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
Vvi4g192 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g193 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g194 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g195 . . . . . . . . . Cmo12g00247 . Cma05g00625 . Car12g00279 Sed01g1300 Cpe07g00254 . Bhi04g01087 Tan02g2614 Cmetu03g1754 . Hepe10g0321 . Lcy13g1353 . . . . . . . . . Cone17ag1080 Cone20ag0632 . . . . . . . Bda13g01300 . . . Bma02g00058 . . . . Cma12g00296 . . . . . . . . . . . . . . . . . . . . Chy03g01195 .
Vvi4g196 Blo01g01340 . Bda01g00674 Bda03g00036 . . Bma04g00034 Bma01g02121 . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1082 Cone20ag0630 . . . . . . . . . Bpe04g00025 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g197 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g198 . . . . . . . . . . . . Car09g00456 . . . Cpe06g00392 . . . . . . . Cla05g01804 Cam05g1926 Cec05g1938 Cco05g2001 Clacu05g1918 Cmu05g1800 Cre05g1926 Cone4ag1857 Cone7ag1764 . . Lsi04g02196 Csa03g04406 . . . . . . . . . . Sed13g2091 . Cmo09g00518 . . . . . . Bhi09g02372 Tan01g3737 Cmetu04g2143 . Hepe01g2090 Mch11g0628 . . . . . . . . . . . .
Vvi4g199 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g200 Blo01g01341 . Bda01g00701 . . . . Bma01g02125 . Cmo12g00245 . Cma05g00629 Car09g00453 Car12g00277 Sed01g1303 Cpe07g00253 Cpe06g00391 Bhi04g01083 Tan02g2620 Cmetu03g2117 . Hepe10g0318 . Lcy13g1351 . . . . . . . . Cone7ag1763 . . Lsi04g02195 Csa03g04405 Chy04g00296 . Blo17g00044 . . Bda13g01298 . . Bma01g01312 Bma02g00056 . . Cmo09g00517 . Cma12g00293 Car01g01191 . . . Bhi09g02366 Tan01g3734 . . . . . . . . . . . . . . Chy03g01193 .
Vvi4g201 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 33883227 33885251 + Bda002710.1 Bda01g00674 674
1 34290950 34293171 + Bda002739.1 Bda01g00701 701
3 501989 504040 + Bda015970.1 Bda03g00036 36
13 35243184 35245130 - Bda000106.1 Bda13g01298 1298
13 35248345 35250160 - Bda000108.1 Bda13g01300 1300
4 26814466 26819490 - XM_039029092.1 Bhi04g01083 1083
4 26882625 26883906 - XM_039028196.1 Bhi04g01087 1087
9 64697927 64702341 - XM_039042112.1 Bhi09g02366 2366
9 64705336 64712906 - XM_039042066.1 Bhi09g02372 2372
1 51014878 51016875 + BLOR01340 Blo01g01340 1340
1 51038022 51040304 + BLOR01341 Blo01g01341 1341
17 288819 290823 - BLOR15865 Blo17g00044 44
1 17911667 17913543 - Bma001631.1 Bma01g01312 1312
1 77629710 77631734 + Bma002957.1 Bma01g02121 2121
1 77736610 77746745 + Bma002964.1 Bma01g02125 2125
2 478451 480404 - Bma014511.1 Bma02g00056 56
2 489380 491063 - Bma014513.1 Bma02g00058 58
4 372870 374921 + Bma018486.1 Bma04g00034 34
4 233252 235303 + Bpe014751.1 Bpe04g00025 25
5 28168500 28176928 - CaPI482276_05g019260.1 Cam05g1926 1926
1 11042271 11046847 - Carg21172-RA Car01g01191 1191
9 2528427 2530915 - Carg02935-RA Car09g00453 453
9 2534323 2542001 - Carg02938-RA Car09g00456 456
12 1833318 1835689 - Carg03884-RA Car12g00277 277
12 1845845 1847459 - Carg03886-RA Car12g00279 279
5 29090748 29099477 - CcPI632755_05g020010.1 Cco05g2001 2001
5 31421084 31429816 - CePI673135_05g019380.1 Cec05g1938 1938
3 15068126 15070786 - Chy3G061730.1 Chy03g01193 1193
3 15088736 15090302 - Chy3G061750.1 Chy03g01195 1195
4 2666617 2679753 + Chy4G070140.1 Chy04g00296 296
5 28371469 28379908 - ClG42_05g0191800.10 Clacu05g1918 1918
5 29934139 29942758 - ClCG05G017600.2 Cla05g01804 1804
5 3139264 3140556 + CmaCh05G006250.1 Cma05g00625 625
5 3152091 3157257 + CmaCh05G006290.1 Cma05g00629 629
12 1504259 1507274 - CmaCh12G002930.1 Cma12g00293 293
12 1517362 1518884 - CmaCh12G002960.1 Cma12g00296 296
3 3789451 3791480 + PI0022286.1 Cmetu03g1754 1754
3 3806861 3812083 + PI0002346.1 Cmetu03g2117 2117
4 30685217 30691626 - PI0006747.1 Cmetu04g2143 2143
9 2405623 2409584 - CmoCh09G005170.1 Cmo09g00517 517
9 2411434 2418695 - CmoCh09G005180.1 Cmo09g00518 518
12 1602941 1606703 - CmoCh12G002450.1 Cmo12g00245 245
12 1615065 1617165 - CmoCh12G002470.1 Cmo12g00247 247
5 28089918 28098353 - CmPI595203_05g018000.1 Cmu05g1800 1800
4 13323711 13324859 + Conep04aG0191600.1 Cone4ag1857 1857
7 11634254 11637663 - Conep07aG0181600.1 Cone7ag1763 1763
7 11638789 11642486 - Conep07aG0181700.1 Cone7ag1764 1764
17 8066007 8067043 - Conep17aG0110800.1 Cone17ag1080 1080
17 8069916 8072924 - Conep17aG0111000.1 Cone17ag1082 1082
20 3788807 3791674 + Conep20aG0064800.1 Cone20ag0630 630
20 3806536 3807314 + Conep20aG0065000.1 Cone20ag0632 632
6 2211868 2216055 - Cp4.1LG06g04630.1 Cpe06g00391 391
6 2217749 2224893 - Cp4.1LG06g04650.1 Cpe06g00392 392
7 1645668 1648474 - Cp4.1LG07g01990.1 Cpe07g00253 253
7 1655932 1659971 - Cp4.1LG07g01980.1 Cpe07g00254 254
5 31410641 31419066 - CrPI670011_05g019260.1 Cre05g1926 1926
3 38407779 38411575 - CsaV3_3G047110.1 Csa03g04405 4405
3 38414553 38420868 - CsaV3_3G047120.1 Csa03g04406 4406
1 85505678 85512229 - Hsped.01g20900.1 Hepe01g2090 2090
10 3390759 3395597 - Hsped.10g03180.1 Hepe10g0318 318
10 3420376 3429516 - Hsped.10g03210.1 Hepe10g0321 321
13 31537748 31543418 - Maker00025575 Lcy13g1351 1351
13 31573398 31575675 - Maker00025566 Lcy13g1353 1353
4 28987328 28991038 - Lsi04G021950.1 Lsi04g02195 2195
4 28993312 29004825 - Lsi04G021960.1 Lsi04g02196 2196
11 4037082 4044498 - MC11g0522 Mch11g0628 628
1 9730163 9731533 + Sed0005624.1 Sed01g1300 1300
1 9751126 9755995 + Sed0025754.1 Sed01g1303 1303
13 25632143 25640913 - Sed0014514.1 Sed13g2091 2091
1 102128077 102132725 - Tan0021711.1 Tan01g3734 3734
1 102135487 102143049 - Tan0006452.1 Tan01g3737 3737
2 94718915 94721002 + Tan0010891.1 Tan02g2614 2614
2 94750318 94755243 + Tan0010895.4 Tan02g2620 2620
4 1899432 1900571 - Vvi4g192 Vvi4g192 192
4 1902516 1909484 + Vvi4g193 Vvi4g193 193
4 1909483 1910022 + Vvi4g194 Vvi4g194 194
4 1910095 1911341 - Vvi4g195 Vvi4g195 195
4 1913810 1923695 - Vvi4g196 Vvi4g196 196
4 1931739 1932417 - Vvi4g197 Vvi4g197 197
4 1937939 1949481 - Vvi4g198 Vvi4g198 198
4 1953598 1957566 + Vvi4g199 Vvi4g199 199
4 1970578 1975867 + Vvi4g200 Vvi4g200 200
4 1976948 1978455 - Vvi4g201 Vvi4g201 201
       

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