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
Vvi5g179 . . . . . Bpe14g01084 . . . . . . . . . Cpe08g00176 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla05g00663 Cam05g0727 Cec05g0734 Cco05g0734 Clacu05g0720 Cmu05g0685 Cre05g0759 . Csa03g01480 . .
Vvi5g180 . . . . . . . . Cmo08g01206 Cmo17g00323 . . Car06g01298 Car14g01434 . Cpe08g00178 Cpe03g01356 . . . . . . . Cla06g00471 Cam06g0505 Cec06g0507 Cco06g0508 Clacu06g0489 Cmu06g0491 Cre06g1263 Cone14ag0754 . Cone7ag0139 . . Csa06g01798 Chy11g01520 . . . . . . Bpe13g00669 . Bma06g01496 Sed04g1786 . Cmo14g01652 Cma08g01231 Cma17g00333 . Car17g00307 Cpe12g00283 Cpe17g00030 Bhi12g02043 Tan06g2689 Cmetu11g2207 . . . Lcy12g0740 . . . . . . . Lsi09g01440 Csa03g01479 . Cme11g02021
Vvi5g181 Blo01g00071 . . . . . . . Cmo08g01205 . . . . . . Cpe08g00179 . . . . . . . . . . . . . . . . . Cone7ag0141 Cone4ag0145 . Csa06g01802 . . . . . . Bpe05g00833 . . . . . . . . . . . Cpe17g00029 Bhi12g02046 . . . . . . . . . . . . . . . . .
Vvi5g182 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g183 . . . . . . . . . Cmo17g00321 . . . . . . . . . . . . . . Cla06g00473 Cam06g0508 Cec06g0509 Cco06g0511 Clacu06g0492 Cmu06g0493 Cre06g1265 . . . . . Csa06g01816 Chy11g01517 . . . . . . . . . . . . . Cma17g00331 . . Cpe12g00281 . . . . . . . . . . . . . . . Lsi09g01438 . . .
Vvi5g184 Blo01g00070 . . Bda08g00378 . . . Bma05g01031 . . . . . . . . . . . . . . . . . . . . . . . . Cone15ag0763 . . . . . . . . . . Bpe05g00831 . . . . . . . . . Car17g00306 . . . . . . . . . . . . . . . . Lsi09g01434 . . Cme11g02020
Vvi5g185 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g186 Blo01g00069 . . Bda08g00295 . . . Bma05g01030 . . . Cma14g01615 . Car14g01438 . . Cpe03g01357 . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe05g00830 . . . . . Cmo14g01653 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g187 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g188 . . . . . . . Bma05g01033 . Cmo17g00319 . . . . . . . . . . . . . . Cla06g00476 Cam06g0510 Cec06g0511 Cco06g0514 Clacu06g0494 Cmu06g0496 Cre06g1267 . . Cone7ag0143 Cone4ag0147 . . Chy11g01513 . . . . . Bpe05g00834 . . . . . . . Cma17g00329 . Car17g00303 Cpe12g00279 . Bhi12g02049 . . . . . . . . . . . . . Lsi09g01433 . . Cme11g02015
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 3086982 3095208 - Bda024729.1 Bda08g00295 295
8 3870823 3878267 + Bda024820.1 Bda08g00378 378
12 63676368 63678268 - XM_039051055.1 Bhi12g02043 2043
12 63775932 63778625 + XM_039050652.1 Bhi12g02046 2046
12 63865845 63868257 + XM_039018806.1 Bhi12g02049 2049
1 875865 889033 + BLOR00069 Blo01g00069 69
1 890912 897102 + BLOR00070 Blo01g00070 70
1 901271 907281 + BLOR00071 Blo01g00071 71
5 48862307 48868894 + Bma022189.1 Bma05g01030 1030
5 48869869 48876326 + Bma031224 Bma05g01031 1031
5 48887080 48888135 - Bma022191.2 Bma05g01033 1033
6 51465214 51466341 - Bma024608.1 Bma06g01496 1496
5 21560373 21568673 + Bpe018243.1 Bpe05g00830 830
5 21569571 21575982 + Bpe018244.1 Bpe05g00831 831
5 21584930 21585714 + Bpe018246.1 Bpe05g00833 833
5 21587325 21588380 - Bpe018247.1 Bpe05g00834 834
13 13448274 13449422 + Bpe010370.1 Bpe13g00669 669
14 8116631 8117260 - Bpe014458.1 Bpe14g01084 1084
5 6312713 6317066 - CaPI482276_05g007270.1 Cam05g0727 727
6 7139277 7140521 - CaPI482276_06g005050.1 Cam06g0505 505
6 7161875 7167619 + CaPI482276_06g005080.1 Cam06g0508 508
6 7173927 7189145 + CaPI482276_06g005100.1 Cam06g0510 510
6 9280650 9281801 + Carg17335-RA Car06g01298 1298
14 11991093 11992187 - Carg19656-RA Car14g01434 1434
14 12076295 12084670 + Carg20102-RA Car14g01438 1438
17 1881998 1883763 - Carg05509-RA Car17g00303 303
17 1900998 1910007 - Carg05512-RA Car17g00306 306
17 1912622 1914180 + Carg05513-RA Car17g00307 307
5 6021848 6027187 - CcPI632755_05g007340.1 Cco05g0734 734
6 5550021 5551265 - CcPI632755_06g005080.1 Cco06g0508 508
6 5584856 5592405 + CcPI632755_06g005110.1 Cco06g0511 511
6 5612918 5614682 + CcPI632755_06g005140.1 Cco06g0514 514
5 6043773 6049052 - CePI673135_05g007340.1 Cec05g0734 734
6 5671562 5672797 - CePI673135_06g005070.1 Cec06g0507 507
6 5694048 5699772 + CePI673135_06g005090.1 Cec06g0509 509
6 5706128 5721329 + CePI673135_06g005110.1 Cec06g0511 511
11 21772637 21773739 - Chy11G200930.1 Chy11g01513 1513
11 21805105 21808828 - Chy11G200970.1 Chy11g01517 1517
11 21824929 21826170 + Chy11G201000.1 Chy11g01520 1520
5 6048335 6052641 - ClG42_05g0072000.10 Clacu05g0720 720
6 5680315 5681838 - ClG42_06g0048900.10 Clacu06g0489 489
6 5703051 5708702 + ClG42_06g0049200.10 Clacu06g0492 492
6 5714865 5730058 + ClG42_06g0049400.10 Clacu06g0494 494
5 6153938 6158244 - ClCG05G006190.2 Cla05g00663 663
6 5729945 5731511 - ClCG06G005040.1 Cla06g00471 471
6 5752549 5758375 + ClCG06G005060.2 Cla06g00473 473
6 5780013 5781535 + ClCG06G005080.1 Cla06g00476 476
8 7556768 7558431 + CmaCh08G012310.1 Cma08g01231 1231
14 12125704 12136301 + CmaCh14G016150.1 Cma14g01615 1615
17 1795664 1796716 - CmaCh17G003290.1 Cma17g00329 329
17 1807686 1811620 - CmaCh17G003310.1 Cma17g00331 331
17 1824299 1825961 + CmaCh17G003330.1 Cma17g00333 333
11 28029237 28030766 - MELO3C021324.2.1 Cme11g02015 2015
11 28053151 28059976 - MELO3C021320.2.1 Cme11g02020 2020
11 28067751 28069316 + MELO3C021319.2.1 Cme11g02021 2021
11 4133694 4135495 - PI0000302.1 Cmetu11g2207 2207
8 7655077 7660830 - CmoCh08G012050.1 Cmo08g01205 1205
8 7662961 7664397 + CmoCh08G012060.1 Cmo08g01206 1206
14 13057918 13059006 - CmoCh14G016520.1 Cmo14g01652 1652
14 13063420 13073569 + CmoCh14G016530.1 Cmo14g01653 1653
17 1924359 1925411 - CmoCh17G003190.1 Cmo17g00319 319
17 1935823 1940118 - CmoCh17G003210.1 Cmo17g00321 321
17 1953504 1954763 + CmoCh17G003230.1 Cmo17g00323 323
5 5891680 5895986 - CmPI595203_05g006850.1 Cmu05g0685 685
6 5482287 5483810 - CmPI595203_06g004910.1 Cmu06g0491 491
6 5504920 5510583 + CmPI595203_06g004930.1 Cmu06g0493 493
6 5530514 5531956 + CmPI595203_06g004960.1 Cmu06g0496 496
4 669160 669766 + Conep04aG0015100.1 Cone4ag0145 145
4 671751 674032 - Conep04aG0015300.1 Cone4ag0147 147
7 577840 579563 - Conep07aG0014000.1 Cone7ag0139 139
7 590529 591126 + Conep07aG0014200.1 Cone7ag0141 141
7 593373 594979 - Conep07aG0014400.1 Cone7ag0143 143
14 4223178 4224347 - Conep14aG0077100.1 Cone14ag0754 754
15 4556201 4561539 + Conep15aG0077800.1 Cone15ag0763 763
3 10976477 10977571 - Cp4.1LG03g11540.1 Cpe03g01356 1356
3 10983701 10992563 + Cp4.1LG03g11670.1 Cpe03g01357 1357
8 1222674 1224231 + Cp4.1LG08g05020.1 Cpe08g00176 176
8 1225704 1226855 - Cp4.1LG08g04880.1 Cpe08g00178 178
8 1232801 1233349 + Cp4.1LG08g04990.1 Cpe08g00179 179
12 1860001 1876466 - Cp4.1LG12g02770.1 Cpe12g00279 279
12 1877593 1881852 - Cp4.1LG12g02800.1 Cpe12g00281 281
12 1895289 1897094 + Cp4.1LG12g02990.1 Cpe12g00283 283
17 196355 202336 - Cp4.1LG17g00560.1 Cpe17g00029 29
17 204466 205902 + Cp4.1LG17g00660.1 Cpe17g00030 30
5 6692522 6697850 - CrPI670011_05g007590.1 Cre05g0759 759
6 6544310 6545557 - CrPI670011_06g012630.1 Cre06g1263 1263
6 6565613 6571334 + CrPI670011_06g012650.1 Cre06g1265 1265
6 6577573 6592802 + CrPI670011_06g012670.1 Cre06g1267 1267
3 10981156 10983185 + CsaV3_3G014790.1 Csa03g01479 1479
3 10984292 10988345 - CsaV3_3G014800.1 Csa03g01480 1480
6 15883235 15886026 - CsaV3_6G023920.1 Csa06g01798 1798
6 15906335 15914473 + CsaV3_6G023960.1 Csa06g01802 1802
6 15980209 15983647 + CsaV3_6G024100.1 Csa06g01816 1816
12 9401172 9402431 + Maker00025054 Lcy12g0740 740
9 22340783 22341841 - Lsi09G014330.1 Lsi09g01433 1433
9 22344595 22349380 - Lsi09G014340.1 Lsi09g01434 1434
9 22361451 22367307 - Lsi09G014380.1 Lsi09g01438 1438
9 22391170 22392408 + Lsi09G014400.1 Lsi09g01440 1440
4 32492312 32494025 - Sed0002765.1 Sed04g1786 1786
6 79320755 79322410 + Tan0000529.1 Tan06g2689 2689
5 1785714 1788540 + Vvi5g179 Vvi5g179 179
5 1791769 1793585 + Vvi5g180 Vvi5g180 180
5 1797069 1798034 - Vvi5g181 Vvi5g181 181
5 1800759 1805109 - Vvi5g182 Vvi5g182 182
5 1806219 1809826 - Vvi5g183 Vvi5g183 183
5 1814419 1837357 - Vvi5g184 Vvi5g184 184
5 1840342 1843831 - Vvi5g185 Vvi5g185 185
5 1845279 1854311 - Vvi5g186 Vvi5g186 186
5 1857659 1860023 + Vvi5g187 Vvi5g187 187
5 1910247 1911449 - Vvi5g188 Vvi5g188 188
       

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