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
Vvi18g10 . . . . . . . . . Cmo12g00648 . . . Car12g00685 . . Cpe07g00604 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma12g00715 . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g11 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo17g00913 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g12 . . . . . . . . . . . Cma09g00004 . . . . . . . . . . . . . . . . . . . . . . Cone20ag0002 . . . . Blo17g00913 . . . . . . . Sed13g1219 . Cmo09g00005 . . . Car09g00004 . . Bhi09g02778 Tan01g5192 Cmetu07g1303 . Hepe01g2387 Mch11g0008 . . . . . . . . . . . .
Vvi18g13 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g14 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g15 Blo01g01662 . . . Bpe02g00280 . . Bma01g02433 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed01g2384 . . . . . . . . Bhi09g02779 Tan01g5191 Cmetu07g1787 . Hepe01g2386 Mch11g0009 . . . . . . . . . . . .
Vvi18g16 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g17 . Blo12g00835 . Bda03g00340 . Bpe04g00300 Bma04g00309 . . . . Cma09g00007 . . . . . . . . . . . . . . . . . . . . . . Cone20ag0003 . Csa04g02754 . . . . . . . . . . . . Cmo09g00008 . . . Car09g00007 . . . . . . . . . . . . . . . . . . . Cme07g00008
Vvi18g18 . Blo12g00836 . Bda03g00339 Bpe02g00281 Bpe04g00299 Bma04g00308 Bma01g02432 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g19 . . . . Bpe02g00282 . . Bma01g02431 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 2871572 2873664 + Bda016300.1 Bda03g00339 339
3 2874279 2886437 + Bda016301.1 Bda03g00340 340
9 74171492 74183012 - XM_039041789.1 Bhi09g02778 2778
9 74250922 74262014 + XM_039042823.1 Bhi09g02779 2779
1 56374969 56381450 - BLOR01662 Blo01g01662 1662
12 26653224 26662485 - BLOR04854 Blo12g00835 835
12 26663288 26665828 - BLOR04855 Blo12g00836 836
17 29972036 29973655 + BLOR08459 Blo17g00913 913
1 81962856 81963455 + Bma003302.1 Bma01g02431 2431
1 81966538 81968765 + Bma003303.1 Bma01g02432 2432
1 81969595 81979726 - Bma003304.1 Bma01g02433 2433
4 2440966 2443873 + Bma018762.1 Bma04g00308 308
4 2444431 2454880 + Bma018763.1 Bma04g00309 309
2 1875469 1877886 + Bpe008124.1 Bpe02g00280 280
2 1878721 1880874 - Bpe008125.1 Bpe02g00281 281
2 1884598 1885239 - Bpe008126.1 Bpe02g00282 282
4 1915103 1917134 + Bpe015001.1 Bpe04g00299 299
4 1917688 1928723 + Bpe015002.1 Bpe04g00300 300
9 10342 16020 + Carg08587-RA Car09g00004 4
9 36009 57155 - Carg08590-RA Car09g00007 7
12 4735071 4738147 + Carg17617-RA Car12g00685 685
9 11369 17765 + CmaCh09G000040.1 Cma09g00004 4
9 38771 60001 - CmaCh09G000070.1 Cma09g00007 7
12 3975161 3978727 + CmaCh12G007150.1 Cma12g00715 715
7 94502 112999 - MELO3C017073.2.1 Cme07g00008 8
7 24750312 24757281 - PI0006631.1 Cmetu07g1303 1303
7 24760817 24779669 + PI0006638.1 Cmetu07g1787 1787
9 11246 17151 + CmoCh09G000050.1 Cmo09g00005 5
9 38741 60450 - CmoCh09G000080.1 Cmo09g00008 8
12 4168500 4171625 + CmoCh12G006480.1 Cmo12g00648 648
20 15709 19016 - Conep20aG0000200.1 Cone20ag0002 2
20 19765 35872 - Conep20aG0000300.1 Cone20ag0003 3
7 4108756 4114300 - Cp4.1LG07g05690.1 Cpe07g00604 604
4 26380202 26391418 + CsaV3_4G037800.1 Csa04g02754 2754
1 88218261 88222136 - Hsped.01g23860.1 Hepe01g2386 2386
1 88228844 88242855 + Hsped.01g23870.1 Hepe01g2387 2387
11 69647 85957 - MC11g0005 Mch11g0008 8
11 90159 96037 + MC11g0006 Mch11g0009 9
1 17908942 17914268 + Sed0015844.2 Sed01g2384 2384
13 17702808 17721492 + Sed0017561.1 Sed13g1219 1219
1 116922223 116924004 - Tan0008656.1 Tan01g5191 5191
1 116935363 116937011 + Tan0004911.1 Tan01g5192 5192
18 178836 216959 - Vvi18g10 Vvi18g10 10
18 227239 228213 + Vvi18g11 Vvi18g11 11
18 228251 232731 - Vvi18g12 Vvi18g12 12
18 233635 236329 - Vvi18g13 Vvi18g13 13
18 237356 246044 - Vvi18g14 Vvi18g14 14
18 249337 255983 + Vvi18g15 Vvi18g15 15
18 257297 263356 + Vvi18g16 Vvi18g16 16
18 263664 297925 - Vvi18g17 Vvi18g17 17
18 299052 304994 - Vvi18g18 Vvi18g18 18
18 307574 308424 - Vvi18g19 Vvi18g19 19
       

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