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
Vvi2g972 . . . . . . . . . Cmo16g00546 . . . . . Cpe14g00423 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma16g00501 . . Cpe01g00547 . . . . . . . . . . . . . . . . Csa04g00718 . .
Vvi2g973 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g974 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g975 Blo02g01234 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g976 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1 . . . . Bpe07g00526 . . . . . Cma02g00375 Cma20g00824 Car02g00242 Car20g00710 . Cpe04g00116 . . . . . . . . Cla02g00501 Cam02g0511 Cec02g0511 Cco02g0519 Clacu02g0513 Cmu02g0509 Cre02g0842 . . . . . . . Cme01g01368 . . . . . . . . Sed01g0278 Cmo02g00382 Cmo20g00835 . . . . . . Bhi10g01967 Tan05g1260 Cmetu11g0821 . . . . . . . . . . . . . Chy01g00763 .
Vvi3g2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g3 . Blo15g00679 Bda06g00991 . . . . Bma12g00550 . . Cma02g00375 Cma20g00824 Car02g00242 Car20g00710 Sed03g1723 . . Bhi05g01788 Tan02g2021 Cmetu03g0999 . . . . . . . . . . . Cone12ag1169 Cone8ag1217 . . Lsi10g00400 . Chy11g00351 . . Blo13g00542 . . . . . . Sed01g0278 Cmo02g00382 Cmo20g00835 . . . . Cpe16g00264 Cpe05g01280 Bhi10g01967 Tan05g1260 Cmetu11g0821 . . . . . . . . . . . . Csa02g01291 . Cme11g00153
Vvi3g4 . . . . . . Bma05g00433 . . . Cma02g00374 Cma20g00823 Car02g00241 Car20g00709 . . . . . . . . . . . . . . . . . Cone12ag1171 Cone8ag1218 Cone3ag1223 Cone10ag1108 Lsi10g00402 . Chy11g00350 . . . . . . . . . Sed02g0459 Cmo02g00381 Cmo20g00834 . . . . Cpe16g00265 Cpe05g01281 Bhi10g01966 Tan05g1259 Cmetu05g0753 . Hepe08g0990 . . . . . . . . . . Csa02g01292 . Cme11g00154
Vvi3g5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 34076733 34078422 - Bda022709.1 Bda06g00991 991
5 56795409 56799533 - XM_039031404.1 Bhi05g01788 1788
10 48974685 48979435 + XM_039045051.1 Bhi10g01966 1966
10 48981958 48989976 - XM_039045807.1 Bhi10g01967 1967
2 44484592 44503260 + BLOR10964 Blo02g01234 1234
13 27279434 27281687 - BLOR05823 Blo13g00542 542
15 21023410 21025149 - BLOR07073 Blo15g00679 679
5 14331507 14338699 + Bma021281.1 Bma05g00433 433
12 22902641 22906772 + Bma007686.1 Bma12g00550 550
7 11162876 11166786 - Bpe021375.1 Bpe07g00526 526
2 5782552 5783930 - CaPI482276_02g005110.1 Cam02g0511 511
2 1634715 1638183 + Carg24145-RA Car02g00241 241
2 1638898 1644785 - Carg24146-RA Car02g00242 242
20 4092444 4096884 + Carg26795-RA Car20g00709 709
20 4098004 4104528 - Carg26794-RA Car20g00710 710
2 4826309 4827734 - CcPI632755_02g005190.1 Cco02g0519 519
2 4793030 4794349 - CePI673135_02g005110.1 Cec02g0511 511
1 5722543 5724440 - Chy1G007630.1 Chy01g00763 763
11 3195879 3198855 + Chy11G189300.1 Chy11g00350 350
11 3201693 3208791 - Chy11G189310.1 Chy11g00351 351
2 4748477 4749857 - ClG42_02g0051300.10 Clacu02g0513 513
2 4965830 4967270 - ClCG02G004770.2 Cla02g00501 501
2 1882851 1886694 + CmaCh02G003740.1 Cma02g00374 374
2 1886998 1893505 - CmaCh02G003750.1 Cma02g00375 375
16 2555440 2557224 + CmaCh16G005010.1 Cma16g00501 501
20 3913634 3917835 + CmaCh20G008230.1 Cma20g00823 823
20 3920382 3926180 - CmaCh20G008240.1 Cma20g00824 824
1 17058700 17063097 - MELO3C013445.2.1 Cme01g01368 1368
11 1640794 1646698 + MELO3C023332.2.1 Cme11g00153 153
11 1651284 1656057 - MELO3C023333.2.1 Cme11g00154 154
3 2090504 2094504 - PI0016140.1 Cmetu03g0999 999
5 21435245 21438742 + PI0022386.1 Cmetu05g0753 753
11 27753355 27761917 + PI0009537.1 Cmetu11g0821 821
2 1948698 1951670 + CmoCh02G003810.1 Cmo02g00381 381
2 1951825 1957671 - CmoCh02G003820.1 Cmo02g00382 382
16 2645574 2647358 + CmoCh16G005460.1 Cmo16g00546 546
20 4158381 4162304 + CmoCh20G008340.1 Cmo20g00834 834
20 4162691 4169119 - CmoCh20G008350.1 Cmo20g00835 835
2 4687053 4688444 - CmPI595203_02g005090.1 Cmu02g0509 509
3 30993176 31009778 + Conep03aG0173000.1 Cone3ag1223 1223
8 10310671 10314758 + Conep08aG0125400.1 Cone8ag1217 1217
8 10314758 10317626 - Conep08aG0125500.1 Cone8ag1218 1218
10 7874223 7883200 + Conep10aG0113800.1 Cone10ag1108 1108
12 9280140 9282382 + Conep12aG0120800.1 Cone12ag1169 1169
12 9284332 9287599 - Conep12aG0121000.1 Cone12ag1171 1171
1 3150152 3151912 - Cp4.1LG01g01120.1 Cpe01g00547 547
4 1039875 1042393 - Cp4.1LG04g00930.1 Cpe04g00116 116
5 8929219 8934424 + Cp4.1LG05g12730.1 Cpe05g01280 1280
5 8935118 8938923 - Cp4.1LG05g12790.1 Cpe05g01281 1281
14 2646000 2647877 + Cp4.1LG14g02990.1 Cpe14g00423 423
16 4642303 4648654 + Cp4.1LG16g02600.1 Cpe16g00264 264
16 4649470 4654725 - Cp4.1LG16g02670.1 Cpe16g00265 265
2 5231379 5232729 - CrPI670011_02g008420.1 Cre02g0842 842
2 12561316 12569367 + CsaV3_2G015070.1 Csa02g01291 1291
2 12571370 12574220 - CsaV3_2G015080.1 Csa02g01292 1292
4 4915379 4917916 - CsaV3_4G007180.1 Csa04g00718 718
8 9375544 9380255 + Hsped.08g09900.1 Hepe08g0990 990
10 6085441 6092395 + Lsi10G004000.1 Lsi10g00400 400
10 6095589 6099550 - Lsi10G004020.1 Lsi10g00402 402
1 2145144 2152172 - Sed0009304.1 Sed01g0278 278
2 41804815 41810812 - Sed0002624.2 Sed02g0459 459
3 11253979 11260761 + Sed0021083.1 Sed03g1723 1723
2 89447452 89451988 - Tan0014732.1 Tan02g2021 2021
5 13579694 13585064 + Tan0012593.1 Tan05g1259 1259
5 13586572 13594789 - Tan0017156.1 Tan05g1260 1260
2 18560292 18594852 - Vvi2g972 Vvi2g972 972
2 18609440 18617224 - Vvi2g973 Vvi2g973 973
2 18715011 18715732 - Vvi2g974 Vvi2g974 974
2 18746618 18751691 + Vvi2g975 Vvi2g975 975
2 18774892 18778611 + Vvi2g976 Vvi2g976 976
3 2917 5568 + Vvi3g1 Vvi3g1 1
3 6505 7685 + Vvi3g2 Vvi3g2 2
3 24425 40615 + Vvi3g3 Vvi3g3 3
3 40974 48142 - Vvi3g4 Vvi3g4 4
3 69710 76504 - Vvi3g5 Vvi3g5 5
       

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