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
Vvi1g751 Blo01g00402 Blo16g01152 Bda01g02229 Bda11g01256 Bpe13g01454 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01256 . . Bma01g00058 Bma06g00627 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g752 Blo01g00403 . . . Bpe13g00488 Bpe10g00829 Bma14g01780 Bma15g00195 Cmo04g01655 . . . . . . . Cpe01g01402 . . . . . . . Cla05g02524 Cam05g2709 Cec05g2742 Cco05g2781 Clacu05g2712 Cmu05g2566 Cre05g2680 Cone13ag1024 Cone19ag1015 . . Lsi04g00525 Csa05g02356 . Cme10g00504 . . Bda07g01589 . . . Bma01g00059 . . . . Cma04g01583 Cma05g00001 Car04g01630 Car05g00001 . . . . . . . . . . . . . . . . . . . .
Vvi1g753 Blo01g00404 . Bda01g02231 . Bpe13g00487 . . . . Cmo18g00829 . Cma18g00826 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma01g00060 Bma06g00628 . Cmo04g02852 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g754 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g755 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g756 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g757 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g758 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g759 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g760 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma06g00629 . . . Cma04g01584 . . . Cpe13g00914 . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 58100675 58112932 + Bda004569.1 Bda01g02229 2229
1 58134013 58135660 + Bda004573.1 Bda01g02231 2231
7 29514952 29516750 + Bda028459.1 Bda07g01589 1589
11 13180439 13186030 - Bda007771.1 Bda11g01256 1256
1 4535835 4541839 + BLOR00402 Blo01g00402 402
1 4542878 4544144 - BLOR00403 Blo01g00403 403
1 4558253 4561731 + BLOR00404 Blo01g00404 404
16 40045815 40051522 - BLOR21939 Blo16g01152 1152
1 599027 601015 + Bma000225.1 Bma01g00058 58
1 610190 611896 - Bma000226.1 Bma01g00059 59
1 617779 619428 + Bma000227.1 Bma01g00060 60
6 33397234 33402333 + Bma031289 Bma06g00627 627
6 33417430 33428765 + Bma023572.1 Bma06g00628 628
6 33430490 33432345 + Bma023573.1 Bma06g00629 629
14 38342757 38344555 + Bma012551.1 Bma14g01780 1780
15 1989429 1991156 - Bma013177.1 Bma15g00195 195
10 14300726 14302456 + Bpe003133.2 Bpe10g00829 829
13 12291206 12292881 - Bpe010198.1 Bpe13g00487 487
13 12301600 12303328 + Bpe010199.1 Bpe13g00488 488
13 19816855 19822397 - Bpe011118.1 Bpe13g01454 1454
5 34459023 34460982 + CaPI482276_05g027090.1 Cam05g2709 2709
4 9407444 9409007 - Carg01770-RA Car04g01630 1630
5 7361 9142 + Carg21801-RA Car05g00001 1
5 35602048 35603954 + CcPI632755_05g027810.1 Cco05g2781 2781
5 37910939 37912909 + CePI673135_05g027420.1 Cec05g2742 2742
5 34666466 34668415 + ClG42_05g0271200.10 Clacu05g2712 2712
5 36591625 36593538 + ClCG05G025150.1 Cla05g02524 2524
4 8017680 8019453 - CmaCh04G015830.1 Cma04g01583 1583
4 8027002 8029654 + CmaCh04G015840.1 Cma04g01584 1584
5 4944 6761 + CmaCh05G000010.1 Cma05g00001 1
18 7215575 7219760 + CmaCh18G008260.1 Cma18g00826 826
10 3238517 3241483 + MELO3C012014.2.1 Cme10g00504 504
4 8431469 8433224 - CmoCh04G016550.1 Cmo04g01655 1655
4 20345051 20348223 + CmoCh04G028520.1 Cmo04g02852 2852
18 9683649 9687903 + CmoCh18G008290.1 Cmo18g00829 829
5 34404429 34406322 + CmPI595203_05g025660.1 Cmu05g2566 2566
13 8539850 8541902 + Conep13aG0105500.1 Cone13ag1024 1024
19 7584888 7586994 + Conep19aG0104700.1 Cone19ag1015 1015
1 8433820 8435729 - Cp4.1LG01g13150.1 Cpe01g01402 1402
13 7778603 7783810 + Cp4.1LG13g08860.1 Cpe13g00914 914
5 37756974 37762701 + CrPI670011_05g026800.1 Cre05g2680 2680
5 25868912 25871372 - CsaV3_5G031750.1 Csa05g02356 2356
4 4858833 4862183 + Lsi04G005250.1 Lsi04g00525 525
1 9040525 9082810 + Vvi1g751 Vvi1g751 751
1 9083834 9085818 - Vvi1g752 Vvi1g752 752
1 9117652 9120234 + Vvi1g753 Vvi1g753 753
1 9151012 9165751 + Vvi1g754 Vvi1g754 754
1 9185075 9187047 - Vvi1g755 Vvi1g755 755
1 9198946 9199984 + Vvi1g756 Vvi1g756 756
1 9205056 9206501 + Vvi1g757 Vvi1g757 757
1 9206549 9207586 - Vvi1g758 Vvi1g758 758
1 9207772 9208125 + Vvi1g759 Vvi1g759 759
1 9240778 9243586 + Vvi1g760 Vvi1g760 760
       

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