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
Vvi18g1750 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1751 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1752 . . . . . . . . . . Cma01g00880 . Car01g00804 . . Cpe06g00948 . . . . . . . . Cla08g00174 . Cec08g0077 Cco08g0239 . Cmu08g0166 Cre08g0157 . . . . . . . Cme09g00120 . . . . . . . . Sed01g3808 Cmo01g00922 Cmo09g01208 . . . Car09g01077 . Cpe02g00984 Bhi06g00114 Tan10g1839 Cmetu09g1280 . . . . . . . . . . . Lsi08g00177 . . .
Vvi18g1753 . . . . . . . . . . . . . . Sed03g0691 . . Bhi04g02540 Tan11g0053 Cmetu03g1265 . Hepe02g3461 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla11g00791 Cam11g0824 Cec11g0806 Cco11g0812 Clacu11g1033 Cmu11g0894 Cre11g1268 . . . .
Vvi18g1754 . . . Bda03g00363 . Bpe04g00325 Bma04g00341 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1755 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1756 . . . Bda03g00364 . Bpe04g00326 . . . . Cma01g00881 . Car01g00805 . . . . . . . . . . . Cla08g00178 . Cec08g0075 . . Cmu08g0168 Cre08g0158 . . . . . . . Cme09g00121 . . . . . . . . Sed08g1728 Cmo01g00923 . . . . . . Cpe02g00983 Bhi06g00113 Tan10g1838 Cmetu09g1050 . . . . . . . . . . . Lsi08g00178 . . .
Vvi18g1757 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1758 Blo01g01688 Blo12g00810 . . Bpe02g00254 Bpe04g00327 . Bma01g02455 . . . . . . . Cpe06g00946 . . . . . . . . Cla08g00181 . Cec08g0069 Cco08g0251 . Cmu08g0171 Cre08g0160 . . . . . . . . . . Bda11g00916 . . . . . Sed08g1872 . Cmo09g01205 . . . Car09g01075 . Cpe02g00981 Bhi06g00110 Tan10g1835 Cmetu11g0599 . . . . . . . . . . . . . . .
Vvi18g1759 Blo01g01689 . . . Bpe02g00253 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 3049964 3053830 - Bda016326.2 Bda03g00363 363
3 3055279 3072893 - Bda016327.1 Bda03g00364 364
11 8965331 8975726 + Bda005671.1 Bda11g00916 916
4 68303598 68305631 - XM_039030646.1 Bhi04g02540 2540
6 2983062 2988841 - XM_039034111.1 Bhi06g00110 110
6 3140253 3151305 + XM_039035136.1 Bhi06g00113 113
6 3158732 3161562 - XM_039033647.1 Bhi06g00114 114
1 56599331 56602074 - BLOR01688 Blo01g01688 1688
1 56603469 56605278 + BLOR01689 Blo01g01689 1689
12 26465242 26486238 + BLOR04829 Blo12g00810 810
1 82148250 82150790 - Bma003325.1 Bma01g02455 2455
4 2765923 2783986 - Bma018800.1 Bma04g00341 341
2 1719713 1720795 - Bpe008098.1 Bpe02g00253 253
2 1722068 1724736 + Bpe008099.1 Bpe02g00254 254
4 2063974 2068036 - Bpe025607 Bpe04g00325 325
4 2069687 2073003 - Bpe015022.1 Bpe04g00326 326
4 2080012 2081207 - Bpe025608 Bpe04g00327 327
11 10494293 10495527 - CaPI482276_11g008240.1 Cam11g0824 824
1 5301655 5303061 + Carg23027-RA Car01g00804 804
1 5303055 5321382 - Carg23028-RA Car01g00805 805
9 9914150 9919389 - Carg27049-RA Car09g01075 1075
9 9999877 10001998 - Carg27051-RA Car09g01077 1077
8 4158530 4160052 + CcPI632755_08g002390.1 Cco08g0239 239
8 4456243 4459258 + CcPI632755_08g002510.1 Cco08g0251 251
11 9311955 9312785 - CcPI632755_11g008120.1 Cco11g0812 812
8 1047930 1051019 - CePI673135_08g000690.1 Cec08g0069 69
8 1255681 1269909 + CePI673135_08g000750.1 Cec08g0075 75
8 1305877 1307375 - CePI673135_08g000770.1 Cec08g0077 77
11 9566741 9567571 - CePI673135_11g008060.1 Cec11g0806 806
11 12797269 12798503 + ClG42_11g0103300.10 Clacu11g1033 1033
8 3527262 3530525 + ClCG08G001740.1 Cla08g00174 174
8 3559896 3568078 - ClCG08G001780.1 Cla08g00178 178
8 3725374 3730084 + ClCG08G001810.1 Cla08g00181 181
11 11397983 11398813 - ClCG11G008270.1 Cla11g00791 791
1 4977130 4979070 + CmaCh01G008800.1 Cma01g00880 880
1 4979449 4994924 - CmaCh01G008810.1 Cma01g00881 881
9 891745 894237 + MELO3C022123.2.1 Cme09g00120 120
9 897751 908053 - MELO3C022122.2.1 Cme09g00121 121
3 26039200 26042008 - PI0028467.1 Cmetu03g1265 1265
9 20917206 20924649 + PI0015305.1 Cmetu09g1050 1050
9 20928593 20931440 - PI0026468.1 Cmetu09g1280 1280
11 921183 922778 + PI0021306.1 Cmetu11g0599 599
1 5226050 5227970 + CmoCh01G009220.1 Cmo01g00922 922
1 5228431 5246377 - CmoCh01G009230.1 Cmo01g00923 923
9 9125440 9132653 - CmoCh09G012050.1 Cmo09g01205 1205
9 9214988 9218174 - CmoCh09G012080.1 Cmo09g01208 1208
8 3485959 3487480 + CmPI595203_08g001660.1 Cmu08g0166 166
8 3516166 3524064 - CmPI595203_08g001680.1 Cmu08g0168 168
8 3674102 3677110 + CmPI595203_08g001710.1 Cmu08g0171 171
11 12126327 12127561 + CmPI595203_11g008940.1 Cmu11g0894 894
2 8815657 8819106 - Cp4.1LG02g09740.1 Cpe02g00981 981
2 8879837 8896259 + Cp4.1LG02g11070.1 Cpe02g00983 983
2 8896313 8898493 - Cp4.1LG02g11010.1 Cpe02g00984 984
6 7882618 7886377 - Cp4.1LG06g09720.1 Cpe06g00946 946
6 8004463 8007597 - Cp4.1LG06g09700.1 Cpe06g00948 948
8 3446545 3448057 + CrPI670011_08g001570.1 Cre08g0157 157
8 3467282 3480161 - CrPI670011_08g001580.1 Cre08g0158 158
8 3651406 3654426 + CrPI670011_08g001600.1 Cre08g0160 160
11 11201102 11201932 - CrPI670011_11g012680.1 Cre11g1268 1268
2 83933558 83934388 - Hsped.02g34610.1 Hepe02g3461 3461
8 3626634 3629415 + Lsi08G001770.1 Lsi08g00177 177
8 3653988 3665131 - Lsi08G001780.1 Lsi08g00178 178
1 67235679 67238167 - Sed0026122.1 Sed01g3808 3808
3 4141422 4143534 - Sed0027115.1 Sed03g0691 691
8 32240759 32246022 + Sed0010977.1 Sed08g1728 1728
8 33260278 33268491 - Sed0009990.1 Sed08g1872 1872
10 57569895 57575870 + Tan0021738.2 Tan10g1835 1835
10 58033529 58049994 + Tan0009417.1 Tan10g1838 1838
10 58061493 58063844 - Tan0006097.1 Tan10g1839 1839
11 792453 794442 + Tan0007934.1 Tan11g0053 53
18 28627960 28629416 - Vvi18g1750 Vvi18g1750 1750
18 28630140 28630427 - Vvi18g1751 Vvi18g1751 1751
18 28686084 28689667 + Vvi18g1752 Vvi18g1752 1752
18 28693227 28694490 + Vvi18g1753 Vvi18g1753 1753
18 28703322 28733078 - Vvi18g1754 Vvi18g1754 1754
18 28739675 28739861 - Vvi18g1755 Vvi18g1755 1755
18 28739955 28746106 - Vvi18g1756 Vvi18g1756 1756
18 28749591 28756756 - Vvi18g1757 Vvi18g1757 1757
18 28763885 28768659 - Vvi18g1758 Vvi18g1758 1758
18 28781439 28786756 - Vvi18g1759 Vvi18g1759 1759
       

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