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
Vvi4g252 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g253 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g254 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g255 Blo01g01355 . Bda01g00715 . . . . Bma01g02143 . . . . Car09g00436 . . . Cpe06g00372 . . . . . . . . . . . . . . Cone4ag1839 Cone7ag1745 . . Lsi04g02172 Csa03g04379 Chy04g00323 . . . . . . . . . Sed05g1660 . Cmo09g00498 . . . . . . Bhi09g02315 Tan01g3700 Cmetu04g3175 . Hepe01g2064 Mch11g0600 . . . . . . . . . . . Cme04g00363
Vvi4g256 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g257 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g258 . . . . . . . . Cmo05g00670 . . Cma05g00642 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car05g00587 Cpe11g00565 . . . . . . . . . . . . . . . Lsi08g01144 . Chy03g01175 .
Vvi4g259 . . . Bda03g00046 . . Bma04g00046 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe04g00034 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g260 . . . . . . . . Cmo05g00669 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma01g01302 . . . . . . . Car05g00586 Cpe11g00564 . . . . . . . . . . . . . . . . Csa02g02331 . .
Vvi4g261 . . . . . . . . . . Cma01g01560 . . . . . . . . . . . . . Cla05g01780 Cam05g1899 Cec05g1910 Cco05g1973 Clacu05g1892 Cmu05g1773 Cre05g1901 . . . . . . . . . . . Bda13g01287 . . . . . Cmo01g01607 . Cma09g00501 . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 34427565 34435385 - Bda002753.1 Bda01g00715 715
3 547743 556643 + Bda015980.1 Bda03g00046 46
13 35179083 35179809 + Bda000094.1 Bda13g01287 1287
9 64066575 64070860 + XM_039043592.1 Bhi09g02315 2315
1 51504688 51508492 - BLOR01355 Blo01g01355 1355
1 17852059 17854204 + Bma030245 Bma01g01302 1302
1 77947567 77951302 - Bma002985.1 Bma01g02143 2143
4 420387 429286 + Bma018497.1 Bma04g00046 46
4 291653 300446 + Bpe025568 Bpe04g00034 34
5 27946530 27948323 + CaPI482276_05g018990.1 Cam05g1899 1899
5 3427978 3430945 - Carg08329-RA Car05g00586 586
5 3432438 3433484 + Carg08330-RA Car05g00587 587
9 2442787 2446076 + Carg02917-RA Car09g00436 436
5 28838963 28840765 + CcPI632755_05g019730.1 Cco05g1973 1973
5 31182567 31185924 + CePI673135_05g019100.1 Cec05g1910 1910
3 14943089 14944144 - Chy3G061550.1 Chy03g01175 1175
4 2849155 2852289 - Chy4G070410.1 Chy04g00323 323
5 28141405 28143179 + ClG42_05g0189200.10 Clacu05g1892 1892
5 29697687 29699461 + ClCG05G017370.1 Cla05g01780 1780
1 10834528 10837276 - CmaCh01G015600.1 Cma01g01560 1560
5 3245728 3246774 + CmaCh05G006420.1 Cma05g00642 642
9 2264374 2269817 + CmaCh09G005010.1 Cma09g00501 501
4 2864937 2868804 - MELO3C003651.2.1 Cme04g00363 363
4 30497044 30500803 + PI0025313.1 Cmetu04g3175 3175
1 12288326 12291263 - CmoCh01G016070.1 Cmo01g01607 1607
5 3395627 3398567 - CmoCh05G006690.1 Cmo05g00669 669
5 3400141 3401187 + CmoCh05G006700.1 Cmo05g00670 670
9 2315772 2320006 + CmoCh09G004980.1 Cmo09g00498 498
5 27859765 27861539 + CmPI595203_05g017730.1 Cmu05g1773 1773
4 13256458 13260068 + Conep04aG0189800.1 Cone4ag1839 1839
7 11554366 11557801 + Conep07aG0179800.1 Cone7ag1745 1745
6 2108248 2112422 + Cp4.1LG06g03580.1 Cpe06g00372 372
11 3349220 3352278 - Cp4.1LG11g05690.1 Cpe11g00564 564
11 3353817 3354860 + Cp4.1LG11g05540.1 Cpe11g00565 565
5 31186424 31188015 + CrPI670011_05g019010.1 Cre05g1901 1901
2 20731294 20735980 + CsaV3_2G031500.1 Csa02g02331 2331
3 38250141 38254192 + CsaV3_3G046850.1 Csa03g04379 4379
1 85323708 85327643 + Hsped.01g20640.1 Hepe01g2064 2064
4 28792004 28803730 + Lsi04G021720.1 Lsi04g02172 2172
8 20080716 20081765 + Lsi08G011440.1 Lsi08g01144 1144
11 3876340 3880983 + MC11g0497 Mch11g0600 600
5 30468098 30475061 - Sed0013692.1 Sed05g1660 1660
1 101893223 101896796 + Tan0001138.1 Tan01g3700 3700
4 2491915 2492832 - Vvi4g252 Vvi4g252 252
4 2492835 2493622 - Vvi4g253 Vvi4g253 253
4 2493626 2494444 - Vvi4g254 Vvi4g254 254
4 2494952 2500388 - Vvi4g255 Vvi4g255 255
4 2501023 2518571 - Vvi4g256 Vvi4g256 256
4 2520410 2529950 - Vvi4g257 Vvi4g257 257
4 2530926 2532401 - Vvi4g258 Vvi4g258 258
4 2534503 2547915 - Vvi4g259 Vvi4g259 259
4 2549157 2554774 - Vvi4g260 Vvi4g260 260
4 2562864 2571626 + Vvi4g261 Vvi4g261 261
       

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