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
Vvi2g162 . Blo03g00258 Bda06g00159 . . . . . . Cmo16g00585 Cma02g00922 . Car02g00671 Car15g01164 . Cpe14g00449 . . . . . . . . Cla07g01086 Cam07g1412 Cec07g1249 Cco07g1226 Clacu07g1150 Cmu07g1130 Cre07g1510 . . Cone6ag0864 Cone9ag0869 . . Chy09g01305 Cme07g01536 . . . . . . . . . Cmo02g00930 . . Cma16g00533 . . . . Bhi12g00124 . . . . . Lcy12g1556 . . . . . . . . Csa04g00677 Chy07g01133 .
Vvi2g163 Blo02g01159 . . . Bpe05g00704 . . Bma14g00677 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda07g00415 . . Bpe11g00592 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g164 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00679 . .
Vvi2g165 Blo02g01160 . . . Bpe05g00705 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g166 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0867 Cone9ag0873 . . . . Blo03g00818 . . Bda09g00704 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00681 Chy07g01132 .
Vvi2g167 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g168 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g169 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme07g01535 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g170 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g171 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00682 Chy07g01131 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 2298415 2302031 + Bda023361.1 Bda06g00159 159
7 5315017 5318066 - Bda025508.1 Bda07g00415 415
9 11201097 11203142 + Bda031369.2 Bda09g00704 704
12 3921639 3928214 + XM_039051103.1 Bhi12g00124 124
2 43222067 43225018 + BLOR10889 Blo02g01159 1159
2 43260055 43262739 + BLOR10890 Blo02g01160 1160
3 5469379 5474403 + BLOR11439 Blo03g00258 258
3 33622228 33623881 + BLOR11999 Blo03g00818 818
14 7319802 7322870 + Bma011128.2 Bma14g00677 677
5 20626998 20630332 + Bpe018117.1 Bpe05g00704 704
5 20630732 20641447 + Bpe018118.1 Bpe05g00705 705
11 4498455 4501504 - Bpe003957.1 Bpe11g00592 592
7 28640738 28645939 + CaPI482276_07g014120.1 Cam07g1412 1412
2 5010194 5016754 - Carg08552-RA Car02g00671 671
15 9141928 9146989 - Carg21288-RA Car15g01164 1164
7 26146254 26149877 - CcPI632755_07g012260.1 Cco07g1226 1226
7 28004971 28008586 - CePI673135_07g012490.1 Cec07g1249 1249
7 16241672 16245735 - Chy7G139610.1 Chy07g01131 1131
7 16252615 16255864 - Chy7G139620.1 Chy07g01132 1132
7 16265895 16269453 - Chy7G139630.1 Chy07g01133 1133
9 15000111 15004635 - Chy9G170210.1 Chy09g01305 1305
7 26172365 26175944 - ClG42_07g0115000.10 Clacu07g1150 1150
7 27556698 27560638 - ClCG07G011440.2 Cla07g01086 1086
2 5485375 5490652 - CmaCh02G009220.1 Cma02g00922 922
16 2722122 2726386 - CmaCh16G005330.1 Cma16g00533 533
7 21201243 21204851 - MELO3C016270.2.1 Cme07g01535 1535
7 21213391 21217670 - MELO3C016272.2.1 Cme07g01536 1536
2 5703867 5709822 - CmoCh02G009300.1 Cmo02g00930 930
16 2822610 2826352 - CmoCh16G005850.1 Cmo16g00585 585
7 26415172 26418750 - CmPI595203_07g011300.1 Cmu07g1130 1130
6 4412479 4416978 + Conep06aG0089100.1 Cone6ag0864 864
6 4426797 4430286 + Conep06aG0089400.1 Cone6ag0867 867
9 4229505 4233448 + Conep09aG0089000.1 Cone9ag0869 869
9 4242036 4246268 + Conep09aG0089400.1 Cone9ag0873 873
14 2820937 2825099 - Cp4.1LG14g02660.1 Cpe14g00449 449
7 30378920 30382530 - CrPI670011_07g015100.1 Cre07g1510 1510
4 4565178 4570274 + CsaV3_4G006770.1 Csa04g00677 677
4 4580397 4583976 + CsaV3_4G006790.1 Csa04g00679 679
4 4618875 4625412 + CsaV3_4G006800.1 Csa04g00681 681
4 4625883 4630137 + CsaV3_4G006820.1 Csa04g00682 682
12 35503175 35510832 + Maker00029310 Lcy12g1556 1556
2 1653586 1657804 + Vvi2g162 Vvi2g162 162
2 1662923 1667111 + Vvi2g163 Vvi2g163 163
2 1667928 1673264 + Vvi2g164 Vvi2g164 164
2 1674270 1678031 + Vvi2g165 Vvi2g165 165
2 1682442 1688345 + Vvi2g166 Vvi2g166 166
2 1690752 1698172 - Vvi2g167 Vvi2g167 167
2 1698357 1698741 + Vvi2g168 Vvi2g168 168
2 1699244 1702798 + Vvi2g169 Vvi2g169 169
2 1703995 1704473 - Vvi2g170 Vvi2g170 170
2 1706215 1710474 + Vvi2g171 Vvi2g171 171
       

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