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
Vvi2g942 . . . . . Bpe07g00049 . . . . . . . . . . Cpe02g00587 . . . . . . . . . . . . . . . . Cone6ag0886 Cone9ag0890 . . . . Blo03g00905 . . . . . . Bma12g00627 . . . . . . . . Cpe06g00592 . . . . . . . . . . . . . . . . . .
Vvi2g943 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g944 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g945 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g946 . . . . . . . . . . . . . . . . Cpe02g00585 . . . . . . . . . . . . . . . . . Cone9ag0351 . . . . . . . . Bpe08g01061 . . . . . . . . . . . Cpe06g00594 . . . . . . . . . . . . . . . . . .
Vvi2g947 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone10ag1268 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g948 . . . . . . Bma07g01219 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda09g00467 . . . . . . . . . . . . Cpe06g00595 . . . . . . . . . . . . . . . . . .
Vvi2g949 . . . . . . . . . . . . . . . . Cpe02g00582 . . . . . . . . . . . . . . . . . . . . . . Blo03g00908 . . . . . . . . . . . . . . . Cpe06g00596 . . . . . . . . . . . . . . . . . .
Vvi2g950 . . . . . . . . . . . . . . . . Cpe02g00580 . . . . . . . . . . . . . . . . . . . . . . Blo03g00910 . . . . . . . . . . . . . . . Cpe06g00597 . . . . . . . . . . . . . . . . . .
Vvi2g951 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe01g00540 Cpe06g00598 . . . . . . . . . . . . . . . Csa04g00712 . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
9 6077795 6079153 + Bda031056.1 Bda09g00467 467
3 35053801 35056814 + BLOR12086 Blo03g00905 905
3 35074742 35078110 + BLOR12089 Blo03g00908 908
3 35092828 35095638 + BLOR12091 Blo03g00910 910
7 47093925 47095427 - Bma026470.1 Bma07g01219 1219
12 27510686 27513709 - Bma007804.1 Bma12g00627 627
7 417633 420625 + Bpe020862.1 Bpe07g00049 49
8 12785330 12786405 - Bpe023186.1 Bpe08g01061 1061
6 4519559 4524175 - Conep06aG0091300.1 Cone6ag0886 886
9 1552638 1554385 - Conep09aG0035800.1 Cone9ag0351 351
9 4339512 4344111 - Conep09aG0091200.1 Cone9ag0890 890
10 9743490 9744810 - Conep10aG0130300.1 Cone10ag1268 1268
1 3101308 3102395 + Cp4.1LG01g01270.1 Cpe01g00540 540
2 3465376 3480091 - Cp4.1LG02g02870.1 Cpe02g00580 580
2 3485937 3489845 - Cp4.1LG02g02880.1 Cpe02g00582 582
2 3496026 3501174 + Cp4.1LG02g02950.1 Cpe02g00585 585
2 3509024 3519978 + Cp4.1LG02g02930.1 Cpe02g00587 587
6 3629339 3631498 - Cp4.1LG06g05980.1 Cpe06g00592 592
6 3651467 3656030 - Cp4.1LG06g05960.1 Cpe06g00594 594
6 3657315 3660713 - Cp4.1LG06g05950.1 Cpe06g00595 595
6 3661348 3665236 + Cp4.1LG06g05900.1 Cpe06g00596 596
6 3673449 3679824 + Cp4.1LG06g05880.1 Cpe06g00597 597
6 3680735 3682565 + Cp4.1LG06g05870.1 Cpe06g00598 598
4 4824506 4826296 + CsaV3_4G007120.1 Csa04g00712 712
2 17792451 17808739 - Vvi2g942 Vvi2g942 942
2 17854732 17865483 + Vvi2g943 Vvi2g943 943
2 17886801 17908532 + Vvi2g944 Vvi2g944 944
2 17912097 17913546 - Vvi2g945 Vvi2g945 945
2 17957866 17976378 - Vvi2g946 Vvi2g946 946
2 17983715 17984127 - Vvi2g947 Vvi2g947 947
2 18028404 18030254 - Vvi2g948 Vvi2g948 948
2 18075927 18088597 + Vvi2g949 Vvi2g949 949
2 18133521 18139501 + Vvi2g950 Vvi2g950 950
2 18145731 18146910 + Vvi2g951 Vvi2g951 951
       

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