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
Vvi4g1322 . Blo16g00554 . . . Bpe13g00054 . Bma15g00776 Cmo02g00650 Cmo20g01056 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo06g00187 . . Bpe10g00266 Bpe06g00305 . Bma06g00472 . . . . Cma20g01050 . . Cpe05g01044 Cpe16g00096 Bhi10g01716 . . . . . . Cla02g00030 . . . . . . Lsi10g00758 . . Cme11g00032
Vvi4g1323 . . . Bda10g00407 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1324 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1325 . . . . . . . Bma15g00775 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo06g00186 . . Bpe10g00267 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1326 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe06g00334 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1327 . Blo16g00578 . . . Bpe13g00067 . . Cmo02g00674 . Cma03g01108 Cma07g00810 Car03g01001 Car07g00797 . Cpe19g00513 Cpe10g00324 . . . . . . . Cla01g01491 Cam01g1559 Cec04g1206 Cco04g1273 Clacu01g1585 Cmu01g1474 Cre04g1155 . . Cone6ag1265 . Lsi01g01169 . . Cme08g01137 . . . . . . . . . Cmo03g01098 Cmo07g00840 . . . . . . . . . . . . . . . . . . . . . Csa06g02741 Chy02g01094 .
Vvi4g1328 . . Bda04g00382 . . . Bma09g00431 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo05g00533 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1329 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1330 . . . . . . . . . . Cma03g01109 Cma07g00811 Car03g01002 Car07g00798 . Cpe19g00512 Cpe10g00323 . . . . . . . Cla01g01490 Cam01g1558 Cec04g1205 Cco04g1272 Clacu01g1584 Cmu01g1473 Cre04g1154 . . Cone6ag1263 . Lsi01g01170 . . Cme08g01138 . . . . . . . . . Cmo03g01099 Cmo07g00841 . . . . . . . . . . . . . . . . . . . . . Csa06g02740 Chy02g01095 .
Vvi4g1331 . . . . . Bpe13g00070 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma06g00432 . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 50727878 50747174 - Bda019326.3 Bda04g00382 382
10 36221701 36239296 - Bda007238.1 Bda10g00407 407
10 43132001 43135806 - XM_039046266.1 Bhi10g01716 1716
5 10102751 10118878 + BLOR15495 Blo05g00533 533
6 7838650 7854410 + BLOR16769 Blo06g00186 186
6 7864244 7872502 + BLOR16770 Blo06g00187 187
16 22812215 22815736 - BLOR07802 Blo16g00554 554
16 23743561 23748090 - BLOR07826 Blo16g00578 578
6 16326767 16331152 + Bma023207.1 Bma06g00432 432
6 22032634 22036166 + Bma023300.1 Bma06g00472 472
9 37672864 37694553 - Bma029426.1 Bma09g00431 431
15 16419280 16445790 + Bma013850.1 Bma15g00775 775
15 16448120 16451090 + Bma013851.2 Bma15g00776 776
6 14360402 14363804 - Bpe019804.1 Bpe06g00305 305
6 14737733 14739764 + Bpe019832.1 Bpe06g00334 334
10 9956217 9959202 - Bpe002603.1 Bpe10g00266 266
10 9961430 9984163 - Bpe024651 Bpe10g00267 267
13 1593019 1596508 - Bpe006140.1 Bpe13g00054 54
13 2462003 2485669 - Bpe006157.2 Bpe13g00067 67
13 2972243 2976576 - Bpe006162.1 Bpe13g00070 70
1 29129189 29132088 + CaPI482276_01g015580.1 Cam01g1558 1558
1 29133776 29138886 - CaPI482276_01g015590.1 Cam01g1559 1559
3 8352128 8356673 + Carg10524-RA Car03g01001 1001
3 8357065 8358431 - Carg10523-RA Car03g01002 1002
7 4212231 4217646 + Carg05321-RA Car07g00797 797
7 4219307 4221472 - Carg05322-RA Car07g00798 798
4 28069501 28072415 + CcPI632755_04g012720.1 Cco04g1272 1272
4 28074155 28079255 - CcPI632755_04g012730.1 Cco04g1273 1273
4 31611910 31614784 + CePI673135_04g012050.1 Cec04g1205 1205
4 31615727 31624676 - CePI673135_04g012060.1 Cec04g1206 1206
2 7703778 7708785 + Chy2G033610.1 Chy02g01094 1094
2 7709058 7712720 - Chy2G033620.1 Chy02g01095 1095
1 27921319 27924214 + ClG42_01g0158400.10 Clacu01g1584 1584
1 27925898 27931001 - ClG42_01g0158500.10 Clacu01g1585 1585
1 29433278 29436173 + ClCG01G015150.1 Cla01g01490 1490
1 29437857 29442958 - ClCG01G015160.2 Cla01g01491 1491
2 381979 385245 + ClCG02G000290.1 Cla02g00030 30
3 7568403 7574432 + CmaCh03G011080.1 Cma03g01108 1108
3 7574527 7576330 - CmaCh03G011090.1 Cma03g01109 1109
7 3728149 3734089 + CmaCh07G008100.1 Cma07g00810 810
7 3735328 3737605 - CmaCh07G008110.1 Cma07g00811 811
20 7838863 7843433 + CmaCh20G010500.1 Cma20g01050 1050
8 8000441 8006804 + MELO3C024602.2.1 Cme08g01137 1137
8 8007667 8009103 - MELO3C033125.2.1 Cme08g01138 1138
11 332278 336098 + MELO3C023218.2.1 Cme11g00032 32
2 4047118 4050650 - CmoCh02G006500.1 Cmo02g00650 650
2 4239599 4246493 - CmoCh02G006740.1 Cmo02g00674 674
3 8891453 8896026 + CmoCh03G010980.1 Cmo03g01098 1098
3 8896065 8897788 - CmoCh03G010990.1 Cmo03g01099 1099
7 3945767 3951729 + CmoCh07G008400.1 Cmo07g00840 840
7 3953016 3955268 - CmoCh07G008410.1 Cmo07g00841 841
20 9746735 9750498 + CmoCh20G010560.1 Cmo20g01056 1056
1 28265133 28268030 + CmPI595203_01g014730.1 Cmu01g1473 1473
1 28269717 28278778 - CmPI595203_01g014740.1 Cmu01g1474 1474
6 10097720 10100625 - Conep06aG0131100.1 Cone6ag1263 1263
6 10107541 10111102 + Conep06aG0131300.1 Cone6ag1265 1265
5 6907209 6910880 + Cp4.1LG05g10440.1 Cpe05g01044 1044
10 1879334 1882763 + Cp4.1LG10g03620.1 Cpe10g00323 323
10 1881249 1889050 - Cp4.1LG10g03560.1 Cpe10g00324 324
16 1789855 1793745 - Cp4.1LG16g00980.1 Cpe16g00096 96
19 4367343 4369830 + Cp4.1LG19g04700.1 Cpe19g00512 512
19 4371711 4379383 - Cp4.1LG19g04610.1 Cpe19g00513 513
4 30143017 30145815 + CrPI670011_04g011540.1 Cre04g1154 1154
4 30147464 30152563 - CrPI670011_04g011550.1 Cre04g1155 1155
6 23947208 23951102 + CsaV3_6G041260.1 Csa06g02740 2740
6 23950544 23956921 - CsaV3_6G041270.1 Csa06g02741 2741
1 9918987 9923926 + Lsi01G011690.1 Lsi01g01169 1169
1 9923566 9928564 - Lsi01G011700.1 Lsi01g01170 1170
10 10394485 10397591 - Lsi10G007580.1 Lsi10g00758 758
4 23153006 23156975 - Vvi4g1322 Vvi4g1322 1322
4 23170211 23225736 - Vvi4g1323 Vvi4g1323 1323
4 23227159 23228312 + Vvi4g1324 Vvi4g1324 1324
4 23237230 23252027 - Vvi4g1325 Vvi4g1325 1325
4 23260405 23277500 + Vvi4g1326 Vvi4g1326 1326
4 23278012 23287916 + Vvi4g1327 Vvi4g1327 1327
4 23288718 23356942 - Vvi4g1328 Vvi4g1328 1328
4 23373475 23378726 + Vvi4g1329 Vvi4g1329 1329
4 23382367 23384135 - Vvi4g1330 Vvi4g1330 1330
4 23401808 23409813 - Vvi4g1331 Vvi4g1331 1331
       

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