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
Vvi18g1700 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1701 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1702 . . . . . . . . . . . . . . . . . . . . . . . . Cla08g00081 Cam08g0078 Cec08g0173 Cco08g0136 Clacu08g0091 Cmu08g0090 Cre08g0079 . . . . . . . Cme09g00081 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1703 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1704 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1705 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1706 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi08g00101 . . .
Vvi18g1707 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1708 Blo01g01679 . . . Bpe02g00262 . . . . . Cma01g00867 . Car01g00794 . . . . . . . . . . . Cla08g00084 Cam08g0082 Cec08g0168 Cco08g0140 Clacu08g0094 Cmu08g0093 Cre08g0082 Cone4ag1157 . . . . . . Cme09g00083 . . Bda11g00924 . . . . . . Cmo01g00910 . . . . . . . . . . . . . . . . . . . . . Lsi08g00103 . . .
Vvi18g1709 Blo01g01680 Blo12g00814 . Bda03g00358 Bpe02g00261 . Bma04g00335 Bma01g02447 . . Cma01g00868 Cma09g01300 . . . Cpe06g00980 . . . . . . . . Cla08g00119 Cam08g0117 Cec08g0139 Cco08g0177 Clacu08g0128 Cmu08g0122 Cre08g0108 Cone4ag1156 . . . . . . Cme09g00085 . . . . . . . . . Cmo01g00911 . . . . Car09g01111 . Cpe02g00991 . . . . . . . . . . . . . . Lsi08g00104 . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 3022885 3024533 - Bda016321.1 Bda03g00358 358
11 9045534 9047573 - Bda005679.3 Bda11g00924 924
1 56520018 56522049 + BLOR01679 Blo01g01679 1679
1 56523057 56524456 - BLOR01680 Blo01g01680 1680
12 26508310 26508978 + BLOR04833 Blo12g00814 814
1 82092052 82093355 - Bma003317.1 Bma01g02447 2447
4 2740791 2742115 - Bma018794.1 Bma04g00335 335
2 1772400 1773548 + Bpe008106.1 Bpe02g00261 261
2 1774631 1776659 - Bpe008107.1 Bpe02g00262 262
8 1415465 1422265 - CaPI482276_08g000780.1 Cam08g0078 78
8 1498552 1501046 + CaPI482276_08g000820.1 Cam08g0082 82
8 2090578 2098339 + CaPI482276_08g001170.1 Cam08g0117 117
1 5204279 5206809 + Carg26286-RA Car01g00794 794
9 11498654 11504420 - Carg24120-RA Car09g01111 1111
8 2149351 2151961 - CcPI632755_08g001360.1 Cco08g0136 136
8 2219689 2222157 + CcPI632755_08g001400.1 Cco08g0140 140
8 2864047 2872283 + CcPI632755_08g001770.1 Cco08g0177 177
8 2619911 2628168 - CePI673135_08g001390.1 Cec08g0139 139
8 3283752 3286272 - CePI673135_08g001680.1 Cec08g0168 168
8 3364144 3371250 + CePI673135_08g001730.1 Cec08g0173 173
8 1819083 1825377 - ClG42_08g0009100.10 Clacu08g0091 91
8 1897250 1899757 + ClG42_08g0009400.10 Clacu08g0094 94
8 2513827 2529684 + ClG42_08g0012800.10 Clacu08g0128 128
8 1679057 1685646 - ClCG08G000790.2 Cla08g00081 81
8 1760468 1764198 + ClCG08G000820.2 Cla08g00084 84
8 2428717 2436713 + ClCG08G001170.2 Cla08g00119 119
1 4894577 4897543 + CmaCh01G008670.1 Cma01g00867 867
1 4901105 4903386 + CmaCh01G008680.1 Cma01g00868 868
9 9050485 9054544 - CmaCh09G013000.1 Cma09g01300 1300
9 602044 606191 - MELO3C022162.2.1 Cme09g00081 81
9 622461 626098 + MELO3C022160.2.1 Cme09g00083 83
9 632441 635273 + MELO3C022158.2.1 Cme09g00085 85
1 5127331 5130102 + CmoCh01G009100.1 Cmo01g00910 910
1 5134195 5136520 + CmoCh01G009110.1 Cmo01g00911 911
8 1737567 1743851 - CmPI595203_08g000900.1 Cmu08g0090 90
8 1815698 1818203 + CmPI595203_08g000930.1 Cmu08g0093 93
8 2432266 2450255 + CmPI595203_08g001220.1 Cmu08g0122 122
4 9893787 9896438 + Conep04aG0120200.1 Cone4ag1156 1156
4 9898954 9900734 - Conep04aG0120300.1 Cone4ag1157 1157
2 8982621 8987768 - Cp4.1LG02g10920.1 Cpe02g00991 991
6 9825165 9828821 - Cp4.1LG06g09810.1 Cpe06g00980 980
8 1673868 1680159 - CrPI670011_08g000790.1 Cre08g0079 79
8 1755128 1757635 + CrPI670011_08g000820.1 Cre08g0082 82
8 2369595 2377868 + CrPI670011_08g001080.1 Cre08g0108 108
8 2086201 2093511 - Lsi08G001010.1 Lsi08g00101 101
8 2164532 2168078 + Lsi08G001030.1 Lsi08g00103 103
8 2173537 2184317 + Lsi08G001040.1 Lsi08g00104 104
18 27859843 27862659 - Vvi18g1700 Vvi18g1700 1700
18 27867277 27871145 - Vvi18g1701 Vvi18g1701 1701
18 27892344 27911348 - Vvi18g1702 Vvi18g1702 1702
18 27912067 27913691 - Vvi18g1703 Vvi18g1703 1703
18 27919149 27920966 - Vvi18g1704 Vvi18g1704 1704
18 27922456 27924085 + Vvi18g1705 Vvi18g1705 1705
18 27926185 27927919 - Vvi18g1706 Vvi18g1706 1706
18 27929369 27938714 - Vvi18g1707 Vvi18g1707 1707
18 27952656 27956129 + Vvi18g1708 Vvi18g1708 1708
18 27960812 27964979 - Vvi18g1709 Vvi18g1709 1709
       

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