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
Vvi18g790 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g791 . . . . . . . . . . . . . . Sed11g0975 . . Bhi04g00318 Tan02g1888 Cmetu03g1774 . Hepe10g0708 . Lcy13g2037 . . . . . . . . Cone7ag1389 . . . . . . Blo17g00843 . Bda08g01336 . . Bpe05g00059 . Bma05g00082 . . . . . . . . . . . . . . . . . . . . . . . . Csa02g01991 . .
Vvi18g792 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g793 . . . . . . . . Cmo05g00202 . . . . . Sed05g3372 . . Bhi04g00317 Tan02g1889 . . Hepe10g0706 . Lcy13g2036 . . . . . . . . . . . . . . . Blo17g00842 . Bda08g01335 . . . . . . . . . Cma05g00202 Car05g00168 . . . . . . . . . . . . . . . . . . . . .
Vvi18g794 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g795 . . . . . . . . . . . . . . . . . Bhi04g00316 . . . Hepe10g0705 . . . . . . . . . . . . . . . . . Blo17g00841 . . . . Bpe05g00060 . Bma05g00084 . . . . . . . . . . . . . . . . . . . . . . . . Csa02g01992 . .
Vvi18g796 . . . . . . . . Cmo05g00203 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda08g01334 . . . . . . . . . Cma05g00203 . . . . . . . . . . . . . . . . . . . . . .
Vvi18g797 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g798 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe05g00061 . . . . . Cma12g00522 . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g799 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda08g01333 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 53499902 53535965 + Bda030377.1 Bda08g01333 1333
8 53657939 53659598 - Bda034052 Bda08g01334 1334
8 53685535 53687131 + Bda034053 Bda08g01335 1335
8 53721523 53723201 - Bda030383.1 Bda08g01336 1336
4 7378299 7386362 + XM_039028567.1 Bhi04g00316 316
4 7438815 7444343 + XM_039030529.1 Bhi04g00317 317
4 7457691 7462012 + XM_039030419.1 Bhi04g00318 318
17 27466270 27474120 + BLOR08387 Blo17g00841 841
17 27511923 27514315 + BLOR08388 Blo17g00842 842
17 27650182 27653007 + BLOR08389 Blo17g00843 843
5 2668147 2669820 + Bma020771.1 Bma05g00082 82
5 2743792 2745459 + Bma020774.1 Bma05g00084 84
5 990972 992639 + Bpe017447.1 Bpe05g00059 59
5 1073195 1075044 - Bpe017448.1 Bpe05g00060 60
5 1098992 1100839 - Bpe017449.1 Bpe05g00061 61
5 870345 877293 - Carg11836-RA Car05g00168 168
5 854187 856160 - CmaCh05G002020.1 Cma05g00202 202
5 858191 860947 - CmaCh05G002030.1 Cma05g00203 203
12 2715043 2721800 + CmaCh12G005220.1 Cma12g00522 522
3 1489846 1493534 - PI0022615.1 Cmetu03g1774 1774
5 874591 876666 - CmoCh05G002020.1 Cmo05g00202 202
5 878928 881567 - CmoCh05G002030.1 Cmo05g00203 203
7 9979565 9981890 - Conep07aG0143000.1 Cone7ag1389 1389
2 18537962 18541109 - CsaV3_2G028100.1 Csa02g01991 1991
2 18543126 18548083 - CsaV3_2G028110.1 Csa02g01992 1992
10 9439565 9445296 + Hsped.10g07050.1 Hepe10g0705 705
10 9480544 9485477 + Hsped.10g07060.1 Hepe10g0706 706
10 9516409 9520199 + Hsped.10g07080.1 Hepe10g0708 708
13 39360885 39372327 + Maker00025240 Lcy13g2036 2036
13 39376073 39379741 + Maker00025148 Lcy13g2037 2037
5 42939361 42956462 + Sed0026615.1 Sed05g3372 3372
11 24469654 24476680 - Sed0020811.1 Sed11g0975 975
2 86903896 86910127 - Tan0014271.1 Tan02g1888 1888
2 86991567 87043423 - Tan0017382.1 Tan02g1889 1889
18 9095606 9096446 + Vvi18g790 Vvi18g790 790
18 9101793 9105297 - Vvi18g791 Vvi18g791 791
18 9114291 9114769 + Vvi18g792 Vvi18g792 792
18 9115081 9117462 - Vvi18g793 Vvi18g793 793
18 9117967 9130712 - Vvi18g794 Vvi18g794 794
18 9147541 9149927 - Vvi18g795 Vvi18g795 795
18 9163500 9165829 - Vvi18g796 Vvi18g796 796
18 9178746 9183975 - Vvi18g797 Vvi18g797 797
18 9187085 9188873 - Vvi18g798 Vvi18g798 798
18 9220505 9229554 - Vvi18g799 Vvi18g799 799
       

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