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
Vvi4g292 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g293 . Blo12g00755 . . Bpe02g01181 . Bma04g00407 . . Cmo12g00207 . Cma05g00733 . Car12g00238 . Cpe07g00217 . Bhi04g00845 . . . Hepe10g0363 . . . . . . . . . . . . . . . . Cme03g01742 . . Bda01g00936 . . Bpe04g00397 . . . . . . Cma12g00254 . Car05g00539 Cpe11g00655 . . . . . . . . Cla08g01224 Cam08g1683 Cec08g1262 Cco08g1382 Clacu08g1381 . Cre08g1166 Lsi08g01087 . Chy03g01247 .
Vvi4g294 Blo01g01393 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag1691 . . . . . . Blo17g00071 . . Bda13g01333 Bpe14g00515 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g295 . . . . Bpe02g01180 . . . . Cmo12g00208 . . . Car12g00239 Sed12g1115 Cpe07g00218 . Bhi04g00842 Tan02g2563 Cmetu04g1511 . Hepe10g0359 . . . . . . . . . . . Cone17ag1121 . . . . Cme03g01739 . . Bda01g00935 . . . . . . . . . Cma12g00255 . . . . . . . . . . . Cla08g01225 Cam08g1684 Cec08g1263 Cco08g1383 Clacu08g1382 . Cre08g1167 Lsi08g01088 . Chy03g01246 .
Vvi4g296 . Blo12g00756 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g02332 Csa03g04551 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g297 . . . . . . . . . . Cma01g01436 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo01g01486 . . . . . . Cpe02g00512 . . . . . . . . . . . . . . . . . Cme04g00176
Vvi4g298 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g299 . . . . . . Bma04g00406 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g04552 Chy04g00151 . . . . . . . . . Sed05g1501 . . . . . . . . Bhi09g02580 Tan01g3935 Cmetu04g3147 . Hepe01g2222 Mch11g0771 . . . . . . . . . . . .
Vvi4g300 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g301 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 42703982 42706607 - Bda003085.2 Bda01g00935 935
1 42732006 42741861 + Bda003087.1 Bda01g00936 936
13 35589119 35591764 - Bda000144.1 Bda13g01333 1333
4 21242318 21246075 - XM_039029280.1 Bhi04g00842 842
4 21296636 21300674 + XM_039029200.1 Bhi04g00845 845
9 70180819 70188430 + XM_039040683.1 Bhi09g02580 2580
1 52248760 52250250 - BLOR01393 Blo01g01393 1393
12 25900444 25902422 - BLOR04774 Blo12g00755 755
12 25903705 25907892 + BLOR04775 Blo12g00756 756
17 540830 543507 - BLOR15892 Blo17g00071 71
4 3302711 3305086 - Bma018869.1 Bma04g00406 406
4 3307752 3309069 + Bma018870.1 Bma04g00407 407
2 15474006 15478245 - Bpe009041.2 Bpe02g01180 1180
2 15481464 15484578 + Bpe009042.1 Bpe02g01181 1181
4 2493289 2494157 + Bpe015081.1 Bpe04g00397 397
14 4532123 4534753 + Bpe007165.1 Bpe14g00515 515
8 23112177 23116019 - CaPI482276_08g016830.1 Cam08g1683 1683
8 23117938 23121289 + CaPI482276_08g016840.1 Cam08g1684 1684
5 3144564 3148722 - Carg08282-RA Car05g00539 539
12 1600880 1604780 - Carg03845-RA Car12g00238 238
12 1606495 1609956 + Carg03846-RA Car12g00239 239
8 25739065 25742887 - CcPI632755_08g013820.1 Cco08g1382 1382
8 25746454 25749147 + CcPI632755_08g013830.1 Cco08g1383 1383
8 24593687 24597708 - CePI673135_08g012620.1 Cec08g1262 1262
8 24601271 24604213 + CePI673135_08g012630.1 Cec08g1263 1263
3 15526277 15529213 - Chy3G062260.1 Chy03g01246 1246
3 15532881 15536385 + Chy3G062270.1 Chy03g01247 1247
4 1345652 1348504 - Chy4G068690.1 Chy04g00151 151
8 23866606 23870466 - ClG42_08g0138100.10 Clacu08g1381 1381
8 23872754 23875673 + ClG42_08g0138200.10 Clacu08g1382 1382
8 25157972 25161843 - ClCG08G012260.2 Cla08g01224 1224
8 25163948 25167252 + ClCG08G012270.1 Cla08g01225 1225
1 10099857 10105030 - CmaCh01G014360.1 Cma01g01436 1436
5 4142791 4147078 - CmaCh05G007330.1 Cma05g00733 733
12 1290000 1294647 - CmaCh12G002540.1 Cma12g00254 254
12 1295756 1299556 + CmaCh12G002550.1 Cma12g00255 255
3 25964014 25968139 - MELO3C011145.2.1 Cme03g01739 1739
3 25970070 25974329 + MELO3C011144.2.1 Cme03g01742 1742
4 1311936 1316293 - MELO3C003462.2.1 Cme04g00176 176
4 7974578 7999621 + PI0024745.1 Cmetu04g1511 1511
4 32104627 32104953 + PI0014594.1 Cmetu04g3147 3147
1 11513752 11518925 - CmoCh01G014860.1 Cmo01g01486 1486
12 1366692 1370099 - CmoCh12G002070.1 Cmo12g00207 207
12 1370979 1375449 + CmoCh12G002080.1 Cmo12g00208 208
7 11293819 11295886 + Conep07aG0174200.1 Cone7ag1691 1691
17 8303373 8305497 - Conep17aG0115000.1 Cone17ag1121 1121
2 3021799 3025712 + Cp4.1LG02g03700.1 Cpe02g00512 512
7 1405571 1409019 - Cp4.1LG07g02230.1 Cpe07g00217 217
7 1410617 1414727 + Cp4.1LG07g02350.1 Cpe07g00218 218
11 4355648 4362328 - Cp4.1LG11g06610.1 Cpe11g00655 655
8 24902791 24906495 - CrPI670011_08g011660.1 Cre08g1166 1166
8 24910190 24913115 + CrPI670011_08g011670.1 Cre08g1167 1167
3 39663250 39666931 + CsaV3_3G048570.1 Csa03g04551 4551
3 39667326 39667699 + CsaV3_3G048580.1 Csa03g04552 4552
1 86908936 86918449 + Hsped.01g22220.1 Hepe01g2222 2222
10 3919324 3920149 - Hsped.10g03590.1 Hepe10g0359 359
10 3943590 3949601 + Hsped.10g03630.1 Hepe10g0363 363
4 30527072 30535424 + Lsi04G023320.1 Lsi04g02332 2332
8 19480194 19484893 - Lsi08G010870.1 Lsi08g01087 1087
8 19487727 19493335 + Lsi08G010880.1 Lsi08g01088 1088
11 5205444 5209414 + MC11g0649 Mch11g0771 771
5 28702356 28708556 - Sed0013565.1 Sed05g1501 1501
12 7286688 7311594 - Sed0008218.1 Sed12g1115 1115
1 104244453 104261248 + Tan0009226.1 Tan01g3935 3935
2 94221999 94225734 + Tan0001466.1 Tan02g2563 2563
4 2794883 2795466 + Vvi4g292 Vvi4g292 292
4 2824571 2831160 - Vvi4g293 Vvi4g293 293
4 2835734 2842423 - Vvi4g294 Vvi4g294 294
4 2843590 2855506 + Vvi4g295 Vvi4g295 295
4 2863081 2866487 + Vvi4g296 Vvi4g296 296
4 2870319 2878007 + Vvi4g297 Vvi4g297 297
4 2880129 2880892 + Vvi4g298 Vvi4g298 298
4 2883264 2886368 + Vvi4g299 Vvi4g299 299
4 2887666 2888436 - Vvi4g300 Vvi4g300 300
4 2889370 2892149 - Vvi4g301 Vvi4g301 301
       

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