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
Vvi2g932 . . . . . Bpe07g00052 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0880 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00700 . .
Vvi2g933 . . . . . . . . . Cmo16g00565 . . . . . Cpe14g00438 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma12g00625 . . . . Cma16g00519 . . . . . . . . . . . . . . . . . . . . . .
Vvi2g934 . . . . . . . . . Cmo16g00562 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g935 Blo02g01172 . . Bda08g00444 Bpe05g00715 . . . . Cmo16g00561 . . . . . Cpe14g00435 . . . . . . . . . . . . . . . . . Cone6ag0881 . . . . . . . . . . . Bma05g00897 . . . . . Cma16g00514 . . . . . . . . . . . . . . . . . . . Csa04g00704 . .
Vvi2g936 . . . . . . . . Cmo06g00577 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma06g00571 . Car06g00508 . . Cpe06g00591 . . . . . . . . . . . . . . . . . .
Vvi2g937 Blo02g01173 . . Bda08g00443 Bpe05g00716 Bpe07g00051 . . . Cmo16g00560 . . . . . Cpe14g00434 . . . . . . . . . . . . . . . . . Cone6ag0883 Cone9ag0887 . . . . . . . . . . Bma05g00898 Bma12g00626 . . . . Cma16g00513 . . Cpe01g00534 . . . . . . . . . . . . . . . . Csa04g00705 . .
Vvi2g938 . . . . . . Bma07g01220 . . Cmo16g00559 . . . . . Cpe14g00433 . . . . . . . . . . . . . . . . . . . . . . . . . . Bda09g00466 . . . . . . . . Cma16g00512 . . . . . . . . . . . . . . . . . . . Csa04g00706 . .
Vvi2g939 . . . . Bpe05g00717 Bpe07g00050 . . . Cmo16g00558 . . . . . Cpe14g00432 . . . . . . . . . . . . . . . . . Cone6ag0884 Cone9ag0888 . . . . . . . . . . Bma05g00899 . . . . . Cma16g00511 . . Cpe01g00536 . . . . . . . . . . . . . . . . Csa04g00707 . .
Vvi2g940 Blo02g01221 . . . Bpe05g00764 . . . . Cmo16g00557 . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0885 Cone9ag0889 . . . . . . . . . . . . . . . . Cma16g00510 . . Cpe01g00537 . . . . . . . . . . . . . . . . Csa04g00708 . .
Vvi2g941 Blo02g01224 . . . Bpe05g00767 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 4535050 4537596 - Bda024893.1 Bda08g00443 443
8 4548153 4549505 + Bda024894.1 Bda08g00444 444
9 6073337 6074697 + Bda034099 Bda09g00466 466
2 43378254 43379597 - BLOR10902 Blo02g01172 1172
2 43410797 43417078 + BLOR10903 Blo02g01173 1173
2 44228800 44248649 - BLOR10951 Blo02g01221 1221
2 44350760 44353798 + BLOR10954 Blo02g01224 1224
5 46820921 46822264 - Bma022016.1 Bma05g00897 897
5 46826758 46829306 + Bma022017.1 Bma05g00898 898
5 46831715 46834677 + Bma022018.1 Bma05g00899 899
7 47098807 47100115 - Bma026471.1 Bma07g01220 1220
12 27497673 27500021 - Bma007801.4 Bma12g00625 625
12 27503088 27505550 + Bma007802.1 Bma12g00626 626
5 20695438 20696781 - Bpe018127.2 Bpe05g00715 715
5 20700071 20702611 + Bpe018128.1 Bpe05g00716 716
5 20704160 20707712 + Bpe018129.1 Bpe05g00717 717
5 21000444 21010794 - Bpe025828 Bpe05g00764 764
5 21046765 21049803 + Bpe018179.1 Bpe05g00767 767
7 422197 425133 - Bpe020863.1 Bpe07g00050 50
7 426041 428730 - Bpe020864.2 Bpe07g00051 51
7 440786 442240 - Bpe020865.3 Bpe07g00052 52
6 2846643 2854003 - Carg16260-RA Car06g00508 508
6 2753710 2760286 - CmaCh06G005710.1 Cma06g00571 571
16 2617685 2626621 - CmaCh16G005100.1 Cma16g00510 510
16 2626985 2630358 - CmaCh16G005110.1 Cma16g00511 511
16 2632384 2634969 - CmaCh16G005120.1 Cma16g00512 512
16 2635616 2639209 - CmaCh16G005130.1 Cma16g00513 513
16 2646097 2647476 + CmaCh16G005140.1 Cma16g00514 514
16 2656463 2659727 + CmaCh16G005190.1 Cma16g00519 519
6 2831015 2837694 - CmoCh06G005770.1 Cmo06g00577 577
16 2713632 2720668 - CmoCh16G005570.1 Cmo16g00557 557
16 2721042 2724079 - CmoCh16G005580.1 Cmo16g00558 558
16 2726719 2728946 - CmoCh16G005590.1 Cmo16g00559 559
16 2729529 2734647 - CmoCh16G005600.1 Cmo16g00560 560
16 2741261 2742640 + CmoCh16G005610.1 Cmo16g00561 561
16 2743860 2746684 + CmoCh16G005620.1 Cmo16g00562 562
16 2751710 2755013 + CmoCh16G005650.1 Cmo16g00565 565
6 4484806 4486296 + Conep06aG0090700.1 Cone6ag0880 880
6 4492845 4494731 + Conep06aG0090800.1 Cone6ag0881 881
6 4503700 4505852 + Conep06aG0091000.1 Cone6ag0883 883
6 4512765 4515672 + Conep06aG0091100.1 Cone6ag0884 884
6 4515872 4519320 + Conep06aG0091200.1 Cone6ag0885 885
9 4326863 4328452 + Conep09aG0090900.1 Cone9ag0887 887
9 4333137 4336191 + Conep09aG0091000.1 Cone9ag0888 888
9 4336429 4339359 + Conep09aG0091100.1 Cone9ag0889 889
1 3073852 3077131 + Cp4.1LG01g01410.1 Cpe01g00534 534
1 3080649 3084998 + Cp4.1LG01g01370.1 Cpe01g00536 536
1 3085495 3096611 + Cp4.1LG01g01400.1 Cpe01g00537 537
6 3620491 3626822 - Cp4.1LG06g05940.1 Cpe06g00591 591
14 2712147 2722965 - Cp4.1LG14g02800.1 Cpe14g00432 432
14 2725072 2727796 - Cp4.1LG14g02790.1 Cpe14g00433 433
14 2728315 2731574 - Cp4.1LG14g02810.1 Cpe14g00434 434
14 2739302 2740681 + Cp4.1LG14g02870.1 Cpe14g00435 435
14 2749558 2754418 + Cp4.1LG14g02880.1 Cpe14g00438 438
4 4729143 4730606 + CsaV3_4G007000.1 Csa04g00700 700
4 4759877 4762161 - CsaV3_4G007040.1 Csa04g00704 704
4 4777839 4781791 + CsaV3_4G007050.1 Csa04g00705 705
4 4782205 4786713 + CsaV3_4G007060.1 Csa04g00706 706
4 4790432 4794552 + CsaV3_4G007070.1 Csa04g00707 707
4 4795128 4801821 + CsaV3_4G007080.1 Csa04g00708 708
2 17600962 17602444 - Vvi2g932 Vvi2g932 932
2 17609689 17614854 - Vvi2g933 Vvi2g933 933
2 17631655 17646964 - Vvi2g934 Vvi2g934 934
2 17661209 17662826 - Vvi2g935 Vvi2g935 935
2 17687720 17713368 - Vvi2g936 Vvi2g936 936
2 17728596 17733321 + Vvi2g937 Vvi2g937 937
2 17738720 17744676 + Vvi2g938 Vvi2g938 938
2 17748344 17758642 + Vvi2g939 Vvi2g939 939
2 17760097 17774855 + Vvi2g940 Vvi2g940 940
2 17785701 17785983 - Vvi2g941 Vvi2g941 941
       

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