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
Vvi2g202 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g203 . . . Bda08g00756 . Bpe07g00255 . . . Cmo16g01268 Cma02g00912 . Car02g00663 . . Cpe14g01011 . . . . . . . . Cla07g00789 Cam07g0852 Cec07g0905 Cco07g0887 Clacu07g0827 Cmu07g0830 Cre07g1188 . . . . Lsi07g01120 . . Cme07g01644 . . . . . . . Bma12g00444 . Cmo02g00919 . . Cma16g01224 . Car16g01152 Cpe08g00909 . . . . . . . . . . . . . . . . . Chy07g01228 .
Vvi2g204 . . . . . . . . . . Cma02g00930 Cma15g01302 Car02g00679 Car15g01173 . . Cpe05g00781 . . . . . . . . . . . . . . . . . . . Csa05g00182 Chy09g01314 . . . . . . . . . . Cmo02g00939 Cmo15g01370 . . . . . . Bhi12g00105 . . . . . . Cla01g00162 Cam01g0168 Cec01g0166 Cco01g0169 Clacu01g0164 Cmu01g0163 Cre09g2343 Lsi09g00154 . . Cme09g01863
Vvi2g205 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g206 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g207 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g208 . . . . . . . . . . Cma02g00931 Cma15g01305 Car02g00680 Car15g01175 . . Cpe05g00780 . . . . . . . . . . . . . . . . . . . Csa05g00028 Chy09g01316 . . . Bda07g01942 . . . . . . Cmo02g00940 Cmo15g01372 . . . . . . Bhi12g00103 . . . . . Lcy12g1541 Cla01g00160 Cam01g0166 Cec01g0164 Cco01g0167 Clacu01g0162 Cmu01g0161 Cre09g2345 Lsi09g00152 . . Cme09g01865
Vvi2g209 . . . . . . . . . . Cma02g00866 Cma15g01306 Car02g00682 Car15g01176 . . . . . . . . . . . . . . . . . . . . . . Csa05g00030 Chy09g01317 . . . Bda07g01944 . . . . . . Cmo02g00942 Cmo15g01373 . . . . . . Bhi12g00102 . . Lac11g1945 Hepe06g1450 . Lcy12g1540 Cla01g00159 Cam01g0165 Cec01g0162 Cco01g0166 Clacu01g0161 Cmu01g0160 Cre09g2346 Lsi09g00151 . . Cme09g01866
Vvi2g210 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g211 . . . . . . . . . . . Cma15g01307 . Car15g01177 . . . . . . . . . . . . . . . . . . . . . . Csa05g00178 Chy09g01318 . . . . . . . . . . . Cmo15g01374 . . . . . . Bhi12g00101 . . Lac11g1944 Hepe06g1449 . Lcy12g1539 Cla01g00158 Cam01g0164 Cec01g0161 Cco01g0165 Clacu01g0160 Cmu01g0159 Cre09g2347 Lsi09g00150 . . Cme09g01867
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 36880142 36883058 - Bda028921.3 Bda07g01942 1942
7 36893264 36894079 + Bda028923.1 Bda07g01944 1944
8 9623640 9626615 + Bda029249.1 Bda08g00756 756
12 3304599 3307667 + XM_039019984.1 Bhi12g00101 101
12 3311893 3313977 - XM_039020258.1 Bhi12g00102 102
12 3462110 3467866 + XM_039051341.1 Bhi12g00103 103
12 3473459 3489515 - XM_039018491.1 Bhi12g00105 105
12 11231440 11234928 + Bma007449.1 Bma12g00444 444
7 1836778 1838366 - Bpe021067.1 Bpe07g00255 255
1 1988457 1989374 + CaPI482276_01g001640.1 Cam01g0164 164
1 1993337 1994800 - CaPI482276_01g001650.1 Cam01g0165 165
1 2026842 2032336 + CaPI482276_01g001660.1 Cam01g0166 166
1 2037754 2042269 - CaPI482276_01g001680.1 Cam01g0168 168
7 21251119 21254871 - CaPI482276_07g008520.1 Cam07g0852 852
2 4965830 4967795 + Carg08560-RA Car02g00663 663
2 5062077 5066386 + Carg08544-RA Car02g00679 679
2 5067072 5071556 - Carg08543-RA Car02g00680 680
2 5080066 5081266 + Carg08541-RA Car02g00682 682
15 9176845 9178825 + Carg21297-RA Car15g01173 1173
15 9182962 9187331 - Carg21299-RA Car15g01175 1175
15 9192432 9193456 + Carg21300-RA Car15g01176 1176
15 9195585 9196460 - Carg21301-RA Car15g01177 1177
16 9820200 9821713 - Carg19489-RA Car16g01152 1152
1 1564323 1565240 + CcPI632755_01g001650.1 Cco01g0165 165
1 1568558 1570798 - CcPI632755_01g001660.1 Cco01g0166 166
1 1609378 1614402 + CcPI632755_01g001670.1 Cco01g0167 167
1 1620306 1624808 - CcPI632755_01g001690.1 Cco01g0169 169
7 20643321 20647113 - CcPI632755_07g008870.1 Cco07g0887 887
1 1559557 1560474 + CePI673135_01g001610.1 Cec01g0161 161
1 1564391 1565853 - CePI673135_01g001620.1 Cec01g0162 162
1 1598381 1603819 + CePI673135_01g001640.1 Cec01g0164 164
1 1609205 1613745 - CePI673135_01g001660.1 Cec01g0166 166
7 22439821 22443475 - CePI673135_07g009050.1 Cec07g0905 905
7 17059251 17073579 - Chy7G140580.1 Chy07g01228 1228
9 15070257 15074691 + Chy9G170300.1 Chy09g01314 1314
9 15079458 15083620 - Chy9G170320.1 Chy09g01316 1316
9 15103796 15105287 + Chy9G170330.1 Chy09g01317 1317
9 15108321 15109199 - Chy9G170340.1 Chy09g01318 1318
1 1608536 1609453 + ClG42_01g0016000.10 Clacu01g0160 160
1 1613349 1614796 - ClG42_01g0016100.10 Clacu01g0161 161
1 1647102 1652532 + ClG42_01g0016200.10 Clacu01g0162 162
1 1658015 1662499 - ClG42_01g0016400.10 Clacu01g0164 164
7 20924519 20928291 - ClG42_07g0082700.10 Clacu07g0827 827
1 1605424 1606341 + ClCG01G001620.1 Cla01g00158 158
1 1609633 1611517 - ClCG01G001630.2 Cla01g00159 159
1 1644424 1649976 + ClCG01G001640.2 Cla01g00160 160
1 1655875 1660631 - ClCG01G001660.1 Cla01g00162 162
7 22056105 22060399 - ClCG07G008270.1 Cla07g00789 789
2 5055907 5057219 + CmaCh02G008660.1 Cma02g00866 866
2 5439191 5441029 + CmaCh02G009120.1 Cma02g00912 912
2 5531103 5535549 + CmaCh02G009300.1 Cma02g00930 930
2 5536316 5540677 - CmaCh02G009310.1 Cma02g00931 931
15 8220029 8221609 + CmaCh15G013020.1 Cma15g01302 1302
15 8225461 8230268 - CmaCh15G013050.1 Cma15g01305 1305
15 8236253 8236954 + CmaCh15G013060.1 Cma15g01306 1306
15 8239120 8242623 - CmaCh15G013070.1 Cma15g01307 1307
16 9262820 9264333 - CmaCh16G012240.1 Cma16g01224 1224
7 22153832 22157979 - MELO3C016368.2.1 Cme07g01644 1644
9 22811718 22816435 + MELO3C005771.2.1 Cme09g01863 1863
9 22820693 22826479 - MELO3C005773.2.1 Cme09g01865 1865
9 22846755 22849025 + MELO3C005774.2.1 Cme09g01866 1866
9 22851710 22854787 - MELO3C005775.2.1 Cme09g01867 1867
2 5656544 5658787 + CmoCh02G009190.1 Cmo02g00919 919
2 5751613 5756846 + CmoCh02G009390.1 Cmo02g00939 939
2 5757688 5761195 - CmoCh02G009400.1 Cmo02g00940 940
2 5770498 5772171 + CmoCh02G009420.1 Cmo02g00942 942
15 9341973 9343656 + CmoCh15G013700.1 Cmo15g01370 1370
15 9347593 9352317 - CmoCh15G013720.1 Cmo15g01372 1372
15 9357157 9358632 + CmoCh15G013730.1 Cmo15g01373 1373
15 9360200 9361099 - CmoCh15G013740.1 Cmo15g01374 1374
16 9040802 9042315 - CmoCh16G012680.1 Cmo16g01268 1268
1 1561866 1562783 + CmPI595203_01g001590.1 Cmu01g0159 159
1 1566680 1568320 - CmPI595203_01g001600.1 Cmu01g0160 160
1 1600276 1605224 + CmPI595203_01g001610.1 Cmu01g0161 161
1 1611182 1615685 - CmPI595203_01g001630.1 Cmu01g0163 163
7 21138414 21142185 - CmPI595203_07g008300.1 Cmu07g0830 830
5 4844469 4848862 + Cp4.1LG05g07800.1 Cpe05g00780 780
5 4849784 4854073 - Cp4.1LG05g07920.1 Cpe05g00781 781
8 7157464 7159954 - Cp4.1LG08g09130.1 Cpe08g00909 909
14 8514045 8516130 - Cp4.1LG14g10120.1 Cpe14g01011 1011
7 24737121 24741027 - CrPI670011_07g011880.1 Cre07g1188 1188
9 42695672 42700200 + CrPI670011_09g023430.1 Cre09g2343 2343
9 42705597 42711093 - CrPI670011_09g023450.1 Cre09g2345 2345
9 42743826 42745318 + CrPI670011_09g023460.1 Cre09g2346 2346
9 42749282 42750199 - CrPI670011_09g023470.1 Cre09g2347 2347
5 125300 128763 - CsaV3_5G000280.1 Csa05g00028 28
5 146419 149861 + CsaV3_5G000300.1 Csa05g00030 30
5 1024935 1028044 + CsaV3_5G001780.1 Csa05g00178 178
5 1059362 1064538 - CsaV3_5G001820.1 Csa05g00182 182
6 65056591 65060614 + Hsped.06g14490.1 Hepe06g1449 1449
6 65065085 65067232 - Hsped.06g14500.1 Hepe06g1450 1450
11 34927039 34927914 + Lag0032582.1 Lac11g1944 1944
11 34933457 34934867 - Lag0032583.1 Lac11g1945 1945
12 35230424 35231692 + Maker00029191 Lcy12g1539 1539
12 35237276 35244777 - Maker00029237 Lcy12g1540 1540
12 35310825 35316307 + Maker00029232 Lcy12g1541 1541
7 16636937 16638595 + Lsi07G011200.1 Lsi07g01120 1120
9 1520835 1525279 + Lsi09G001500.1 Lsi09g00150 150
9 1530361 1531425 - Lsi09G001510.1 Lsi09g00151 151
9 1590257 1595263 + Lsi09G001520.1 Lsi09g00152 152
9 1601575 1606713 - Lsi09G001540.1 Lsi09g00154 154
2 1943328 1943906 - Vvi2g202 Vvi2g202 202
2 1944047 1946224 + Vvi2g203 Vvi2g203 203
2 1947973 1953908 + Vvi2g204 Vvi2g204 204
2 1964781 1965840 + Vvi2g205 Vvi2g205 205
2 1969469 1970524 - Vvi2g206 Vvi2g206 206
2 1971915 1976531 + Vvi2g207 Vvi2g207 207
2 1998984 2003828 - Vvi2g208 Vvi2g208 208
2 2012749 2013969 + Vvi2g209 Vvi2g209 209
2 2016485 2019135 - Vvi2g210 Vvi2g210 210
2 2020338 2023481 - Vvi2g211 Vvi2g211 211
       

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