpe18g00758 . . . . . . . . . . . . . . Lsi06g01332 Csa01g00383 Chy02g02363 Cme02g01741
Vvi17g323 . . . . . . . . . . . Cma11g00268 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa01g00382 Chy02g02364 .
Vvi17g324 . Blo16g00138 . . . Bpe13g00347 Bma06g00038 . . . . . . . . . . . . . . . . . . . . . . . . Cone2ag0716 Cone16ag0580 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g325 . . Bda06g00804 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0285 . . . . . . Blo15g00073 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 11267894 11287202 + Bda024131.2 Bda06g00804 804
6 11303406 11309005 - Bda024135.1 Bda06g00806 806
14 7379896 7381184 + Bda027712.1 Bda14g00929 929
15 8233872 8236804 - Bda012346.1 Bda15g00516 516
15 8243656 8246068 + Bda012347.1 Bda15g00517 517
8 38189932 38193504 + XM_039038294.1 Bhi08g01231 1231
8 38193667 38201453 - XM_039038293.1 Bhi08g01232 1232
4 7649135 7650327 - BLOR13687 Blo04g00775 775
4 8647564 8667093 - BLOR13735 Blo04g00823 823
13 5835299 5849480 - BLOR05445 Blo13g00164 164
13 5851079 5854099 + BLOR05446 Blo13g00165 165
15 589887 597053 + BLOR06464 Blo15g00070 70
15 601408 603312 - BLOR06465 Blo15g00071 71
15 615216 621056 - BLOR06467 Blo15g00073 73
16 3089301 3090182 + BLOR07384 Blo16g00136 136
16 3111198 3111966 - BLOR07386 Blo16g00138 138
3 8758240 8777735 - Bma017216.1 Bma03g00894 894
6 651157 652018 + Bma022645.1 Bma06g00038 38
8 775073 777933 - Bma027059.1 Bma08g00062 62
8 779667 781566 + Bma027060.1 Bma08g00063 63
12 45245427 45247321 + Bma008595.1 Bma12g01231 1231
7 15871621 15873490 + Bpe021879.1 Bpe07g01035 1035
12 12493330 12494858 - Bpe005950.1 Bpe12g00690 690
12 12495568 12498467 + Bpe005951.1 Bpe12g00691 691
13 11286685 11287549 + Bpe006474.1 Bpe13g00347 347
13 11317684 11321686 - Bpe006478.2 Bpe13g00351 351
15 16390907 16401256 - Bpe001456.1 Bpe15g00523 523
4 25518254 25525444 + CaPI482276_04g011440.1 Cam04g1144 1144
4 25526141 25529260 - CaPI482276_04g011450.1 Cam04g1145 1145
6 27644066 27656843 + CaPI482276_06g016190.1 Cam06g1619 1619
6 27669524 27673340 + CaPI482276_06g016210.1 Cam06g1621 1621
10 1041832 1047565 + Carg17926-RA Car10g00217 217
10 1048000 1051997 + Carg17925-RA Car10g00218 218
10 1053015 1054414 - Carg17924-RA Car10g00219 219
10 1056006 1058855 + Carg17923-RA Car10g00220 220
11 1376436 1379373 - Carg09143-RA Car11g00246 246
11 1384503 1389020 - Carg09141-RA Car11g00248 248
11 1389566 1394471 - Carg09140-RA Car11g00249 249
13 9140461 9146141 + Carg04813-RA Car13g00859 859
13 9146483 9149687 - Carg04812-RA Car13g00860 860
18 151771 154340 + Carg22751-RA Car18g00035 35
18 154739 160419 - Carg22750-RA Car18g00036 36
1 29757193 29764391 + CcPI632755_01g017030.1 Cco01g1703 1703
1 29765092 29768223 - CcPI632755_01g017040.1 Cco01g1704 1704
6 27321915 27334645 + CcPI632755_06g016740.1 Cco06g1674 1674
6 27347699 27351542 + CcPI632755_06g016760.1 Cco06g1676 1676
1 31202665 31209755 + CePI673135_01g016540.1 Cec01g1654 1654
1 31210452 31213567 - CePI673135_01g016550.1 Cec01g1655 1655
6 30402870 30406925 + CePI673135_06g016820.1 Cec06g1682 1682
6 30419761 30423607 + CePI673135_06g016840.1 Cec06g1684 1684
2 27474784 27487359 + Chy2G046270.1 Chy02g02360 2360
2 27489544 27491197 - Chy2G046290.1 Chy02g02362 2362
2 27498074 27501630 + Chy2G046300.1 Chy02g02363 2363
2 27508971 27509718 + Chy2G046310.1 Chy02g02364 2364
12 18388118 18395078 + Chy12G220390.1 Chy12g01439 1439
12 18395788 18399149 - Chy12G220400.1 Chy12g01440 1440
4 25908380 25915497 + ClG42_04g0117200.10 Clacu04g1172 1172
4 25916198 25919319 - ClG42_04g0117300.10 Clacu04g1173 1173
6 26709471 26713522 + ClG42_06g0158400.10 Clacu06g1584 1584
6 26726286 26730095 + ClG42_06g0158600.10 Clacu06g1586 1586
4 26116435 26123828 + ClCG04G011120.2 Cla04g01093 1093
4 26124529 26127650 - ClCG04G011130.2 Cla04g01094 1094
6 28204565 28226763 + ClCG06G014770.2 Cla06g01466 1466
6 28228130 28231310 - ClCG06G014790.2 Cla06g01467 1467
6 28238616 28242425 + ClCG06G014800.2 Cla06g01468 1468
10 1031940 1042543 + CmaCh10G002320.1 Cma10g00232 232
10 1043530 1044800 - CmaCh10G002330.1 Cma10g00233 233
10 1046548 1052356 + CmaCh10G002340.1 Cma10g00234 234
11 1360435 1362530 - CmaCh11G002680.1 Cma11g00268 268
11 1363997 1366969 - CmaCh11G002690.1 Cma11g00269 269
11 1368848 1371938 + CmaCh11G002700.1 Cma11g00270 270
11 1371544 1376184 - CmaCh11G002710.1 Cma11g00271 271
11 1376519 1381690 - CmaCh11G002730.1 Cma11g00273 273
13 7847124 7853481 + CmaCh13G010240.1 Cma13g01024 1024
13 7853291 7857115 - CmaCh13G010250.1 Cma13g01025 1025
18 161955 165004 + CmaCh18G000410.1 Cma18g00041 41
18 165157 170981 - CmaCh18G000420.1 Cma18g00042 42
2 24364212 24371060 + MELO3C017311.2.1 Cme02g01738 1738
2 24397342 24402466 + MELO3C017309.2.1 Cme02g01739 1739
2 24403900 24406248 - MELO3C017308.2.1 Cme02g01740 1740
2 24411435 24416028 + MELO3C017307.2.1 Cme02g01741 1741
12 24957117 24964553 + MELO3C002088.2.1 Cme12g01877 1877
12 24965266 24969191 - MELO3C002087.2.1 Cme12g01878 1878
12 1253104 1260991 - PI0026684.1 Cmetu12g1130 1130
12 1248736 1253109 + PI0016791.1 Cmetu12g1774 1774
10 1086364 1096746 + CmoCh10G002450.1 Cmo10g00245 245
10 1097090 1101656 + CmoCh10G002460.1 Cmo10g00246 246
10 1102143 1103651 - CmoCh10G002480.1 Cmo10g00248 248
10 1105407 1110346 + CmoCh10G002490.1 Cmo10g00249 249
11 1343340 1346009 - CmoCh11G002750.1 Cmo11g00275 275
11 1348230 1349479 + CmoCh11G002760.1 Cmo11g00276 276
11 1351036 1355729 - CmoCh11G002770.1 Cmo11g00277 277
11 1355854 1361181 - CmoCh11G002780.1 Cmo11g00278 278
13 8849908 8856029 + CmoCh13G010650.1 Cmo13g01065 1065
13 8856004 8859827 - CmoCh13G010660.1 Cmo13g01066 1066
18 200638 203432 + CmoCh18G000340.1 Cmo18g00034 34
18 203546 209133 - CmoCh18G000350.1 Cmo18g00035 35
4 26090398 26097515 + CmPI595203_04g011530.1 Cmu04g1153 1153
4 26098216 26101340 - CmPI595203_04g011540.1 Cmu04g1154 1154
6 26612434 26616485 + CmPI595203_06g015350.1 Cmu06g1535 1535
6 26629269 26633109 + CmPI595203_06g015370.1 Cmu06g1537 1537
2 32789302 32790909 + Conep02aG0172900.1 Cone2ag0716 716
13 2060549 2069169 + Conep13aG0029800.1 Cone13ag0280 280
13 2074872 2080272 + Conep13aG0029900.1 Cone13ag0281 281
13 2094453 2096617 - Conep13aG0030000.1 Cone13ag0282 282
13 2111285 2114346 + Conep13aG0030100.1 Cone13ag0283 283
13 2125706 2131093 - Conep13aG0030300.1 Cone13ag0285 285
16 7599707 7601168 - Conep16aG0294100.1 Cone16ag0580 580
19 2014602 2017185 - Conep19aG0029100.1 Cone19ag0281 281
4 11314103 11323725 + Cp4.1LG04g14020.1 Cpe04g01403 1403
4 11329232 11332333 + Cp4.1LG04g14010.1 Cpe04g01405 1405
9 9741524 9747314 + Cp4.1LG09g11450.1 Cpe09g01138 1138
9 9747403 9751269 - Cp4.1LG09g11330.1 Cpe09g01139 1139
18 7283773 7287650 - Cp4.1LG18g07510.1 Cpe18g00758 758
18 7290899 7295348 - Cp4.1LG18g07720.1 Cpe18g00760 760
20 667866 672285 + Cp4.1LG20g01090.1 Cpe20g00120 120
20 671208 677283 - Cp4.1LG20g01160.1 Cpe20g00121 121
1 27733699 27740775 + CrPI670011_01g014480.1 Cre01g1448 1448
1 27741476 27744589 - CrPI670011_01g014490.1 Cre01g1449 1449
6 31397524 31410345 + CrPI670011_06g023460.1 Cre06g2346 2346
6 31423330 31427171 + CrPI670011_06g023480.1 Cre06g2348 2348
1 1548860 1551112 + CsaV3_1G002470.1 Csa01g00247 247
1 2372211 2374433 - CsaV3_1G003820.1 Csa01g00382 382
1 2377357 2381680 - CsaV3_1G003830.1 Csa01g00383 383
1 2392644 2396031 - CsaV3_1G003860.1 Csa01g00386 386
1 2397832 2405260 - CsaV3_1G003870.1 Csa01g00387 387
1 4259515 4263442 + CsaV3_1G006630.1 Csa01g00663 663
1 4263073 4271287 - CsaV3_1G006640.1 Csa01g00664 664
7 68281632 68290230 + Hsped.07g23930.1 Hepe07g2393 2393
7 68290404 68293761 - Hsped.07g23940.1 Hepe07g2394 2394
10 1834127 1837318 + Lag0024280.1 Lac10g0235 235
10 1838094 1845053 - Lag0024281.1 Lac10g0236 236
2 1534632 1538492 + Lsi02G001800.1 Lsi02g00180 180
2 1537898 1546982 - Lsi02G001810.1 Lsi02g00181 181
6 23873869 23887579 + Lsi06G013290.1 Lsi06g01329 1329
6 23902789 23905361 + Lsi06G013320.1 Lsi06g01332 1332
8 35707433 35711821 + Sed0008793.3 Sed08g2180 2180
8 35712444 35720396 - Sed0017030.1 Sed08g2181 2181
5 73977657 73984648 + Tan0021875.1 Tan05g2269 2269
5 73985374 73988923 - Tan0001604.1 Tan05g2270 2270
17 3517940 3530407 + Vvi17g316 Vvi17g316 316
17 3531078 3538891 + Vvi17g317 Vvi17g317 317
17 3540736 3546974 - Vvi17g318 Vvi17g318 318
17 3553074 3561452 + Vvi17g319 Vvi17g319 319
17 3562313 3570422 + Vvi17g320 Vvi17g320 320
17 3581767 3583750 - Vvi17g321 Vvi17g321 321
17 3607715 3610689 + Vvi17g322 Vvi17g322 322
17 3612189 3618035 + Vvi17g323 Vvi17g323 323
17 3623090 3624481 - Vvi17g324 Vvi17g324 324
17 3626430 3634245 - Vvi17g325 Vvi17g325 325
       

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