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
Vvi18g1660 Blo01g01668 Blo12g00832 . . Bpe02g00274 Bpe04g00304 . . . . Cma01g00840 . . . . . . Bhi04g02590 . . . . . . . . . . . . . . . . . . . . Cme09g00036 . . Bda11g00935 . . . . . . Cmo01g00880 Cmo09g01300 . . . Car09g01143 . . . . . . . . . . . . . . . . Lsi08g00047 . . .
Vvi18g1661 . . . . . . . Bma01g02439 . . . . Car01g00778 . . . . . . . . . . . . . . . . . . . . . . . . . Cme09g00039 . . . . . . . . . . . . . . . . Cpe02g01018 . . . . . . . Cla11g00844 Cam11g0875 Cec11g0875 Cco11g0870 Clacu11g0987 Cmu11g0838 Cre11g1319 Lsi08g00048 . . .
Vvi18g1662 . Blo12g00831 . . . . . . . . . . . . . . . . . . . . . . Cla08g00064 Cam08g0061 Cec08g0190 Cco08g0119 Clacu08g0076 Cmu08g0074 Cre08g0066 . . . . . . . Cme09g00041 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi08g00050 . . .
Vvi18g1663 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1664 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1665 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1666 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi06g00189 . . . . . . . . . . . . . . . . .
Vvi18g1667 . Blo12g00830 . Bda03g00345 . Bpe04g00305 Bma04g00316 . . . . . . . . Cpe06g01005 . . . . . . . . Cla08g00065 Cam08g0062 Cec08g0189 Cco08g0120 Clacu08g0077 Cmu08g0075 Cre08g0067 . . . . . . . Cme09g00042 . . . . . . . . . . Cmo09g01299 . . . Car09g01142 . . . . . . . . . . . . . . . . Lsi08g00051 . . .
Vvi18g1668 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1669 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 2912657 2919290 - Bda016306.1 Bda03g00345 345
11 9129505 9131279 + Bda005690.1 Bda11g00935 935
4 69589046 69590892 + XM_039028403.1 Bhi04g02590 2590
6 4626657 4632019 + XM_039033214.1 Bhi06g00189 189
1 56428859 56430373 - BLOR01668 Blo01g01668 1668
12 26624659 26626342 + BLOR04849 Blo12g00830 830
12 26626756 26631711 - BLOR04850 Blo12g00831 831
12 26632195 26633707 + BLOR04851 Blo12g00832 832
1 82017806 82019355 - Bma003310.1 Bma01g02439 2439
4 2525723 2533410 - Bma018771.1 Bma04g00316 316
2 1842290 1843798 + Bpe008118.1 Bpe02g00274 274
4 1954608 1955094 - Bpe015004.1 Bpe04g00304 304
4 1959419 1962812 - Bpe025603 Bpe04g00305 305
8 1235142 1239784 + CaPI482276_08g000610.1 Cam08g0061 61
8 1240067 1244270 - CaPI482276_08g000620.1 Cam08g0062 62
11 11998981 12000377 + CaPI482276_11g008750.1 Cam11g0875 875
1 4781447 4787929 - Carg21725-RA Car01g00778 778
9 11923190 11926032 + Carg27645-RA Car09g01142 1142
9 11928378 11930142 - Carg27644-RA Car09g01143 1143
8 1945504 1950155 + CcPI632755_08g001190.1 Cco08g0119 119
8 1950438 1954757 - CcPI632755_08g001200.1 Cco08g0120 120
11 10942642 10961433 + CcPI632755_11g008700.1 Cco11g0870 870
8 3542589 3546743 + CePI673135_08g001890.1 Cec08g0189 189
8 3547026 3551617 - CePI673135_08g001900.1 Cec08g0190 190
11 11321048 11322455 + CePI673135_11g008750.1 Cec11g0875 875
8 1633456 1638054 + ClG42_08g0007600.10 Clacu08g0076 76
8 1638337 1642626 - ClG42_08g0007700.10 Clacu08g0077 77
11 11298299 11299694 - ClG42_11g0098700.10 Clacu11g0987 987
8 1488814 1493438 + ClCG08G000630.1 Cla08g00064 64
8 1493721 1497997 - ClCG08G000640.1 Cla08g00065 65
11 12963403 12964798 + ClCG11G008800.1 Cla11g00844 844
1 4599705 4602148 - CmaCh01G008400.1 Cma01g00840 840
9 299035 301748 + MELO3C022201.2.1 Cme09g00036 36
9 307379 309815 + MELO3C022200.2.1 Cme09g00039 39
9 317088 320724 + MELO3C022199.2.1 Cme09g00041 41
9 320278 324391 - MELO3C022198.2.1 Cme09g00042 42
1 4787577 4790028 - CmoCh01G008800.1 Cmo01g00880 880
9 11517428 11520873 + CmoCh09G012990.1 Cmo09g01299 1299
9 11521885 11526444 - CmoCh09G013000.1 Cmo09g01300 1300
8 1552434 1557032 + CmPI595203_08g000740.1 Cmu08g0074 74
8 1557315 1561604 - CmPI595203_08g000750.1 Cmu08g0075 75
11 10626220 10627613 - CmPI595203_11g008380.1 Cmu11g0838 838
2 9366898 9369187 + Cp4.1LG02g10750.1 Cpe02g01018 1018
6 10172427 10176144 + Cp4.1LG06g10030.1 Cpe06g01005 1005
8 1494531 1499211 + CrPI670011_08g000660.1 Cre08g0066 66
8 1499494 1503728 - CrPI670011_08g000670.1 Cre08g0067 67
11 12861832 12863210 + CrPI670011_11g013190.1 Cre11g1319 1319
8 1137806 1145584 + Lsi08G000470.1 Lsi08g00047 47
8 1153043 1158194 + Lsi08G000480.1 Lsi08g00048 48
8 1212161 1216348 + Lsi08G000500.1 Lsi08g00050 50
8 1215734 1221955 - Lsi08G000510.1 Lsi08g00051 51
18 27298742 27301524 + Vvi18g1660 Vvi18g1660 1660
18 27303884 27305837 - Vvi18g1661 Vvi18g1661 1661
18 27308719 27312220 + Vvi18g1662 Vvi18g1662 1662
18 27319001 27324143 - Vvi18g1663 Vvi18g1663 1663
18 27324194 27327611 - Vvi18g1664 Vvi18g1664 1664
18 27337564 27339270 + Vvi18g1665 Vvi18g1665 1665
18 27341190 27342959 + Vvi18g1666 Vvi18g1666 1666
18 27344310 27347675 - Vvi18g1667 Vvi18g1667 1667
18 27357686 27357962 - Vvi18g1668 Vvi18g1668 1668
18 27367071 27377291 + Vvi18g1669 Vvi18g1669 1669
       

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