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
Vvi19g774 . . . . . . . . . . . Cma09g01036 . Car09g00943 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo09g01040 . . . . . . . . . . . . . . . . . . . . . . Chy01g01022 Cme01g01097
Vvi19g775 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla09g02105 Cam09g2191 Cec09g2262 . . . . . . Chy01g01021 .
Vvi19g776 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g777 . . . . . . . . . . . . . . . Cpe06g00844 Cpe02g00842 . . . . . . . . . . . . . . . . . . . Csa07g01057 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy01g01017 Cme01g01095
Vvi19g778 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy01g01016 Cme01g01093
Vvi19g779 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g780 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa07g01058 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy01g01015 Cme01g01089
Vvi19g781 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1241 Cone15ag1266 . Csa07g01059 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme01g01088
Vvi19g782 . . . . . . Bma10g00615 . . Cmo06g00672 . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1269 Cone15ag1295 . . . . Blo07g00858 . Bda05g00660 . . Bpe03g00737 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g783 Blo03g00480 Blo03g01493 Bda07g00435 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1270 Cone15ag1296 . . . . . . . . Bpe11g00613 . . Bma14g00658 . . Cmo09g00636 . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 54948986 54953388 - Bda021793.1 Bda05g00660 660
7 5573036 5575612 + Bda025531.1 Bda07g00435 435
3 16697226 16703553 - BLOR11661 Blo03g00480 480
3 41778073 41781066 + BLOR12674 Blo03g01493 1493
7 26992515 26999967 + BLOR18790 Blo07g00858 858
10 8225013 8229383 + Bma030365 Bma10g00615 615
14 7104284 7106862 - Bma011104.2 Bma14g00658 658
3 27480402 27484828 - Bpe012645.1 Bpe03g00737 737
11 4663659 4666232 + Bpe003978.1 Bpe11g00613 613
9 36428971 36430501 - CaPI482276_09g021910.1 Cam09g2191 2191
9 5803003 5805894 - Carg24731-RA Car09g00943 943
9 39462813 39464174 - CePI673135_09g022620.1 Cec09g2262 2262
1 10709206 10710639 + Chy1G010150.1 Chy01g01015 1015
1 10724888 10725916 + Chy1G010160.1 Chy01g01016 1016
1 10730282 10731154 - Chy1G010170.1 Chy01g01017 1017
1 10783443 10791916 - Chy1G010210.1 Chy01g01021 1021
1 10795953 10796769 - Chy1G010220.1 Chy01g01022 1022
9 38597468 38604899 - ClCG09G021640.1 Cla09g02105 2105
9 5347876 5350741 - CmaCh09G010360.1 Cma09g01036 1036
1 13685454 13693262 + MELO3C013202.2.1 Cme01g01088 1088
1 13694258 13696090 + MELO3C013203.2.1 Cme01g01089 1089
1 13740004 13741041 + MELO3C013205.2.1 Cme01g01093 1093
1 13746942 13747862 - MELO3C013206.2.1 Cme01g01095 1095
1 13782011 13783838 - MELO3C013207.2.1 Cme01g01097 1097
6 3393288 3399277 + CmoCh06G006720.1 Cmo06g00672 672
9 3188960 3194836 + CmoCh09G006360.1 Cmo09g00636 636
9 5574828 5577714 - CmoCh09G010400.1 Cmo09g01040 1040
14 10030719 10034882 - Conep14aG0127300.1 Cone14ag1241 1241
14 10165879 10167293 - Conep14aG0130100.1 Cone14ag1269 1269
14 10167595 10171421 + Conep14aG0130200.1 Cone14ag1270 1270
15 9970346 9973401 - Conep15aG0129500.1 Cone15ag1266 1266
15 10138307 10142141 - Conep15aG0132400.1 Cone15ag1295 1295
15 10143063 10146990 + Conep15aG0132500.1 Cone15ag1296 1296
2 5408632 5409525 - Cp4.1LG02g00330.1 Cpe02g00842 842
6 5428642 5429505 - Cp4.1LG06g08060.1 Cpe06g00844 844
7 10067148 10068023 + CsaV3_7G021460.1 Csa07g01057 1057
7 10084559 10085888 - CsaV3_7G021470.1 Csa07g01058 1058
7 10086934 10093432 - CsaV3_7G021480.1 Csa07g01059 1059
19 10312757 10326282 - Vvi19g774 Vvi19g774 774
19 10326385 10327742 - Vvi19g775 Vvi19g775 775
19 10327786 10329303 - Vvi19g776 Vvi19g776 776
19 10331313 10331967 + Vvi19g777 Vvi19g777 777
19 10332462 10337676 - Vvi19g778 Vvi19g778 778
19 10385172 10388468 + Vvi19g779 Vvi19g779 779
19 10399637 10401741 - Vvi19g780 Vvi19g780 780
19 10402251 10419777 - Vvi19g781 Vvi19g781 781
19 10434341 10444022 - Vvi19g782 Vvi19g782 782
19 10455399 10463846 + Vvi19g783 Vvi19g783 783
       

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