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
Vvi18g1390 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1391 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1227 Cone7ag0908 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1392 . . . . . . . . . . . Cma09g01147 . . . . . . . . . . . . . . . . . . . Cone4ag1226 Cone7ag0909 . . . . . . . . . . . . . . . . Cmo09g01158 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1393 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1394 . . . . . . . . . . . Cma09g01145 . . . . . . . . . . . . . . . . . . . Cone4ag1225 Cone7ag0911 . . . . . . . . . . . . . . . . Cmo09g01156 . . . Car09g01039 . . . . . . . . . . . . . . . . . . . .
Vvi18g1395 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1396 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1397 . . . . . . . . . . . . . . Sed03g3083 . . Bhi04g02527 Tan11g0060 Cmetu03g2067 . Hepe02g3457 . Lcy10g2348 . . . . . . . . . . . . . . . Blo17g00151 . . Bda13g01440 . Bpe14g00416 . Bma02g00184 . . . . . . . . . . . . . . . . Cla11g00787 Cam11g0821 Cec11g0801 Cco11g0806 Clacu11g1037 Cmu11g0898 Cre11g1264 . . . .
Vvi18g1398 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag1025 Cone5ag0732 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1399 . . . . . . . . . . . Cma09g01142 . . . . . . . . . . . . . . . . . . . Cone4ag1222 Cone7ag0913 . . . . . . . . . . . . . . . . Cmo09g01152 . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
13 37152359 37155727 - Bda000273.1 Bda13g01440 1440
4 68122182 68126898 + XM_039028104.1 Bhi04g02527 2527
17 1411327 1414819 - BLOR15972 Blo17g00151 151
2 1682415 1685830 - Bma014641.1 Bma02g00184 184
14 3849838 3853259 + Bpe024978 Bpe14g00416 416
11 10440270 10443398 + CaPI482276_11g008210.1 Cam11g0821 821
9 7421149 7426241 - Carg27509-RA Car09g01039 1039
11 9265801 9269047 + CcPI632755_11g008060.1 Cco11g0806 806
11 9498391 9501322 + CePI673135_11g008010.1 Cec11g0801 801
11 12842907 12846040 - ClG42_11g0103700.10 Clacu11g1037 1037
11 11349291 11352374 + ClCG11G008230.1 Cla11g00787 787
9 6476356 6484814 - CmaCh09G011420.1 Cma09g01142 1142
9 6503269 6508880 - CmaCh09G011450.1 Cma09g01145 1145
9 6561937 6563448 + CmaCh09G011470.1 Cma09g01147 1147
3 25984618 25987542 + PI0020325.1 Cmetu03g2067 2067
9 7192181 7201900 - CmoCh09G011520.1 Cmo09g01152 1152
9 7219107 7224026 - CmoCh09G011560.1 Cmo09g01156 1156
9 7299396 7300916 + CmoCh09G011580.1 Cmo09g01158 1158
11 12171974 12175107 - CmPI595203_11g008980.1 Cmu11g0898 898
1 55137199 55139137 - Conep01aG0107300.1 Cone1ag1025 1025
4 10210000 10212598 - Conep04aG0126800.1 Cone4ag1222 1222
4 10221131 10223054 + Conep04aG0127100.1 Cone4ag1225 1225
4 10224325 10226785 + Conep04aG0127200.1 Cone4ag1226 1226
4 10227013 10230165 - Conep04aG0127300.1 Cone4ag1227 1227
5 3154646 3156647 - Conep05aG0075700.1 Cone5ag0732 732
7 7129507 7132988 + Conep07aG0093700.1 Cone7ag0908 908
7 7133436 7135833 - Conep07aG0093800.1 Cone7ag0909 909
7 7148645 7152229 - Conep07aG0094000.1 Cone7ag0911 911
7 7160534 7163491 + Conep07aG0094200.1 Cone7ag0913 913
11 11147055 11150004 + CrPI670011_11g012640.1 Cre11g1264 1264
2 83899235 83901418 + Hsped.02g34570.1 Hepe02g3457 3457
10 47037112 47041058 + Maker00039830 Lcy10g2348 2348
3 47539174 47567424 - Sed0016017.1 Sed03g3083 3083
11 823072 826938 - Tan0016533.1 Tan11g0060 60
18 20159284 20168711 + Vvi18g1390 Vvi18g1390 1390
18 20203330 20206775 + Vvi18g1391 Vvi18g1391 1391
18 20207846 20209652 - Vvi18g1392 Vvi18g1392 1392
18 20209651 20211072 - Vvi18g1393 Vvi18g1393 1393
18 20224368 20234931 - Vvi18g1394 Vvi18g1394 1394
18 20255145 20255684 + Vvi18g1395 Vvi18g1395 1395
18 20255698 20261741 + Vvi18g1396 Vvi18g1396 1396
18 20267069 20299113 - Vvi18g1397 Vvi18g1397 1397
18 20311698 20316360 + Vvi18g1398 Vvi18g1398 1398
18 20331032 20346348 - Vvi18g1399 Vvi18g1399 1399
       

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