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
Vvi4g1152 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma03g00940 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1153 . . . . Bpe15g00482 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1695 Cone9ag1619 . . . . . . . Bda14g01069 . . . . . . . Cma16g01246 . . . . . . . . . . . . . . . . . . . Lsi07g01091 . . .
Vvi4g1154 . . . . . . . . . Cmo20g01136 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed01g0197 . . . Cma20g01106 . . Cpe05g01103 . Bhi10g01854 Tan05g1142 Cmetu11g0032 . Hepe08g0290 . . . . . . . . . . . . .
Vvi4g1155 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma06g00533 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1156 Blo04g00979 Blo16g00089 . . Bpe15g00483 Bpe13g00407 . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0862 Cone12ag0826 . . . . . . . . Bda11g01828 . . . . Bma06g00090 Sed01g0196 . . . . . . . . Bhi10g01852 Tan05g1137 Cmetu11g1470 . Hepe08g0292 . . . . . . . . . Lsi07g01090 . . .
Vvi4g1157 . Blo16g00090 . . Bpe15g00484 Bpe13g00406 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0827 . . . . . . . . Bda11g01827 . . . Bma03g01040 Bma06g00089 . . . Cma16g01247 . . . . . . . . . . . . . . . . . . . Lsi07g01089 . . .
Vvi4g1158 . Blo16g00091 . . . Bpe13g00405 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1696 Cone9ag1620 . . . . . . Bda11g01826 . . . . Bma06g00088 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1159 . . . . . . . . . . . Cma07g00412 . Car07g00362 . Cpe19g00872 . . . . . . . . Cla01g01995 Cam01g2093 Cec04g1751 Cco04g1816 Clacu01g2111 Cmu01g1988 Cre04g1664 . . . . Lsi01g00581 . . Cme08g00951 . . . . . . . . . . Cmo07g00407 . . . . . . . . . . . . . . . . . . . . . Csa06g03349 Chy02g00552 .
Vvi4g1160 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1161 . Blo16g00092 . . . . . . . . . . . . Sed14g1206 . . Bhi03g00834 Tan03g2103 Cmetu11g1017 . Hepe04g1611 . . . . . . . . . . Cone12ag0829 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 53501994 53504075 + Bda008762.1 Bda11g01826 1826
11 53505304 53520759 + Bda008763.1 Bda11g01827 1827
11 53522876 53525072 - Bda008764.1 Bda11g01828 1828
14 9265435 9267626 + Bda027886.1 Bda14g01069 1069
3 15336645 15337819 + XM_039027559.1 Bhi03g00834 834
10 46040956 46044117 - XM_039046218.1 Bhi10g01852 1852
10 46073809 46087884 - XM_039045391.1 Bhi10g01854 1854
4 12394390 12395958 - BLOR13891 Blo04g00979 979
16 2258854 2261101 + BLOR07337 Blo16g00089 89
16 2262959 2274019 - BLOR07338 Blo16g00090 90
16 2275139 2277213 - BLOR07339 Blo16g00091 91
16 2281027 2281368 - BLOR07340 Blo16g00092 92
3 9921252 9922517 + Bma017274.1 Bma03g00940 940
3 12145522 12150823 + Bma017399.1 Bma03g01040 1040
6 1366674 1368738 + Bma022706.1 Bma06g00088 88
6 1369582 1378753 + Bma022707.1 Bma06g00089 89
6 1380648 1382873 - Bma022708.1 Bma06g00090 90
6 27321590 27326681 + Bma023414.1 Bma06g00533 533
13 11764961 11767052 + Bpe006529.1 Bpe13g00405 405
13 11768105 11777190 + Bpe006530.1 Bpe13g00406 406
13 11779128 11781273 - Bpe006531.1 Bpe13g00407 407
15 16128280 16131131 + Bpe001416.1 Bpe15g00482 482
15 16133342 16135172 + Bpe001417.2 Bpe15g00483 483
15 16137086 16144939 - Bpe001418.1 Bpe15g00484 484
1 33940782 33948641 - CaPI482276_01g020930.1 Cam01g2093 2093
7 1818463 1819029 + Carg07942-RA Car07g00362 362
4 33024160 33025675 - CcPI632755_04g018160.1 Cco04g1816 1816
4 36509469 36510803 - CePI673135_04g017510.1 Cec04g1751 1751
2 3322075 3322632 + Chy2G028190.1 Chy02g00552 552
1 32799279 32800739 - ClG42_01g0211100.10 Clacu01g2111 2111
1 34595443 34596902 - ClCG01G020470.1 Cla01g01995 1995
7 1785172 1785971 + CmaCh07G004120.1 Cma07g00412 412
16 9414446 9424673 + CmaCh16G012460.1 Cma16g01246 1246
16 9424372 9436768 - CmaCh16G012470.1 Cma16g01247 1247
20 8683216 8687446 - CmaCh20G011060.1 Cma20g01106 1106
8 6244937 6246158 - MELO3C007926.2.1 Cme08g00951 951
11 28581892 28591686 + PI0010703.1 Cmetu11g0032 32
11 4519049 4519649 + PI0017501.1 Cmetu11g1017 1017
11 28602934 28606288 + PI0028275.1 Cmetu11g1470 1470
7 1870509 1871295 + CmoCh07G004070.1 Cmo07g00407 407
20 11049738 11053244 - CmoCh20G011360.1 Cmo20g01136 1136
1 33136844 33138304 - CmPI595203_01g019880.1 Cmu01g1988 1988
6 12809812 12813268 + Conep06aG0176000.1 Cone6ag1695 1695
6 12813466 12816272 - Conep06aG0176100.1 Cone6ag1696 1696
8 8523859 8526758 + Conep08aG0088800.1 Cone8ag0862 862
9 11547438 11551323 + Conep09aG0166900.1 Cone9ag1619 1619
9 11555427 11558472 - Conep09aG0167000.1 Cone9ag1620 1620
12 7498383 7500565 + Conep12aG0085100.1 Cone12ag0826 826
12 7501315 7508889 - Conep12aG0085200.1 Cone12ag0827 827
12 7514253 7514618 - Conep12aG0085400.1 Cone12ag0829 829
5 7395915 7400813 + Cp4.1LG05g11030.1 Cpe05g01103 1103
19 6409036 6409773 - Cp4.1LG19g08630.1 Cpe19g00872 872
4 34980254 34988559 - CrPI670011_04g016640.1 Cre04g1664 1664
6 27941854 27942670 - CsaV3_6G047350.1 Csa06g03349 3349
4 71554610 71556272 - Hsped.04g16110.1 Hepe04g1611 1611
8 2627081 2642972 + Hsped.08g02900.1 Hepe08g0290 290
8 2652502 2654721 + Hsped.08g02920.1 Hepe08g0292 292
1 4637937 4639490 + Lsi01G005810.1 Lsi01g00581 581
7 16281650 16293330 + Lsi07G010890.1 Lsi07g01089 1089
7 16297269 16301667 - Lsi07G010900.1 Lsi07g01090 1090
7 16304282 16307805 - Lsi07G010910.1 Lsi07g01091 1091
1 1510907 1514806 - Sed0011175.2 Sed01g0196 196
1 1519695 1532563 - Sed0004775.1 Sed01g0197 197
14 21312227 21314050 - Sed0025208.1 Sed14g1206 1206
3 75893251 75894952 - Tan0018260.1 Tan03g2103 2103
5 10171347 10174878 - Tan0012242.1 Tan05g1137 1137
5 10187885 10205395 - Tan0010641.1 Tan05g1142 1142
4 20315431 20318762 + Vvi4g1152 Vvi4g1152 1152
4 20321484 20326332 + Vvi4g1153 Vvi4g1153 1153
4 20327037 20339205 + Vvi4g1154 Vvi4g1154 1154
4 20339632 20342566 - Vvi4g1155 Vvi4g1155 1155
4 20350178 20354875 + Vvi4g1156 Vvi4g1156 1156
4 20357828 20371146 - Vvi4g1157 Vvi4g1157 1157
4 20372150 20375416 - Vvi4g1158 Vvi4g1158 1158
4 20382439 20383630 - Vvi4g1159 Vvi4g1159 1159
4 20384128 20390368 + Vvi4g1160 Vvi4g1160 1160
4 20391433 20391823 - Vvi4g1161 Vvi4g1161 1161
       

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