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
Vvi2g152 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0245 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g153 . . . . . . . . . . Cma02g00926 . Car02g00674 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo02g00934 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g154 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag0982 Cone5ag0687 . Cone15ag0013 . . . Cme06g02403 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g155 . . . . . . . . . . Cma02g00925 . Car02g00673 . . . Cpe05g00787 . . . . . . . . . . . . . . . . . . . Csa05g00188 . . . . . . . . . . . Cmo02g00933 . . . . . . . . . . . . . . Cla01g00171 Cam01g0175 Cec01g0173 Cco01g0176 Clacu01g0171 Cmu01g0169 Cre09g2336 Lsi09g00159 . . .
Vvi2g156 . Blo03g00257 Bda06g00156 . . Bpe07g00062 . . . Cmo16g00590 . . . . . Cpe14g00453 . . . . . . . . Cla07g01091 Cam07g1407 Cec07g1254 Cco07g1231 Clacu07g1156 Cmu07g1135 Cre07g1515 . . Cone6ag0862 Cone9ag0864 Lsi07g01122 . . Cme07g01541 . . . . . . . Bma12g00615 . . . . Cma16g00538 . . . . . . . . . . . . . . . . . . . Csa04g00672 Chy07g01138 .
Vvi2g157 Blo02g01158 . . Bda08g00460 Bpe05g00703 . . . . . . . . . . . . . . . . . . . Cla07g01090 Cam07g1408 Cec07g1253 Cco07g1230 Clacu07g1155 Cmu07g1134 Cre07g1514 . . . . . . . Cme07g01540 . . . . . . Bma05g00887 . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00673 Chy07g01137 .
Vvi2g158 . . Bda06g00157 . . Bpe07g00061 . . Cmo06g01034 Cmo16g00589 . . . . . Cpe14g00452 . . . . . . . . Cla07g01089 Cam07g1409 Cec07g1252 Cco07g1229 Clacu07g1154 Cmu07g1133 Cre07g1513 . . . Cone9ag0866 . . . . . . . . . . . Bma12g00616 . . . Cma06g01014 Cma16g00536 Car06g00852 . . . . . . . . . . . . . . . . . . Csa04g00674 Chy07g01136 .
Vvi2g159 . . . . . . . . . . Cma02g00924 . Car02g00672 . . . . . . . . . . . . . . . . . . Cone8ag0238 Cone12ag0601 . . . . . . . . . . . . . . . Cmo02g00931 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g160 . . . . . . Bma07g01687 . . Cmo16g00586 . . . . . Cpe14g00450 . . . . . . . . Cla07g01087 Cam07g1411 Cec07g1250 Cco07g1227 Clacu07g1152 Cmu07g1131 Cre07g1511 . . . . . . . Cme07g01537 . Blo19g00370 . Bda09g00012 Bpe08g01522 . . . . . . . Cma16g00534 . . . . . . . . . . . . . . . . . . . Csa04g00676 Chy07g01134 .
Vvi2g161 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0236 Cone12ag0241 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 2281601 2283477 + Bda023358.2 Bda06g00156 156
6 2284899 2286224 + Bda023359.1 Bda06g00157 157
8 4797101 4798788 - Bda024912.1 Bda08g00460 460
9 275251 276539 + Bda030530.1 Bda09g00012 12
2 43201649 43220993 + BLOR10888 Blo02g01158 1158
3 5449817 5456099 + BLOR11438 Blo03g00257 257
19 23477578 23479083 - BLOR09713 Blo19g00370 370
5 46623783 46624692 + Bma022005.1 Bma05g00887 887
7 52433319 52434620 - Bma026984.1 Bma07g01687 1687
12 27449527 27451398 + Bma030507 Bma12g00615 615
12 27452656 27453919 + Bma007792.1 Bma12g00616 616
5 20615889 20617050 + Bpe018116.1 Bpe05g00703 703
7 487618 488946 - Bpe020873.1 Bpe07g00061 61
7 490288 492161 - Bpe020874.1 Bpe07g00062 62
8 15868846 15870055 - Bpe023634.1 Bpe08g01522 1522
1 2094923 2098102 + CaPI482276_01g001750.1 Cam01g0175 175
7 28588462 28590703 + CaPI482276_07g014070.1 Cam07g1407 1407
7 28592267 28595442 + CaPI482276_07g014080.1 Cam07g1408 1408
7 28597264 28598462 + CaPI482276_07g014090.1 Cam07g1409 1409
7 28609083 28610635 - CaPI482276_07g014110.1 Cam07g1411 1411
2 5020718 5022522 - Carg08551-RA Car02g00672 672
2 5023973 5026065 - Carg08550-RA Car02g00673 673
2 5026800 5041253 - Carg08549-RA Car02g00674 674
6 6676123 6677400 - Carg20898-RA Car06g00852 852
1 1677157 1680367 + CcPI632755_01g001760.1 Cco01g0176 176
7 26182393 26183951 + CcPI632755_07g012270.1 Cco07g1227 1227
7 26195173 26196360 - CcPI632755_07g012290.1 Cco07g1229 1229
7 26198082 26201209 - CcPI632755_07g012300.1 Cco07g1230 1230
7 26202780 26205017 - CcPI632755_07g012310.1 Cco07g1231 1231
1 1672351 1675547 + CePI673135_01g001730.1 Cec01g0173 173
7 28038756 28040313 + CePI673135_07g012500.1 Cec07g1250 1250
7 28051808 28053007 - CePI673135_07g012520.1 Cec07g1252 1252
7 28054792 28057854 - CePI673135_07g012530.1 Cec07g1253 1253
7 28059456 28061702 - CePI673135_07g012540.1 Cec07g1254 1254
7 16293859 16295481 + Chy7G139640.1 Chy07g01134 1134
7 16308863 16309986 - Chy7G139660.1 Chy07g01136 1136
7 16323142 16324306 - Chy7G139670.1 Chy07g01137 1137
7 16325674 16327848 - Chy7G139680.1 Chy07g01138 1138
1 1716271 1719321 + ClG42_01g0017100.10 Clacu01g0171 171
7 26208108 26209657 + ClG42_07g0115200.10 Clacu07g1152 1152
7 26220676 26221872 - ClG42_07g0115400.10 Clacu07g1154 1154
7 26223651 26226757 - ClG42_07g0115500.10 Clacu07g1155 1155
7 26228315 26230551 - ClG42_07g0115600.10 Clacu07g1156 1156
1 1714337 1717465 + ClCG01G001740.1 Cla01g00171 171
7 27592280 27594386 + ClCG07G011450.1 Cla07g01087 1087
7 27604987 27606782 - ClCG07G011480.1 Cla07g01089 1089
7 27609967 27611508 - ClCG07G011490.2 Cla07g01090 1090
7 27612737 27615622 - ClCG07G011500.1 Cla07g01091 1091
2 5495314 5496885 - CmaCh02G009240.1 Cma02g00924 924
2 5497142 5500149 - CmaCh02G009250.1 Cma02g00925 925
2 5500505 5518471 - CmaCh02G009260.1 Cma02g00926 926
6 6854389 6858994 - CmaCh06G010140.1 Cma06g01014 1014
16 2735278 2737648 + CmaCh16G005340.1 Cma16g00534 534
16 2743423 2745863 - CmaCh16G005360.1 Cma16g00536 536
16 2748333 2750955 - CmaCh16G005380.1 Cma16g00538 538
6 31201575 31213186 - MELO3C013786.2.1 Cme06g02403 2403
7 21251993 21255526 + MELO3C016273.2.1 Cme07g01537 1537
7 21273515 21280800 - MELO3C016276.2.1 Cme07g01540 1540
7 21281554 21284759 - MELO3C016277.2.1 Cme07g01541 1541
2 5709856 5716461 - CmoCh02G009310.1 Cmo02g00931 931
2 5718062 5719758 - CmoCh02G009330.1 Cmo02g00933 933
2 5720343 5735590 - CmoCh02G009340.1 Cmo02g00934 934
6 8079916 8083369 - CmoCh06G010340.1 Cmo06g01034 1034
16 2836960 2839063 + CmoCh16G005860.1 Cmo16g00586 586
16 2842571 2845257 - CmoCh16G005890.1 Cmo16g00589 589
16 2846961 2850535 - CmoCh16G005900.1 Cmo16g00590 590
1 1648398 1672539 + CmPI595203_01g001690.1 Cmu01g0169 169
7 26451007 26452556 + CmPI595203_07g011310.1 Cmu07g1131 1131
7 26463568 26464764 - CmPI595203_07g011330.1 Cmu07g1133 1133
7 26466535 26469641 - CmPI595203_07g011340.1 Cmu07g1134 1134
7 26471199 26473435 - CmPI595203_07g011350.1 Cmu07g1135 1135
1 54923415 54925474 - Conep01aG0102700.1 Cone1ag0982 982
5 2947117 2949199 - Conep05aG0071100.1 Cone5ag0687 687
6 4395691 4402125 + Conep06aG0088900.1 Cone6ag0862 862
8 1348429 1354641 - Conep08aG0024500.1 Cone8ag0236 236
8 1359960 1361009 - Conep08aG0024700.1 Cone8ag0238 238
9 4212352 4214243 + Conep09aG0088500.1 Cone9ag0864 864
9 4216267 4217151 + Conep09aG0088700.1 Cone9ag0866 866
12 1297460 1300330 - Conep12aG0024600.1 Cone12ag0241 241
12 1310681 1313376 + Conep12aG0025000.1 Cone12ag0245 245
12 5339269 5340222 - Conep12aG0062200.1 Cone12ag0601 601
15 114500 116378 + Conep15aG0001400.1 Cone15ag0013 13
5 4870501 4891361 + Cp4.1LG05g07850.1 Cpe05g00787 787
14 2838600 2840398 + Cp4.1LG14g02750.1 Cpe14g00450 450
14 2844655 2846615 - Cp4.1LG14g02620.1 Cpe14g00452 452
14 2848287 2851580 - Cp4.1LG14g02700.1 Cpe14g00453 453
7 30413856 30415401 + CrPI670011_07g015110.1 Cre07g1511 1511
7 30426260 30427458 - CrPI670011_07g015130.1 Cre07g1513 1513
7 30429222 30432318 - CrPI670011_07g015140.1 Cre07g1514 1514
7 30433499 30436137 - CrPI670011_07g015150.1 Cre07g1515 1515
9 42639929 42643126 - CrPI670011_09g023360.1 Cre09g2336 2336
4 4515404 4518591 + CsaV3_4G006720.1 Csa04g00672 672
4 4518921 4525750 + CsaV3_4G006730.1 Csa04g00673 673
4 4526957 4529061 + CsaV3_4G006740.1 Csa04g00674 674
4 4541191 4544207 - CsaV3_4G006760.1 Csa04g00676 676
5 1104335 1108422 + CsaV3_5G001880.1 Csa05g00188 188
7 16656788 16668882 - Lsi07G011220.1 Lsi07g01122 1122
9 1638535 1671281 + Lsi09G001590.1 Lsi09g00159 159
2 1579134 1583057 - Vvi2g152 Vvi2g152 152
2 1585585 1594666 + Vvi2g153 Vvi2g153 153
2 1595084 1600755 - Vvi2g154 Vvi2g154 154
2 1605078 1609494 + Vvi2g155 Vvi2g155 155
2 1610313 1615187 + Vvi2g156 Vvi2g156 156
2 1617929 1624103 + Vvi2g157 Vvi2g157 157
2 1624198 1627954 + Vvi2g158 Vvi2g158 158
2 1628584 1630021 + Vvi2g159 Vvi2g159 159
2 1637890 1640114 - Vvi2g160 Vvi2g160 160
2 1643879 1646665 + Vvi2g161 Vvi2g161 161
       

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