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
Vvi19g1174 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1175 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1176 . Blo13g00609 . . . . Bma08g00828 . . . . . . . . . Cpe16g00702 . . . . . . . Cla02g01835 . . . . . . . . . . . . . Cme11g01646 . . . . . . . . . . . . . . . . Cpe05g01027 Bhi10g00926 . . . . . . . . . . . . . . Csa06g01144 . .
Vvi19g1177 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1178 . . . . Bpe07g00479 . . . . . . . . . . . . . . . . . . . Cla02g01838 Cam02g1945 Cec02g1972 Cco02g2011 Clacu02g1925 Cmu02g1874 Cre02g2187 . . . . . . . Cme11g01653 Blo15g00647 . . . . . . Bma12g00563 Sed05g3318 . . . . . . . Cpe05g01025 Bhi10g00923 Tan05g0574 Cmetu11g0931 . Hepe08g0657 . . . . . . . . . . Csa06g01142 Chy11g01050 .
Vvi19g1179 . . . . Bpe07g00480 . . . . . . . . . . . . . . . . . . . Cla02g01840 Cam02g1946 Cec02g1973 Cco02g2012 . . Cre02g2188 . . . . . . . Cme11g01654 . . . . . . . . Sed05g3319 . . . . . . . Cpe05g01024 Bhi10g00922 Tan05g0573 Cmetu11g1928 . Hepe08g0658 . . . . . . . . . . Csa06g01141 Chy11g01051 .
Vvi19g1180 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1181 . . . . Bpe07g00481 . . . . . . . . . . . . . . . . . . . Cla02g01841 Cam02g1947 Cec02g1974 Cco02g2013 Clacu02g1928 Cmu02g1877 Cre02g2189 . . . . . . . Cme11g01655 . . . . . . . Bma12g00561 . . . . . . . . Cpe05g01023 Bhi10g00921 . . . . . . . . . . . . . . Csa06g01139 Chy11g01053 .
Vvi19g1182 Blo04g00453 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe15g00927 . Bma03g00487 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1183 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
10 18907019 18932882 - XM_039045141.1 Bhi10g00921 921
10 18942708 18953086 + XM_039045413.1 Bhi10g00922 922
10 18953482 18954799 - XM_039045414.1 Bhi10g00923 923
10 19045281 19050380 + XM_039046601.1 Bhi10g00926 926
4 3778021 3779637 + BLOR13365 Blo04g00453 453
13 28516477 28518043 - BLOR19661 Blo13g00609 609
15 17755180 17756543 + BLOR07041 Blo15g00647 647
3 3824590 3826211 + Bma030974 Bma03g00487 487
8 46122609 46125179 - Bma028224.1 Bma08g00828 828
12 23995634 24037829 - Bma007706.1 Bma12g00561 561
12 24369234 24372243 + Bma007713.1 Bma12g00563 563
7 8358529 8359941 + Bpe021317.1 Bpe07g00479 479
7 8445802 8453338 - Bpe021318.1 Bpe07g00480 480
7 8640676 8692021 + Bpe021319.2 Bpe07g00481 481
15 19033013 19034622 - Bpe001848.1 Bpe15g00927 927
2 32560179 32561323 + CaPI482276_02g019450.1 Cam02g1945 1945
2 32562279 32570660 - CaPI482276_02g019460.1 Cam02g1946 1946
2 32586614 32605716 + CaPI482276_02g019470.1 Cam02g1947 1947
2 33070919 33072064 + CcPI632755_02g020110.1 Cco02g2011 2011
2 33072731 33080552 - CcPI632755_02g020120.1 Cco02g2012 2012
2 33084925 33117406 + CcPI632755_02g020130.1 Cco02g2013 2013
2 37571981 37573127 + CePI673135_02g019720.1 Cec02g1972 1972
2 37573750 37582475 - CePI673135_02g019730.1 Cec02g1973 1973
2 37584048 37617410 + CePI673135_02g019740.1 Cec02g1974 1974
11 14997669 14998889 + Chy11G196300.1 Chy11g01050 1050
11 14999918 15006051 - Chy11G196310.1 Chy11g01051 1051
11 15014726 15041995 + Chy11G196330.1 Chy11g01053 1053
2 32815065 32816210 + ClG42_02g0192500.10 Clacu02g1925 1925
2 32825758 32857922 + ClG42_02g0192800.10 Clacu02g1928 1928
2 33491641 33496029 - ClCG02G018760.2 Cla02g01835 1835
2 33524596 33527699 + ClCG02G018790.2 Cla02g01838 1838
2 33526793 33527668 - ClCG02G018805.1 Cla02g01840 1840
2 33535376 33570405 + ClCG02G018810.2 Cla02g01841 1841
11 24327479 24328174 - MELO3C019620.2.1 Cme11g01646 1646
11 24372089 24375632 + MELO3C019617.2.1 Cme11g01653 1653
11 24374234 24383529 - MELO3C019616.2.1 Cme11g01654 1654
11 24394751 24426957 + MELO3C019615.2.1 Cme11g01655 1655
11 8446557 8448769 - PI0026651.1 Cmetu11g0931 931
11 8436583 8446551 + PI0027769.1 Cmetu11g1928 1928
2 32677304 32678449 + CmPI595203_02g018740.1 Cmu02g1874 1874
2 32688064 32720314 + CmPI595203_02g018770.1 Cmu02g1877 1877
5 6673778 6708971 - Cp4.1LG05g10330.1 Cpe05g01023 1023
5 6709489 6715944 + Cp4.1LG05g10260.1 Cpe05g01024 1024
5 6714777 6717272 - Cp4.1LG05g10280.1 Cpe05g01025 1025
5 6733243 6735820 + Cp4.1LG05g10240.1 Cpe05g01027 1027
16 7220040 7222462 + Cp4.1LG16g07040.1 Cpe16g00702 702
2 35525922 35527067 + CrPI670011_02g021870.1 Cre02g2187 2187
2 35527708 35531981 - CrPI670011_02g021880.1 Cre02g2188 2188
2 35552393 35571639 + CrPI670011_02g021890.1 Cre02g2189 2189
6 9464269 9492387 - CsaV3_6G013370.1 Csa06g01139 1139
6 9497206 9506310 + CsaV3_6G013390.1 Csa06g01141 1141
6 9504780 9507654 - CsaV3_6G013400.1 Csa06g01142 1142
6 9536058 9540856 + CsaV3_6G013420.1 Csa06g01144 1144
8 5867474 5868568 + Hsped.08g06570.1 Hepe08g0657 657
8 5869266 5879953 - Hsped.08g06580.1 Hepe08g0658 658
5 42522762 42525099 + Sed0024280.1 Sed05g3318 3318
5 42525306 42535651 - Sed0018347.1 Sed05g3319 3319
5 4143281 4149648 + Tan0001806.1 Tan05g0573 573
5 4150399 4151600 - Tan0009541.1 Tan05g0574 574
19 23447077 23447990 + Vvi19g1174 Vvi19g1174 1174
19 23462616 23464298 + Vvi19g1175 Vvi19g1175 1175
19 23474520 23476369 - Vvi19g1176 Vvi19g1176 1176
19 23490154 23490538 - Vvi19g1177 Vvi19g1177 1177
19 23495532 23508846 + Vvi19g1178 Vvi19g1178 1178
19 23508848 23538511 - Vvi19g1179 Vvi19g1179 1179
19 23540098 23540654 - Vvi19g1180 Vvi19g1180 1180
19 23555076 23625967 + Vvi19g1181 Vvi19g1181 1181
19 23626247 23627989 - Vvi19g1182 Vvi19g1182 1182
19 23630850 23634422 + Vvi19g1183 Vvi19g1183 1183
       

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