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
Vvi5g889 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma06g01302 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g890 . . . . . . . . . . Cma06g01250 Cma14g01886 Car06g01074 Car14g01689 Sed02g1485 Cpe08g00393 Cpe03g01585 Bhi01g00041 Tan10g0534 Cmetu06g0221 . . . Lcy11g1765 . . . . . . . . Cone15ag0302 . . Lsi05g01829 . . Cme06g00391 . . . Bda13g00497 . . . . . Cmo06g01261 Cmo14g01936 . . . . . . . . . . . . . Cla05g00356 Cam05g0388 Cec05g0393 Cco05g0392 Clacu05g0383 Cmu05g0368 Cre05g0431 . Csa03g01107 Chy06g00377 .
Vvi5g891 . . Bda03g01123 . . . . . . . . . . . . . . . . . . . . . Cla06g00749 Cam06g0802 Cec06g0809 . Clacu06g0804 Cmu06g0777 Cre06g1554 . . . . . Csa02g00933 Chy05g00553 . . . . . . . . Bma06g01285 . . . . . Car08g00904 . . . Bhi12g01505 . . . . . Lcy13g0457 . . . . . . . Lsi09g01150 . . Cme05g00710
Vvi5g892 Blo01g00325 Blo12g00119 . Bda08g00030 Bpe04g01065 Bpe14g00840 Bma04g01049 . Cmo08g01001 . Cma06g01246 Cma14g01889 Car06g01072 Car14g01691 Sed02g1489 Cpe08g00395 Cpe03g01588 Bhi01g00243 Tan10g0528 Cmetu06g1184 Lac12g2058 Hepe05g1754 . Lcy11g1768 . . . . . . . . . Cone7ag0385 . Lsi05g01832 Csa02g00930 . Cme06g00388 . . . Bda13g00492 Bpe05g01135 . Bma02g01208 . . Cmo06g01258 Cmo14g01940 Cma08g01029 Cma17g00108 . . Cpe12g00096 Cpe17g00248 . . . . . . . Cla05g00354 Cam05g0385 Cec05g0389 Cco05g0389 Clacu05g0380 Cmu05g0364 Cre05g0428 . Csa03g01103 Chy06g00374 .
Vvi5g893 . . . . . Bpe14g00842 . . . . . Cma14g01891 . Car14g01693 Sed02g1492 . Cpe03g01591 Bhi01g00241 Tan10g0526 Cmetu06g0437 . Hepe05g1757 . Lcy11g1771 . . . . . . . . . Cone7ag0388 . Lsi05g01835 . . Cme06g00385 . . . Bda13g00490 . . Bma02g01206 . . . Cmo14g01943 . . . . . . . . . . . . . Cla05g00351 Cam05g0383 Cec05g0386 Cco05g0386 Clacu05g0377 Cmu05g0361 Cre05g0426 . Csa03g01101 Chy06g00371 .
Vvi5g894 . . . . . Bpe14g00844 . . . . . Cma14g01894 Car06g01068 Car14g01696 . Cpe08g00397 Cpe03g01593 Bhi01g00235 . . . . . . . . . . . . . . . Cone7ag0390 . Lsi05g01838 . . Cme06g00381 . . . Bda13g00487 . . Bma02g01204 Bma06g01283 . Cmo06g01253 Cmo14g01946 . . . . . . . . . . . . . Cla05g00348 Cam05g0378 Cec05g0383 Cco05g0383 Clacu05g0372 Cmu05g0357 Cre05g0421 . Csa03g01095 Chy06g00365 .
Vvi5g895 . . . . . . . . . . . Cma14g01895 Car06g01066 Car14g01697 Sed12g0379 Cpe08g00398 Cpe03g01594 Bhi01g00233 Tan10g0519 Cmetu06g0638 . . . . . . . . . . . . . Cone7ag0391 . Lsi05g01843 . . Cme06g00380 . . . . . . . . . Cmo06g01252 Cmo14g01947 . . . . . . . . . . . . . Cla05g00347 Cam05g0377 Cec05g0382 Cco05g0382 Clacu05g0371 Cmu05g0356 Cre05g0420 . Csa03g01094 Chy06g00363 .
Vvi5g896 . . . Bda08g00033 . . . . Cmo08g00998 Cmo17g00106 . . . . . . . . . . . . . . Cla06g00751 . . . . . . . . . . . . Chy05g00555 . . . . . . . . . . . . Cma08g01026 Cma17g00103 Car08g00903 Car17g00092 Cpe12g00092 Cpe17g00250 Bhi12g01503 . . . . . Lcy13g0459 . . . . . . . Lsi09g01148 . . Cme05g00712
Vvi5g897 . . . . . . . . . . . . Car06g01059 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla05g00336 . Cec05g0372 . . . . . . . .
Vvi5g898 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 11801146 11802879 + Bda033516 Bda03g01123 1123
8 269519 271248 + Bda024421.1 Bda08g00030 30
8 284642 287287 - Bda024424.2 Bda08g00033 33
13 5755722 5758016 - Bda001392.1 Bda13g00487 487
13 5769953 5771184 - Bda001396.1 Bda13g00490 490
13 5777469 5779211 - Bda001398.1 Bda13g00492 492
13 5863315 5865267 + Bda001403.1 Bda13g00497 497
1 813492 817889 + XM_039029849.1 Bhi01g00041 41
1 4358065 4366259 - XM_039036277.1 Bhi01g00233 233
1 4370350 4374918 - XM_039022116.1 Bhi01g00235 235
1 4540204 4545673 - XM_039031899.1 Bhi01g00241 241
1 4584838 4589313 - XM_039028451.1 Bhi01g00243 243
12 48486153 48489075 + XM_039019923.1 Bhi12g01503 1503
12 48520617 48522638 - XM_039050639.1 Bhi12g01505 1505
1 3969360 3971074 + BLOR00325 Blo01g00325 325
12 8496770 8500992 + BLOR04138 Blo12g00119 119
2 54120400 54122531 - Bma016045.2 Bma02g01204 1204
2 54127610 54128843 - Bma016047.1 Bma02g01206 1206
2 54136393 54138122 - Bma016049.1 Bma02g01208 1208
4 19103069 19104933 + Bma019676.1 Bma04g01049 1049
6 49912101 49914873 - Bma024391.1 Bma06g01283 1283
6 49940034 49941594 - Bma024393.1 Bma06g01285 1285
6 50046308 50052344 + Bma024410.1 Bma06g01302 1302
4 8012924 8014747 + Bpe015735.1 Bpe04g01065 1065
5 23664068 23665596 + Bpe018553.1 Bpe05g01135 1135
14 6310566 6312282 + Bpe014216.1 Bpe14g00840 840
14 6318173 6319647 + Bpe014218.1 Bpe14g00842 842
14 6325672 6327964 + Bpe014220.2 Bpe14g00844 844
5 3470890 3477144 - CaPI482276_05g003770.1 Cam05g0377 377
5 3480599 3484369 - CaPI482276_05g003780.1 Cam05g0378 378
5 3518326 3523528 - CaPI482276_05g003830.1 Cam05g0383 383
5 3535615 3542025 - CaPI482276_05g003850.1 Cam05g0385 385
5 3576140 3582668 + CaPI482276_05g003880.1 Cam05g0388 388
6 11055952 11057493 + CaPI482276_06g008020.1 Cam06g0802 802
6 7944283 7960208 + Carg06300-RA Car06g01059 1059
6 8026824 8029630 - Carg06293-RA Car06g01066 1066
6 8032374 8034461 - Carg06291-RA Car06g01068 1068
6 8056991 8058969 - Carg06287-RA Car06g01072 1072
6 8079330 8084119 + Carg06285-RA Car06g01074 1074
8 6052480 6054978 + Carg11021-RA Car08g00903 903
8 6056915 6058491 - Carg11020-RA Car08g00904 904
14 13431178 13434991 - Carg24756-RA Car14g01689 1689
14 13453270 13454956 + Carg24758-RA Car14g01691 1691
14 13466480 13468382 + Carg24760-RA Car14g01693 1693
14 13483448 13487548 + Carg24763-RA Car14g01696 1696
14 13488320 13491119 + Carg24764-RA Car14g01697 1697
17 535220 537697 + Carg10140-RA Car17g00092 92
5 3102752 3110260 - CcPI632755_05g003820.1 Cco05g0382 382
5 3112556 3116305 - CcPI632755_05g003830.1 Cco05g0383 383
5 3149754 3158208 - CcPI632755_05g003860.1 Cco05g0386 386
5 3171211 3173105 - CcPI632755_05g003890.1 Cco05g0389 389
5 3212868 3218680 + CcPI632755_05g003920.1 Cco05g0392 392
5 3032281 3043930 + CePI673135_05g003720.1 Cec05g0372 372
5 3119842 3121067 - CePI673135_05g003820.1 Cec05g0382 382
5 3124482 3128214 - CePI673135_05g003830.1 Cec05g0383 383
5 3162439 3167562 - CePI673135_05g003860.1 Cec05g0386 386
5 3182238 3186040 - CePI673135_05g003890.1 Cec05g0389 389
5 3221131 3227737 + CePI673135_05g003930.1 Cec05g0393 393
6 9971963 9973507 + CePI673135_06g008090.1 Cec06g0809 809
5 6030321 6040665 + Chy5G095990.1 Chy05g00553 553
5 6050804 6052456 - Chy5G096010.1 Chy05g00555 555
6 2430598 2431665 - Chy6G108910.1 Chy06g00363 363
6 2434197 2437593 - Chy6G108930.1 Chy06g00365 365
6 2484401 2486975 - Chy6G108990.1 Chy06g00371 371
6 2501354 2503242 - Chy6G109020.1 Chy06g00374 374
6 2535796 2545015 + Chy6G109050.1 Chy06g00377 377
5 3184755 3192219 - ClG42_05g0037100.10 Clacu05g0371 371
5 3194446 3198188 - ClG42_05g0037200.10 Clacu05g0372 372
5 3232928 3238168 - ClG42_05g0037700.10 Clacu05g0377 377
5 3252082 3255792 - ClG42_05g0038000.10 Clacu05g0380 380
5 3289993 3296564 + ClG42_05g0038300.10 Clacu05g0383 383
6 9703830 9705376 + ClG42_06g0080400.10 Clacu06g0804 804
5 3045131 3056688 + ClCG05G003200.2 Cla05g00336 336
5 3129391 3135952 - ClCG05G003300.2 Cla05g00347 347
5 3139401 3143807 - ClCG05G003320.2 Cla05g00348 348
5 3180812 3186655 - ClCG05G003350.2 Cla05g00351 351
5 3202413 3204280 - ClCG05G003380.2 Cla05g00354 354
5 3238839 3245944 + ClCG05G003400.2 Cla05g00356 356
6 9986980 9988930 + ClCG06G007730.1 Cla06g00749 749
6 10001268 10003763 - ClCG06G007750.1 Cla06g00751 751
6 8297784 8299697 - CmaCh06G012460.1 Cma06g01246 1246
6 8321911 8326242 + CmaCh06G012500.1 Cma06g01250 1250
8 6416449 6418953 + CmaCh08G010260.1 Cma08g01026 1026
8 6435483 6437376 - CmaCh08G010290.1 Cma08g01029 1029
14 13349812 13353624 - CmaCh14G018860.1 Cma14g01886 1886
14 13372199 13374446 + CmaCh14G018890.1 Cma14g01889 1889
14 13384125 13387337 + CmaCh14G018910.1 Cma14g01891 1891
14 13402453 13408311 + CmaCh14G018940.1 Cma14g01894 1894
14 13408335 13409727 + CmaCh14G018950.1 Cma14g01895 1895
17 503276 505753 + CmaCh17G001030.1 Cma17g00103 103
17 524868 529733 - CmaCh17G001080.1 Cma17g00108 108
5 8305425 8307343 + MELO3C020452.2.1 Cme05g00710 710
5 8316206 8318759 - MELO3C020450.2.1 Cme05g00712 712
6 2386192 2388884 - MELO3C006312.2.1 Cme06g00380 380
6 2389842 2394238 - MELO3C006313.2.1 Cme06g00381 381
6 2420541 2425261 - MELO3C006315.2.1 Cme06g00385 385
6 2438136 2440939 - MELO3C006317.2.1 Cme06g00388 388
6 2491513 2495739 + MELO3C006320.2.1 Cme06g00391 391
6 2684409 2688196 + PI0024770.1 Cmetu06g0221 221
6 2627820 2633077 - PI0005719.1 Cmetu06g0437 437
6 2603413 2606245 - PI0000361.3 Cmetu06g0638 638
6 2647421 2649330 - PI0020396.1 Cmetu06g1184 1184
6 9464088 9467147 - CmoCh06G012520.1 Cmo06g01252 1252
6 9468323 9472100 - CmoCh06G012530.1 Cmo06g01253 1253
6 9494495 9496718 - CmoCh06G012580.1 Cmo06g01258 1258
6 9517417 9522045 + CmoCh06G012610.1 Cmo06g01261 1261
8 6470819 6473362 + CmoCh08G009980.1 Cmo08g00998 998
8 6487936 6490050 - CmoCh08G010010.1 Cmo08g01001 1001
14 14340834 14344564 - CmoCh14G019360.1 Cmo14g01936 1936
14 14363407 14365662 + CmoCh14G019400.1 Cmo14g01940 1940
14 14376752 14378632 + CmoCh14G019430.1 Cmo14g01943 1943
14 14393688 14400483 + CmoCh14G019460.1 Cmo14g01946 1946
14 14400529 14401898 + CmoCh14G019470.1 Cmo14g01947 1947
17 575710 578187 + CmoCh17G001060.1 Cmo17g00106 106
5 3023207 3030676 - CmPI595203_05g003560.1 Cmu05g0356 356
5 3032904 3036646 - CmPI595203_05g003570.1 Cmu05g0357 357
5 3070903 3076137 - CmPI595203_05g003610.1 Cmu05g0361 361
5 3087444 3093798 - CmPI595203_05g003640.1 Cmu05g0364 364
5 3128004 3134575 + CmPI595203_05g003680.1 Cmu05g0368 368
6 9521323 9522869 + CmPI595203_06g007770.1 Cmu06g0777 777
7 1700698 1703114 + Conep07aG0039400.1 Cone7ag0385 385
7 1711919 1714084 + Conep07aG0039700.1 Cone7ag0388 388
7 1718930 1721356 + Conep07aG0039900.1 Cone7ag0390 390
7 1725255 1726337 + Conep07aG0040000.1 Cone7ag0391 391
15 1409536 1414622 - Conep15aG0030800.1 Cone15ag0302 302
3 12243314 12247101 - Cp4.1LG03g18100.1 Cpe03g01585 1585
3 12266689 12268369 + Cp4.1LG03g18410.1 Cpe03g01588 1588
3 12276560 12284104 + Cp4.1LG03g18420.1 Cpe03g01591 1591
3 12298519 12302320 + Cp4.1LG03g18020.1 Cpe03g01593 1593
3 12304742 12305902 + Cp4.1LG03g18050.1 Cpe03g01594 1594
8 2475840 2480460 - Cp4.1LG08g02880.1 Cpe08g00393 393
8 2503821 2508263 + Cp4.1LG08g02740.1 Cpe08g00395 395
8 2528331 2533573 + Cp4.1LG08g02780.1 Cpe08g00397 397
8 2535043 2537863 + Cp4.1LG08g02810.1 Cpe08g00398 398
12 548387 551623 + Cp4.1LG12g00870.1 Cpe12g00092 92
12 574549 577271 - Cp4.1LG12g00910.1 Cpe12g00096 96
17 1635834 1638550 + Cp4.1LG17g03350.1 Cpe17g00248 248
17 1652524 1656723 - Cp4.1LG17g03230.1 Cpe17g00250 250
5 3802880 3810394 - CrPI670011_05g004200.1 Cre05g0420 420
5 3812518 3816260 - CrPI670011_05g004210.1 Cre05g0421 421
5 3850628 3855782 - CrPI670011_05g004260.1 Cre05g0426 426
5 3870508 3874249 - CrPI670011_05g004280.1 Cre05g0428 428
5 3909291 3915954 + CrPI670011_05g004310.1 Cre05g0431 431
6 10711489 10713033 + CrPI670011_06g015540.1 Cre06g1554 1554
2 8779877 8783679 + CsaV3_2G011460.1 Csa02g00930 930
2 8806267 8808266 + CsaV3_2G011490.1 Csa02g00933 933
3 8671508 8674208 - CsaV3_3G010940.1 Csa03g01094 1094
3 8674955 8679477 - CsaV3_3G010950.1 Csa03g01095 1095
3 8707121 8711973 - CsaV3_3G011010.1 Csa03g01101 1101
3 8719914 8725611 - CsaV3_3G011030.1 Csa03g01103 1103
3 8756736 8760992 + CsaV3_3G011070.1 Csa03g01107 1107
5 67859560 67862072 + Hsped.05g17540.1 Hepe05g1754 1754
5 67888506 67891825 + Hsped.05g17570.1 Hepe05g1757 1757
12 37689147 37691373 - Lag0016430.1 Lac12g2058 2058
11 41448710 41453221 - Maker00031888 Lcy11g1765 1765
11 41494911 41499788 + Maker00031588 Lcy11g1768 1768
11 41518815 41524020 + Maker00032116 Lcy11g1771 1771
13 5464482 5466641 + Maker00023320 Lcy13g0457 457
13 5480749 5483244 - Maker00023685 Lcy13g0459 459
5 25559297 25571269 - Lsi05G018290.1 Lsi05g01829 1829
5 25611094 25615839 + Lsi05G018320.1 Lsi05g01832 1832
5 25630566 25635763 + Lsi05G018350.1 Lsi05g01835 1835
5 25663614 25670407 + Lsi05G018380.1 Lsi05g01838 1838
5 25689556 25691733 + Lsi05G018430.1 Lsi05g01843 1843
9 18426235 18428721 + Lsi09G011480.1 Lsi09g01148 1148
9 18445172 18447255 - Lsi09G011500.1 Lsi09g01150 1150
2 50812155 50816901 - Sed0022855.1 Sed02g1485 1485
2 50839758 50842943 + Sed0011038.1 Sed02g1489 1489
2 50855331 50858547 + Sed0018555.2 Sed02g1492 1492
12 2301165 2304918 - Sed0001038.2 Sed12g0379 379
10 4148061 4151178 - Tan0002009.2 Tan10g0519 519
10 4203530 4209958 - Tan0021683.2 Tan10g0526 526
10 4237488 4240387 - Tan0009188.1 Tan10g0528 528
10 4304719 4309359 + Tan0015340.1 Tan10g0534 534
5 13719219 13791705 - Vvi5g889 Vvi5g889 889
5 13901213 13919034 + Vvi5g890 Vvi5g890 890
5 13951046 13954128 - Vvi5g891 Vvi5g891 891
5 14028571 14031484 + Vvi5g892 Vvi5g892 892
5 14065431 14067113 + Vvi5g893 Vvi5g893 893
5 14128822 14143945 + Vvi5g894 Vvi5g894 894
5 14146033 14151956 + Vvi5g895 Vvi5g895 895
5 14152438 14154922 - Vvi5g896 Vvi5g896 896
5 14171951 14187569 + Vvi5g897 Vvi5g897 897
5 14187584 14189829 + Vvi5g898 Vvi5g898 898
       

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