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
Vvi1g1211 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1212 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1213 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi12g02464 . . . . . . . . . . . . . . . . .
Vvi1g1214 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00217 . . . . . . Cone14ag0689 Cone15ag0711 . . . . . . . . . . . . . . . . . . . . . Cpe17g01086 . . . . . . . . . . . . . . . . . . .
Vvi1g1215 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00311 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1216 . . . . . . Bma14g01982 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1217 . . . . . Bpe10g00787 . Bma15g00234 Cmo04g01924 . . . . . . . Cpe01g01611 Bhi07g01912 . . . . . . . . . . . . . . . . . Lsi04g00669 . . Cme10g00648 Blo06g00832 . . . . . . . . . . Cma04g01827 . Car04g01841 . . . . . . . . . . Cla11g01350 Cam11g1408 Cec11g1434 Cco11g1428 Clacu11g1565 Cmu11g1386 Cre11g1806 . . . .
Vvi1g1218 . . . . . Bpe10g00788 . Bma15g00233 Cmo04g01925 Cmo18g00695 . Cma18g00706 . Car18g00652 Sed06g1743 Cpe09g00582 Cpe01g01612 Bhi07g01913 Tan04g0060 Cmetu10g0980 Lac13g0060 Hepe10g1524 . . . . . . . . . . . . . Lsi04g00670 . . Cme10g00649 Blo06g00833 . . . . . . . . . . Cma04g01829 . Car04g01843 . . . . . . . . . . Cla11g01349 Cam11g1407 Cec11g1433 Cco11g1427 Clacu11g1564 Cmu11g1385 Cre11g1805 . . . .
Vvi1g1219 Blo01g00180 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma01g00015 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1220 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 51135223 51156479 + XM_039036161.1 Bhi07g01912 1912
7 51160881 51165398 - XM_039037498.1 Bhi07g01913 1913
12 77517300 77521335 - XM_039051214.1 Bhi12g02464 2464
1 2446182 2447366 - BLOR00180 Blo01g00180 180
6 31557340 31565616 + BLOR17415 Blo06g00832 832
6 31566590 31572931 - BLOR17416 Blo06g00833 833
1 295468 296798 + Bma000186.1 Bma01g00015 15
14 43155458 43158804 - Bma012790.1 Bma14g01982 1982
15 2339292 2342004 + Bma013219.2 Bma15g00233 233
15 2343225 2353509 - Bma013220.1 Bma15g00234 234
10 14032995 14043073 + Bpe003092.1 Bpe10g00787 787
10 14044295 14046841 - Bpe003093.1 Bpe10g00788 788
11 26735576 26740039 + CaPI482276_11g014070.1 Cam11g1407 1407
11 26742479 26753499 - CaPI482276_11g014080.1 Cam11g1408 1408
4 10667207 10673152 + Carg14264-RA Car04g01841 1841
4 10677127 10678365 - Carg14262-RA Car04g01843 1843
18 7792654 7797288 + Carg21235-RA Car18g00652 652
11 27027521 27031999 + CcPI632755_11g014270.1 Cco11g1427 1427
11 27034486 27046953 - CcPI632755_11g014280.1 Cco11g1428 1428
11 28482456 28486904 + CePI673135_11g014330.1 Cec11g1433 1433
11 28489375 28501615 - CePI673135_11g014340.1 Cec11g1434 1434
11 26758132 26762838 + ClG42_11g0156400.10 Clacu11g1564 1564
11 26765048 26776950 - ClG42_11g0156500.10 Clacu11g1565 1565
6 2575877 2583138 - ClCG06G002340.2 Cla06g00217 217
11 26958143 26963002 + ClCG11G013770.1 Cla11g01349 1349
11 26964949 26977956 - ClCG11G013780.1 Cla11g01350 1350
4 9220355 9229617 + CmaCh04G018270.1 Cma04g01827 1827
4 9230834 9234738 - CmaCh04G018290.1 Cma04g01829 1829
18 6436388 6443548 + CmaCh18G007060.1 Cma18g00706 706
10 4140181 4152736 + MELO3C011876.2.1 Cme10g00648 648
10 4153389 4158117 - MELO3C011875.2.1 Cme10g00649 649
10 17776109 17780197 + PI0022105.1 Cmetu10g0980 980
4 9826724 9835975 + CmoCh04G019240.1 Cmo04g01924 1924
4 9836668 9841381 - CmoCh04G019250.1 Cmo04g01925 1925
18 8821070 8826350 + CmoCh18G006950.1 Cmo18g00695 695
11 26010285 26014991 + CmPI595203_11g013850.1 Cmu11g1385 1385
11 26017201 26029106 - CmPI595203_11g013860.1 Cmu11g1386 1386
14 3576641 3578871 - Conep14aG0070400.1 Cone14ag0689 689
15 3908900 3910505 - Conep15aG0072500.1 Cone15ag0711 711
1 9846494 9856073 + Cp4.1LG01g16150.1 Cpe01g01611 1611
1 9856966 9861785 - Cp4.1LG01g16190.1 Cpe01g01612 1612
9 4024880 4029670 - Cp4.1LG09g05960.1 Cpe09g00582 582
17 8235964 8239939 + Cp4.1LG17g10730.1 Cpe17g01086 1086
11 29631706 29636447 + CrPI670011_11g018050.1 Cre11g1805 1805
11 29638704 29650526 - CrPI670011_11g018060.1 Cre11g1806 1806
4 1904896 1919818 + CsaV3_4G003110.1 Csa04g00311 311
10 51977426 51981081 + Hsped.10g15240.1 Hepe10g1524 1524
13 435823 439800 + Lag0039856.1 Lac13g0060 60
4 6140648 6154369 + Lsi04G006690.1 Lsi04g00669 669
4 6156046 6161014 - Lsi04G006700.1 Lsi04g00670 670
6 42129956 42139359 - Sed0028059.1 Sed06g1743 1743
4 513349 518039 + Tan0003157.1 Tan04g0060 60
1 20492301 20493162 + Vvi1g1211 Vvi1g1211 1211
1 20529404 20530313 + Vvi1g1212 Vvi1g1212 1212
1 20542069 20544780 + Vvi1g1213 Vvi1g1213 1213
1 20564869 20568070 - Vvi1g1214 Vvi1g1214 1214
1 20569148 20570248 - Vvi1g1215 Vvi1g1215 1215
1 20592974 20594160 + Vvi1g1216 Vvi1g1216 1216
1 20625400 20652989 + Vvi1g1217 Vvi1g1217 1217
1 20653443 20660585 - Vvi1g1218 Vvi1g1218 1218
1 20661351 20663794 - Vvi1g1219 Vvi1g1219 1219
1 20663796 20665821 - Vvi1g1220 Vvi1g1220 1220
       

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