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
Vvi18g1400 . . . . . . . . . . . . . . Sed03g0686 . . Bhi04g02525 Tan11g0061 Cmetu03g1701 . Hepe02g3456 . Lcy10g2347 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla11g00786 Cam11g0818 Cec11g0800 Cco11g0805 Clacu11g1038 Cmu11g0899 Cre11g1262 . . . .
Vvi18g1401 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1402 . . . . . . . . . . Cma01g00920 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1403 . . . . . . . . . . Cma01g00919 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car09g01038 . . . . . . . . . . . . . . . . . . . .
Vvi18g1404 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1405 . . . . . . . . . . . . . . Sed08g1886 . . Bhi04g02524 Tan11g0063 Cmetu01g0080 . Hepe02g3454 . Lcy10g2345 Cla08g00076 Cam08g0073 Cec08g0178 Cco08g0131 Clacu08g0087 Cmu08g0084 Cre08g0074 Cone4ag1221 . . . . . . . . . . . . . . . . . . . . . . . . Bhi09g01450 . . . . . . Cla09g00889 Cam09g0940 Cec09g0944 Cco09g0947 . . Cre09g0911 . . . .
Vvi18g1406 . Blo12g00800 . Bda03g00373 . Bpe04g00337 Bma04g00352 . . . . Cma09g01129 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo09g01139 . . . Car09g01023 . . . . . . . . . . . . . . . . . . . .
Vvi18g1407 . . . . . . . . . . . Cma09g01113 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo01g01016 Cmo09g01119 . . . Car09g01002 . . . . . . . . . . . . . . . . . . . Cme01g00805
Vvi18g1408 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo17g00152 Blo18g00164 . Bda13g01442 . Bpe14g00413 . Bma02g00186 . Cmo01g00999 . . . . . . . . . . . . . . . . . . . . . . . . Cme01g00849
Vvi18g1409 . Blo12g00802 . . . Bpe04g00334 Bma04g00349 Bma01g02470 . . . . . . . . . . . . . . . . Cla08g00187 . . . . . . Cone4ag1213 . . . . . . . . . Bda11g00903 . . . . . . Cmo01g00998 . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 3132868 3137438 - Bda016336.1 Bda03g00373 373
11 8842658 8844352 - Bda005657.1 Bda11g00903 903
13 37160589 37163294 + Bda000275.1 Bda13g01442 1442
4 68066013 68071244 + XM_039029275.1 Bhi04g02524 2524
4 68073881 68080922 - XM_039030790.1 Bhi04g02525 2525
9 36889803 36900386 - XM_039043668.1 Bhi09g01450 1450
12 26392223 26397226 + BLOR04819 Blo12g00800 800
12 26407253 26419443 - BLOR04821 Blo12g00802 802
17 1425600 1428105 + BLOR15973 Blo17g00152 152
18 1544945 1547192 + BLOR08652 Blo18g00164 164
1 82367898 82369320 + Bma003343.1 Bma01g02470 2470
2 1725532 1727124 + Bma014643.1 Bma02g00186 186
4 2837346 2839185 + Bma018808.1 Bma04g00349 349
4 2846443 2851118 - Bma018811.1 Bma04g00352 352
4 2130253 2131275 + Bpe015030.1 Bpe04g00334 334
4 2138192 2142848 - Bpe025609 Bpe04g00337 337
14 3838599 3841312 - Bpe007066.1 Bpe14g00413 413
8 1336491 1340165 - CaPI482276_08g000730.1 Cam08g0073 73
9 9666297 9673658 - CaPI482276_09g009400.1 Cam09g0940 940
11 10417117 10423112 - CaPI482276_11g008180.1 Cam11g0818 818
9 6640658 6648715 - Carg23302-RA Car09g01002 1002
9 6896265 6906052 + Carg27446-RA Car09g01023 1023
9 7414281 7418906 - Carg27508-RA Car09g01038 1038
8 2038133 2041864 - CcPI632755_08g001310.1 Cco08g0131 131
9 8911480 8918717 - CcPI632755_09g009470.1 Cco09g0947 947
11 9248147 9254113 - CcPI632755_11g008050.1 Cco11g0805 805
8 3445754 3449468 + CePI673135_08g001780.1 Cec08g0178 178
9 8958603 8966200 - CePI673135_09g009440.1 Cec09g0944 944
11 9468007 9473982 - CePI673135_11g008000.1 Cec11g0800 800
8 1740302 1743968 - ClG42_08g0008700.10 Clacu08g0087 87
11 12861469 12867466 + ClG42_11g0103800.10 Clacu11g1038 1038
8 1599438 1603777 - ClCG08G000745.1 Cla08g00076 76
8 3840670 3844494 + ClCG08G001870.2 Cla08g00187 187
9 9166879 9174610 - ClCG09G009500.1 Cla09g00889 889
11 11325123 11334311 - ClCG11G008220.2 Cla11g00786 786
1 5582542 5585041 + CmaCh01G009190.1 Cma01g00919 919
1 5585414 5589003 - CmaCh01G009200.1 Cma01g00920 920
9 6120191 6130515 - CmaCh09G011130.1 Cma09g01113 1113
9 6305713 6316923 + CmaCh09G011290.1 Cma09g01129 1129
1 8598675 8606263 - MELO3C024083.2.1 Cme01g00805 805
1 9630426 9634345 + MELO3C024120.2.1 Cme01g00849 849
1 19089926 19095876 + PI0017350.1 Cmetu01g0080 80
3 25976960 25982870 - PI0022608.1 Cmetu03g1701 1701
1 6943848 6945057 + CmoCh01G009980.1 Cmo01g00998 998
1 6961517 6966223 + CmoCh01G009990.1 Cmo01g00999 999
1 7691207 7693231 + CmoCh01G010160.1 Cmo01g01016 1016
9 6378377 6387406 - CmoCh09G011190.1 Cmo09g01119 1119
9 6590948 6601791 + CmoCh09G011390.1 Cmo09g01139 1139
8 1658793 1662460 - CmPI595203_08g000840.1 Cmu08g0084 84
11 12190518 12196534 + CmPI595203_11g008990.1 Cmu11g0899 899
4 10173872 10175248 - Conep04aG0125900.1 Cone4ag1213 1213
4 10205345 10209817 + Conep04aG0126700.1 Cone4ag1221 1221
8 1586892 1590565 - CrPI670011_08g000740.1 Cre08g0074 74
9 9160048 9167256 - CrPI670011_09g009110.1 Cre09g0911 911
11 11103630 11115445 - CrPI670011_11g012620.1 Cre11g1262 1262
2 83884178 83890747 + Hsped.02g34540.1 Hepe02g3454 3454
2 83893490 83898330 - Hsped.02g34560.1 Hepe02g3456 3456
10 47018676 47024307 + Maker00039165 Lcy10g2345 2345
10 47028143 47036486 - Maker00039943 Lcy10g2347 2347
3 4111695 4116331 - Sed0002212.2 Sed03g0686 686
8 33395676 33399852 - Sed0016174.2 Sed08g1886 1886
11 830062 841013 + Tan0000498.1 Tan11g0061 61
11 845494 849600 - Tan0019590.1 Tan11g0063 63
18 20356681 20367644 - Vvi18g1400 Vvi18g1400 1400
18 20396917 20422554 + Vvi18g1401 Vvi18g1401 1401
18 20434240 20441673 + Vvi18g1402 Vvi18g1402 1402
18 20442855 20449338 - Vvi18g1403 Vvi18g1403 1403
18 20461677 20465965 - Vvi18g1404 Vvi18g1404 1404
18 20473465 20492229 - Vvi18g1405 Vvi18g1405 1405
18 20503033 20524687 - Vvi18g1406 Vvi18g1406 1406
18 20544978 20556621 - Vvi18g1407 Vvi18g1407 1407
18 20571196 20583726 - Vvi18g1408 Vvi18g1408 1408
18 20598143 20599942 - Vvi18g1409 Vvi18g1409 1409
       

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