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
Vvi3g776 Blo02g00915 . . . . . . Bma12g00305 . . . . . . . . . . . . . . . . Cla10g00958 Cam10g0981 Cec10g1012 . Clacu10g1003 Cmu10g1786 Cre10g1159 . . Cone3ag1049 Cone10ag1065 . . . . . . . . . . . . Sed13g0417 Cmo04g00459 Cmo16g00320 . . . . Cpe14g00250 Cpe01g00385 Bhi11g01098 Tan01g0601 Cmetu07g1160 . Hepe07g0391 Mch10g0405 . . . . . . . . Lsi03g01003 . . Cme07g02214
Vvi3g777 . Blo03g00057 Bda06g01152 . Bpe07g00295 . . Bma12g00306 . . . . . . . . . . . . . . . . Cla10g00957 Cam10g0980 Cec10g1011 Cco10g0974 Clacu10g1002 Cmu10g1784 Cre10g1158 . . Cone3ag1050 Cone10ag1066 . . . . . . . . . . . . Sed07g1150 Cmo04g00458 Cmo16g00319 . . . . Cpe14g00249 Cpe01g00384 Bhi11g01096 Tan01g0600 Cmetu07g2217 . . Mch10g0404 . . . . . . . . Lsi03g01002 . . Cme07g02215
Vvi3g778 . . . Bda08g00692 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1051 Cone10ag1067 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g779 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda15g00471 . . . . Bma08g00020 . . . . . . . . . . . . . . . . . . . . . . . . . . Cme07g02216
Vvi3g780 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g781 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g782 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g783 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g784 . . . . . Bpe12g00730 . . . . . . . . . . . . . . . . . . Cla10g00956 Cam10g0979 Cec10g1010 Cco10g0973 Clacu10g1001 Cmu10g1783 Cre10g1157 . . . . . . . . . . . . . . . . Sed14g1573 Cmo04g00457 . . . . . . Cpe01g00383 Bhi11g01095 Tan01g0599 Cmetu07g0995 . Hepe07g0389 Mch10g0403 . . . . . . . . Lsi03g01001 . . .
Vvi3g785 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 40604394 40609305 - Bda022954.3 Bda06g01152 1152
8 7358513 7358950 - Bda029150.1 Bda08g00692 692
15 7897208 7897771 - Bda012301.1 Bda15g00471 471
11 32317641 32321367 + XM_039048387.1 Bhi11g01095 1095
11 32410264 32419334 - XM_039049207.1 Bhi11g01096 1096
11 32453935 32460616 + XM_039047512.1 Bhi11g01098 1098
2 35340637 35343266 + BLOR10645 Blo02g00915 915
3 2149505 2155092 - BLOR11238 Blo03g00057 57
8 390608 391291 - Bma027012.1 Bma08g00020 20
12 4319675 4321834 - Bma007211.5 Bma12g00305 305
12 4323954 4328889 + Bma007212.1 Bma12g00306 306
7 2128023 2144992 + Bpe021105.3 Bpe07g00295 295
12 12803394 12804077 + Bpe005991.1 Bpe12g00730 730
10 21887853 21889038 - CaPI482276_10g009790.1 Cam10g0979 979
10 21895071 21903686 - CaPI482276_10g009800.1 Cam10g0980 980
10 21928266 21931857 + CaPI482276_10g009810.1 Cam10g0981 981
10 21076500 21077615 - CcPI632755_10g009730.1 Cco10g0973 973
10 21083784 21092138 - CcPI632755_10g009740.1 Cco10g0974 974
10 22767397 22768505 - CePI673135_10g010100.1 Cec10g1010 1010
10 22774451 22782780 - CePI673135_10g010110.1 Cec10g1011 1011
10 22803767 22807419 + CePI673135_10g010120.1 Cec10g1012 1012
10 21543036 21544219 - ClG42_10g0100100.10 Clacu10g1001 1001
10 21550010 21558553 - ClG42_10g0100200.10 Clacu10g1002 1002
10 21585138 21588694 + ClG42_10g0100300.10 Clacu10g1003 1003
10 22531738 22532921 - ClCG10G009960.1 Cla10g00956 956
10 22538322 22554344 - ClCG10G009970.1 Cla10g00957 957
10 22581580 22585315 + ClCG10G009980.1 Cla10g00958 958
7 26349349 26353108 - MELO3C018028.2.1 Cme07g02214 2214
7 26355376 26364572 + MELO3C018029.2.1 Cme07g02215 2215
7 26366715 26367831 + MELO3C018030.2.1 Cme07g02216 2216
7 226587 227518 - PI0025718.1 Cmetu07g0995 995
7 242436 246030 + PI0005620.2 Cmetu07g1160 1160
7 230539 240108 - PI0024458.1 Cmetu07g2217 2217
4 2268965 2269712 - CmoCh04G004570.1 Cmo04g00457 457
4 2271230 2278979 - CmoCh04G004580.1 Cmo04g00458 458
4 2280384 2285622 + CmoCh04G004590.1 Cmo04g00459 459
16 1458000 1462345 - CmoCh16G003190.1 Cmo16g00319 319
16 1463782 1468783 + CmoCh16G003200.1 Cmo16g00320 320
10 22151009 22152191 - CmPI595203_10g017830.1 Cmu10g1783 1783
10 22157938 22166639 - CmPI595203_10g017840.1 Cmu10g1784 1784
10 22195380 22198936 + CmPI595203_10g017860.1 Cmu10g1786 1786
3 29249088 29251741 - Conep03aG0155000.1 Cone3ag1049 1049
3 29252977 29257885 + Conep03aG0155100.1 Cone3ag1050 1050
3 29259270 29259929 + Conep03aG0155200.1 Cone3ag1051 1051
10 7401892 7404686 - Conep10aG0109200.1 Cone10ag1065 1065
10 7407498 7412249 + Conep10aG0109300.1 Cone10ag1066 1066
10 7414742 7415536 + Conep10aG0109400.1 Cone10ag1067 1067
1 2209097 2209833 - Cp4.1LG01g02710.1 Cpe01g00383 383
1 2211397 2219216 - Cp4.1LG01g02740.1 Cpe01g00384 384
1 2220566 2224912 + Cp4.1LG01g02790.1 Cpe01g00385 385
14 1441289 1448852 - Cp4.1LG14g04700.1 Cpe14g00249 249
14 1449787 1453963 + Cp4.1LG14g04750.1 Cpe14g00250 250
10 23827779 23829094 - CrPI670011_10g011570.1 Cre10g1157 1157
10 23840880 23849009 - CrPI670011_10g011580.1 Cre10g1158 1158
10 23861527 23865110 + CrPI670011_10g011590.1 Cre10g1159 1159
7 3973210 3974186 - Hsped.07g03890.1 Hepe07g0389 389
7 3987109 3991134 + Hsped.07g03910.1 Hepe07g0391 391
3 19289582 19291400 - Lsi03G010010.1 Lsi03g01001 1001
3 19294076 19303847 - Lsi03G010020.1 Lsi03g01002 1002
3 19310453 19314457 + Lsi03G010030.1 Lsi03g01003 1003
10 2662183 2663013 - MC10g0330 Mch10g0403 403
10 2664991 2672356 - MC10g0331 Mch10g0404 404
10 2674436 2678383 + MC10g0332 Mch10g0405 405
7 8618891 8629684 + Sed0011100.1 Sed07g1150 1150
13 2739428 2743916 + Sed0020853.1 Sed13g0417 417
14 23831013 23831714 + Sed0027724.1 Sed14g1573 1573
1 5490800 5491907 - Tan0020373.1 Tan01g0599 599
1 5495119 5504570 - Tan0005974.1 Tan01g0600 600
1 5510468 5514396 + Tan0018804.1 Tan01g0601 601
3 8657004 8658460 - Vvi3g776 Vvi3g776 776
3 8660791 8679474 + Vvi3g777 Vvi3g777 777
3 8696025 8697570 + Vvi3g778 Vvi3g778 778
3 8744236 8744878 + Vvi3g779 Vvi3g779 779
3 8765038 8765911 - Vvi3g780 Vvi3g780 780
3 8765957 8766906 - Vvi3g781 Vvi3g781 781
3 8766966 8773391 - Vvi3g782 Vvi3g782 782
3 8776001 8776646 + Vvi3g783 Vvi3g783 783
3 8793245 8793890 + Vvi3g784 Vvi3g784 784
3 8820034 8820694 + Vvi3g785 Vvi3g785 785
       

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