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
Vvi1g1241 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1242 . . . . . . . . . Cmo18g00685 . Cma18g00699 . Car18g00648 . . . Bhi07g01922 . . . Hepe10g1518 . . . . . . . . . . . . . Lsi04g00679 . . Cme10g00659 . . . . . . . . . . . . . . . . . . . . . . . . Cla11g01341 . . . . . . . . . .
Vvi1g1243 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1244 Blo01g00357 . . . Bpe13g00531 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1245 . . . . Bpe13g00532 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1246 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1247 . . . . . Bpe10g00769 . Bma15g00253 Cmo04g01928 Cmo18g00684 . Cma18g00698 . Car18g00647 Sed06g1751 Cpe09g00588 Cpe01g01614 Bhi07g01923 Tan04g0049 Cmetu10g1680 Lac13g0054 Hepe10g1517 . . . . . . . . . . . . . Lsi04g00680 . . Cme10g00660 Blo06g00814 . . . . . . . . . . Cma04g01832 . . . . . . . . . . . . Cla11g01340 Cam11g1398 Cec11g1420 Cco11g1417 Clacu11g1555 Cmu11g1376 Cre11g1796 . . . .
Vvi1g1248 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1249 Blo01g00355 . Bda01g02178 . . . . . Cmo04g01930 Cmo18g00683 . Cma18g00696 . Car18g00646 Sed06g1752 Cpe09g00589 Cpe01g01615 Bhi07g01925 Tan04g0046 Cmetu10g1535 . . . . . . . . . . . . . . . Lsi04g00681 . . Cme10g00662 . . . . . . Bma01g00008 . . . . Cma04g01834 . . . . . . . . . . . . Cla11g01339 Cam11g1397 Cec11g1419 Cco11g1416 Clacu11g1554 Cmu11g1375 Cre11g1795 . . . .
Vvi1g1250 . . . . . . . . Cmo04g01932 . . . . . Sed06g1754 Cpe09g00591 Cpe01g01617 Bhi07g01927 Tan04g0044 Cmetu10g0959 Lac13g0050 Hepe10g1514 . . . . . . . . . . . . . Lsi04g00683 . . Cme10g00664 . . . . . . . . . . . Cma04g01836 . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57771968 57772243 + Bda032994 Bda01g02178 2178
7 51469909 51472757 + XM_039037499.1 Bhi07g01922 1922
7 51533842 51535649 + XM_039037163.1 Bhi07g01923 1923
7 51558955 51560788 - XM_039035507.1 Bhi07g01925 1925
7 51621075 51623322 + XM_039036995.1 Bhi07g01927 1927
1 4219520 4219795 + BLOR00355 Blo01g00355 355
1 4233062 4246522 - BLOR00357 Blo01g00357 357
6 31389665 31391628 - BLOR17397 Blo06g00814 814
1 233638 233910 + Bma030160 Bma01g00008 8
15 2522639 2523833 + Bma013238.1 Bma15g00253 253
10 13913614 13914795 - Bpe003074.1 Bpe10g00769 769
13 12586534 12594213 + Bpe010235.2 Bpe13g00531 531
13 12595323 12599354 + Bpe010236.2 Bpe13g00532 532
11 26638017 26639597 + CaPI482276_11g013970.1 Cam11g1397 1397
11 26641194 26642489 - CaPI482276_11g013980.1 Cam11g1398 1398
18 7732721 7734082 + Carg21229-RA Car18g00646 646
18 7735574 7737308 - Carg21230-RA Car18g00647 647
18 7740965 7743255 - Carg21231-RA Car18g00648 648
11 26920835 26921110 + CcPI632755_11g014160.1 Cco11g1416 1416
11 26923552 26924874 - CcPI632755_11g014170.1 Cco11g1417 1417
11 28390171 28391766 + CePI673135_11g014190.1 Cec11g1419 1419
11 28393363 28394658 - CePI673135_11g014200.1 Cec11g1420 1420
11 26653349 26659913 + ClG42_11g0155400.10 Clacu11g1554 1554
11 26661551 26662848 - ClG42_11g0155500.10 Clacu11g1555 1555
11 26855870 26857669 + ClCG11G013680.1 Cla11g01339 1339
11 26858787 26860586 - ClCG11G013690.1 Cla11g01340 1340
11 26865856 26869378 - ClCG11G013700.1 Cla11g01341 1341
4 9250045 9251393 + CmaCh04G018320.1 Cma04g01832 1832
4 9252598 9253451 - CmaCh04G018340.1 Cma04g01834 1834
4 9264652 9265625 + CmaCh04G018360.1 Cma04g01836 1836
18 6370210 6371444 + CmaCh18G006960.1 Cma18g00696 696
18 6372938 6374457 - CmaCh18G006980.1 Cma18g00698 698
18 6378834 6381937 - CmaCh18G006990.1 Cma18g00699 699
10 4202033 4207454 + MELO3C011869.2.1 Cme10g00659 659
10 4213715 4215863 + MELO3C011868.2.1 Cme10g00660 660
10 4217404 4219203 - MELO3C011867.2.1 Cme10g00662 662
10 4242300 4243846 + MELO3C011865.2.1 Cme10g00664 664
10 17679190 17681295 - PI0013385.1 Cmetu10g0959 959
10 17705805 17707849 + PI0004277.2 Cmetu10g1535 1535
10 17708842 17710725 - PI0008048.1 Cmetu10g1680 1680
4 9856602 9858376 + CmoCh04G019280.1 Cmo04g01928 1928
4 9859334 9860734 - CmoCh04G019300.1 Cmo04g01930 1930
4 9872268 9873331 + CmoCh04G019320.1 Cmo04g01932 1932
18 8745760 8747056 + CmoCh18G006830.1 Cmo18g00683 683
18 8748415 8750322 - CmoCh18G006840.1 Cmo18g00684 684
18 8754063 8755888 - CmoCh18G006850.1 Cmo18g00685 685
11 25905537 25912103 + CmPI595203_11g013750.1 Cmu11g1375 1375
11 25913741 25915038 - CmPI595203_11g013760.1 Cmu11g1376 1376
1 9872358 9879355 + Cp4.1LG01g16130.1 Cpe01g01614 1614
1 9879808 9880896 - Cp4.1LG01g16220.1 Cpe01g01615 1615
1 9892903 9893985 + Cp4.1LG01g16270.1 Cpe01g01617 1617
9 4083721 4085651 + Cp4.1LG09g06040.1 Cpe09g00588 588
9 4086957 4088199 - Cp4.1LG09g05980.1 Cpe09g00589 589
9 4104797 4106210 + Cp4.1LG09g05910.1 Cpe09g00591 591
11 29536055 29537669 + CrPI670011_11g017950.1 Cre11g1795 1795
11 29539292 29540589 - CrPI670011_11g017960.1 Cre11g1796 1796
10 51884660 51887331 - Hsped.10g15140.1 Hepe10g1514 1514
10 51928758 51930230 - Hsped.10g15170.1 Hepe10g1517 1517
10 51937015 51940482 - Hsped.10g15180.1 Hepe10g1518 1518
13 357170 361973 - Lag0039846.1 Lac13g0050 50
13 381510 383308 - Lag0039850.1 Lac13g0054 54
4 6214116 6217586 + Lsi04G006790.1 Lsi04g00679 679
4 6229398 6230731 + Lsi04G006800.1 Lsi04g00680 680
4 6236427 6236702 - Lsi04G006810.1 Lsi04g00681 681
4 6266236 6267920 + Lsi04G006830.1 Lsi04g00683 683
6 42226288 42228472 + Sed0008682.1 Sed06g1751 1751
6 42229359 42231631 - Sed0026530.1 Sed06g1752 1752
6 42277273 42279315 + Sed0007152.1 Sed06g1754 1754
4 410879 413017 - Tan0017128.1 Tan04g0044 44
4 443002 444181 + Tan0015763.1 Tan04g0046 46
4 444926 446946 - Tan0017213.3 Tan04g0049 49
1 20879330 20883898 + Vvi1g1241 Vvi1g1241 1241
1 20910080 20913536 + Vvi1g1242 Vvi1g1242 1242
1 20923224 20925144 + Vvi1g1243 Vvi1g1243 1243
1 20925189 20932874 + Vvi1g1244 Vvi1g1244 1244
1 20933416 20934933 + Vvi1g1245 Vvi1g1245 1245
1 20935035 20939592 + Vvi1g1246 Vvi1g1246 1246
1 20940811 20944087 + Vvi1g1247 Vvi1g1247 1247
1 20944605 20952346 - Vvi1g1248 Vvi1g1248 1248
1 20952346 20953480 - Vvi1g1249 Vvi1g1249 1249
1 20954685 20957185 - Vvi1g1250 Vvi1g1250 1250
       

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