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
Vvi18g610 . . . . . . . . Cmo05g00127 Cmo12g00549 . . . Car12g00554 Sed10g1155 . Cpe07g00531 Bhi04g00455 Tan02g1694 Cmetu03g2102 . Hepe08g1352 . Lcy13g2153 Cla08g01640 Cam08g2144 Cec08g1731 Cco08g1851 Clacu08g1832 . Cre08g1615 Cone4ag1632 . . . . . . Cme03g02124 . . . . . Bpe05g00047 . . . . . Cma12g00613 Cma05g00123 Car05g00105 . . . . . . . . . . . . . . . . . Lsi08g01546 Csa02g01872 Chy03g01614 .
Vvi18g611 Blo01g01487 Blo12g00997 . Bda03g00161 . Bpe04g00143 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag1318 . . Lsi04g01457 Csa04g02503 . . . . . . . . . Bma05g00060 . . . . . . . . Cpe02g00237 . . . . . . . . . . . . . . . . Chy07g00210 .
Vvi18g612 Blo01g01488 Blo12g00996 Bda01g00599 Bda03g00162 Bpe02g00463 Bpe04g00144 . . Cmo05g00128 Cmo12g00548 . . . Car12g00553 . . Cpe07g00530 Bhi04g00454 Tan02g1695 . . Hepe08g1351 . . Cla08g01639 Cam08g2143 Cec08g1730 Cco08g1850 Clacu08g1831 . Cre08g1614 Cone4ag1631 Cone7ag1319 Cone17ag0901 Cone20ag0243 . . . Cme03g02123 . Blo18g00727 . Bda01g01584 Bpe02g01773 . Bma01g00682 . . . . Cma12g00612 Cma05g00124 Car05g00106 . Cpe11g00107 . . . . . . . . . . . . . . . Lsi08g01545 Csa02g01873 Chy03g01613 .
Vvi18g613 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g614 . Blo12g00995 . Bda03g00163 . Bpe04g00145 . . . . Cma01g01771 Cma09g00307 Car01g01380 . . Cpe06g00216 . . . . . . . . . . . . . . . . . Cone17ag0900 Cone20ag0242 Lsi04g01460 Csa04g02500 . . . . . . . Bpe05g00461 . . Sed13g1825 Cmo01g01829 Cmo09g00308 . . . Car09g00259 . Cpe02g00234 Bhi09g03198 Tan01g4668 Cmetu07g0441 . Hepe01g1848 Mch11g0381 . . . . . . . . . . Chy07g00208 .
Vvi18g615 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g616 . . . . . . . . . Cmo12g00547 . . . Car12g00552 . . Cpe07g00529 Bhi04g00452 . . . . . . Cla08g01638 Cam08g2142 Cec08g1729 Cco08g1849 Clacu08g1830 . Cre08g1613 . . Cone17ag0899 Cone20ag0241 . . . Cme03g02122 . . . . . . . . . . . Cma12g00609 . . . . . . . . . . . . . . . . . . . Lsi08g01544 Csa02g01874 Chy03g01612 .
Vvi18g617 . . . . . . . . Cmo05g00132 . . . . . Sed10g1161 . . Bhi04g00450 Tan02g1701 Cmetu03g2266 . Hepe08g1348 . Lcy13g2150 Cla08g01637 Cam08g2141 Cec08g1728 Cco08g1848 Clacu08g1829 . Cre08g1612 . . Cone17ag0898 Cone20ag0240 . . . Cme03g02120 . . . Bda01g01640 . . . . . . . . Cma05g00127 Car05g00108 . Cpe11g00108 . . . . . . . . . . . . . . . Lsi08g01542 Csa02g01876 Chy03g01610 .
Vvi18g618 . Blo12g00994 . . . Bpe04g00147 . . . . . Cma09g00304 Car01g01382 . . . . . . . . . . . . . . . . . . . . . . Lsi04g01464 Csa04g02497 . . . . . . . . . . Sed01g3816 Cmo01g01831 Cmo09g00304 . . . Car09g00256 . . Bhi09g03203 Tan01g4672 Cmetu09g0436 . . . . . . . . . . . . . Chy07g00206 .
Vvi18g619 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 32991420 32993077 - Bda002622.1 Bda01g00599 599
1 51668301 51670939 - Bda003851.1 Bda01g01584 1584
1 52377903 52383417 + Bda032967 Bda01g01640 1640
3 1325594 1326998 - Bda016103.1 Bda03g00161 161
3 1328343 1330486 + Bda016104.1 Bda03g00162 162
3 1334422 1343802 + Bda016105.1 Bda03g00163 163
4 11252434 11260461 + XM_039030152.1 Bhi04g00450 450
4 11347422 11352909 + XM_039028621.1 Bhi04g00452 452
4 11393763 11396248 + XM_039030764.1 Bhi04g00454 454
4 11513712 11516244 + XM_039028069.1 Bhi04g00455 455
9 82127755 82138870 + XM_039041447.1 Bhi09g03198 3198
9 82215847 82218082 - XM_039041806.1 Bhi09g03203 3203
1 54317540 54318941 - BLOR01487 Blo01g01487 1487
1 54322892 54328423 + BLOR01488 Blo01g01488 1488
12 27963548 27968644 + BLOR05013 Blo12g00994 994
12 27971385 27980953 - BLOR05014 Blo12g00995 995
12 27982827 27984929 - BLOR05015 Blo12g00996 996
12 27986449 27987856 + BLOR05016 Blo12g00997 997
18 18767842 18770500 - BLOR09215 Blo18g00727 727
1 6263962 6265740 + Bma000892.1 Bma01g00682 682
5 2474971 2479064 - Bma020751.2 Bma05g00060 60
2 3013606 3015250 - Bpe008304.1 Bpe02g00463 463
2 20047582 20050225 - Bpe009605.1 Bpe02g01773 1773
4 962777 964182 - Bpe014862.1 Bpe04g00143 143
4 965595 967713 + Bpe014863.1 Bpe04g00144 144
4 971559 979022 + Bpe014864.1 Bpe04g00145 145
4 982786 983103 - Bpe025579 Bpe04g00147 147
5 855598 857171 - Bpe017434.1 Bpe05g00047 47
5 18944837 18961789 - Bpe017880.1 Bpe05g00461 461
8 26777048 26777497 + CaPI482276_08g021410.1 Cam08g2141 2141
8 26786442 26791644 + CaPI482276_08g021420.1 Cam08g2142 2142
8 26813217 26816237 + CaPI482276_08g021430.1 Cam08g2143 2143
8 26818809 26820860 + CaPI482276_08g021440.1 Cam08g2144 2144
1 12090529 12101115 + Carg10657-RA Car01g01380 1380
1 12105325 12107375 - Carg10655-RA Car01g01382 1382
5 554153 556265 - Carg11899-RA Car05g00105 105
5 557111 559855 - Carg11898-RA Car05g00106 106
5 574137 581305 - Carg11896-RA Car05g00108 108
9 1407931 1408269 + Carg21765-RA Car09g00256 256
9 1415422 1425172 - Carg21762-RA Car09g00259 259
12 3668374 3673633 + Carg16382-RA Car12g00552 552
12 3686750 3688961 + Carg16381-RA Car12g00553 553
12 3689881 3692328 + Carg16380-RA Car12g00554 554
8 29475829 29476278 + CcPI632755_08g018480.1 Cco08g1848 1848
8 29485241 29491356 + CcPI632755_08g018490.1 Cco08g1849 1849
8 29511862 29514892 + CcPI632755_08g018500.1 Cco08g1850 1850
8 29517544 29519595 + CcPI632755_08g018510.1 Cco08g1851 1851
8 28385001 28385450 + CePI673135_08g017280.1 Cec08g1728 1728
8 28394505 28399675 + CePI673135_08g017290.1 Cec08g1729 1729
8 28421174 28424183 + CePI673135_08g017300.1 Cec08g1730 1730
8 28426410 28428476 + CePI673135_08g017310.1 Cec08g1731 1731
3 18025611 18031864 + Chy3G065900.1 Chy03g01610 1610
3 18048479 18053332 + Chy3G065920.1 Chy03g01612 1612
3 18070744 18073382 + Chy3G065930.1 Chy03g01613 1613
3 18075939 18078120 + Chy3G065940.1 Chy03g01614 1614
7 1661637 1667573 + Chy7G130360.1 Chy07g00206 206
7 1675951 1688742 - Chy7G130380.1 Chy07g00208 208
7 1696029 1697190 + Chy7G130400.1 Chy07g00210 210
8 27530879 27531328 + ClG42_08g0182900.10 Clacu08g1829 1829
8 27540381 27546961 + ClG42_08g0183000.10 Clacu08g1830 1830
8 27567003 27570038 + ClG42_08g0183100.10 Clacu08g1831 1831
8 27572604 27574921 + ClG42_08g0183200.10 Clacu08g1832 1832
8 28958744 28969657 + ClCG08G016670.2 Cla08g01637 1637
8 28980545 28986933 + ClCG08G016690.1 Cla08g01638 1638
8 29008933 29012408 + ClCG08G016700.1 Cla08g01639 1639
8 29014768 29016817 + ClCG08G016710.1 Cla08g01640 1640
1 11880975 11892452 + CmaCh01G017710.1 Cma01g01771 1771
5 542154 545359 - CmaCh05G001230.1 Cma05g00123 123
5 545401 548469 - CmaCh05G001240.1 Cma05g00124 124
5 563635 570904 - CmaCh05G001270.1 Cma05g00127 127
9 1251143 1251927 + CmaCh09G003040.1 Cma09g00304 304
9 1259927 1270338 - CmaCh09G003070.1 Cma09g00307 307
12 3198121 3203416 + CmaCh12G006090.1 Cma12g00609 609
12 3214305 3217017 + CmaCh12G006120.1 Cma12g00612 612
12 3217589 3220217 + CmaCh12G006130.1 Cma12g00613 613
3 28413248 28430256 + MELO3C010789.2.1 Cme03g02120 2120
3 28438833 28443681 + MELO3C010787.2.1 Cme03g02122 2122
3 28459954 28463461 + MELO3C010786.2.1 Cme03g02123 2123
3 28464880 28467386 + MELO3C010785.2.1 Cme03g02124 2124
3 844525 846499 - PI0011775.1 Cmetu03g2102 2102
3 887771 895422 - PI0006545.1 Cmetu03g2266 2266
7 23062288 23071954 - PI0014885.1 Cmetu07g0441 441
9 140388 140980 + PI0019440.1 Cmetu09g0436 436
1 13376230 13387986 + CmoCh01G018290.1 Cmo01g01829 1829
1 13391208 13394014 - CmoCh01G018310.1 Cmo01g01831 1831
5 553372 555528 - CmoCh05G001270.1 Cmo05g00127 127
5 555941 559124 - CmoCh05G001280.1 Cmo05g00128 128
5 573874 582196 - CmoCh05G001320.1 Cmo05g00132 132
9 1314204 1315798 + CmoCh09G003040.1 Cmo09g00304 304
9 1323391 1331450 - CmoCh09G003080.1 Cmo09g00308 308
12 3357010 3362330 + CmoCh12G005470.1 Cmo12g00547 547
12 3374799 3378492 + CmoCh12G005480.1 Cmo12g00548 548
12 3379219 3381697 + CmoCh12G005490.1 Cmo12g00549 549
4 12338304 12339935 - Conep04aG0168400.1 Cone4ag1631 1631
4 12346006 12347809 + Conep04aG0168500.1 Cone4ag1632 1632
7 9666753 9668290 - Conep07aG0135700.1 Cone7ag1318 1318
7 9673572 9675425 + Conep07aG0135800.1 Cone7ag1319 1319
17 7054412 7058197 + Conep17aG0092000.1 Cone17ag0898 898
17 7058806 7063116 + Conep17aG0092100.1 Cone17ag0899 899
17 7063693 7071256 - Conep17aG0092200.1 Cone17ag0900 900
17 7079973 7081344 - Conep17aG0092400.1 Cone17ag0901 901
20 1043500 1047111 + Conep20aG0025100.1 Cone20ag0240 240
20 1050096 1054447 + Conep20aG0025200.1 Cone20ag0241 241
20 1054438 1062850 - Conep20aG0025300.1 Cone20ag0242 242
20 1067208 1069814 - Conep20aG0025400.1 Cone20ag0243 243
2 1201398 1213335 - Cp4.1LG02g06390.1 Cpe02g00234 234
2 1218494 1219766 + Cp4.1LG02g06460.1 Cpe02g00237 237
6 1147651 1157009 - Cp4.1LG06g02210.1 Cpe06g00216 216
7 3487991 3493433 + Cp4.1LG07g04750.1 Cpe07g00529 529
7 3504740 3507294 + Cp4.1LG07g04760.1 Cpe07g00530 530
7 3508030 3509883 + Cp4.1LG07g04740.1 Cpe07g00531 531
11 595413 602134 - Cp4.1LG11g01220.1 Cpe11g00107 107
11 613013 623469 - Cp4.1LG11g01240.1 Cpe11g00108 108
8 28582932 28583381 + CrPI670011_08g016120.1 Cre08g1612 1612
8 28592391 28597580 + CrPI670011_08g016130.1 Cre08g1613 1613
8 28619683 28622713 + CrPI670011_08g016140.1 Cre08g1614 1614
8 28625354 28627687 + CrPI670011_08g016150.1 Cre08g1615 1615
2 17804023 17806796 - CsaV3_2G025920.1 Csa02g01872 1872
2 17808687 17812470 - CsaV3_2G025930.1 Csa02g01873 1873
2 17829860 17834863 - CsaV3_2G025940.1 Csa02g01874 1874
2 17843440 17851021 - CsaV3_2G025960.1 Csa02g01876 1876
4 24826494 24832222 + CsaV3_4G035230.1 Csa04g02497 2497
4 24840899 24850635 - CsaV3_4G035260.1 Csa04g02500 2500
4 24865920 24867143 + CsaV3_4G035290.1 Csa04g02503 2503
1 83375235 83389390 - Hsped.01g18480.1 Hepe01g1848 1848
8 15553109 15564844 + Hsped.08g13480.1 Hepe08g1348 1348
8 15641797 15645007 + Hsped.08g13510.1 Hepe08g1351 1351
8 15655258 15659956 + Hsped.08g13520.1 Hepe08g1352 1352
13 40379382 40388975 + Maker00025356 Lcy13g2150 2150
13 40431885 40434571 + Maker00025419 Lcy13g2153 2153
4 22334896 22335627 - Lsi04G014570.1 Lsi04g01457 1457
4 22344929 22358121 + Lsi04G014600.1 Lsi04g01460 1460
4 22377895 22378209 - Lsi04G014640.1 Lsi04g01464 1464
8 23445528 23453915 + Lsi08G015420.1 Lsi08g01542 1542
8 23464377 23470820 + Lsi08G015440.1 Lsi08g01544 1544
8 23501206 23505022 + Lsi08G015450.1 Lsi08g01545 1545
8 23507841 23510244 + Lsi08G015460.1 Lsi08g01546 1546
11 2381181 2394903 - MC11g0302 Mch11g0381 381
1 67343882 67346188 - Sed0015662.1 Sed01g3816 3816
10 16346158 16348648 - Sed0020426.3 Sed10g1155 1155
10 16701443 16713306 - Sed0019663.3 Sed10g1161 1161
13 23184481 23204147 - Sed0026244.1 Sed13g1825 1825
1 112644800 112659628 + Tan0022410.1 Tan01g4668 4668
1 112677275 112678457 - Tan0014212.1 Tan01g4672 4672
2 79607219 79609912 - Tan0004493.2 Tan02g1694 1694
2 79638106 79640378 - Tan0013895.2 Tan02g1695 1695
2 79815465 79834248 - Tan0003458.2 Tan02g1701 1701
18 7062628 7067154 - Vvi18g610 Vvi18g610 610
18 7074317 7076680 - Vvi18g611 Vvi18g611 611
18 7086632 7089964 + Vvi18g612 Vvi18g612 612
18 7098704 7099199 + Vvi18g613 Vvi18g613 613
18 7107576 7146936 + Vvi18g614 Vvi18g614 614
18 7151907 7153160 - Vvi18g615 Vvi18g615 615
18 7156539 7166217 - Vvi18g616 Vvi18g616 616
18 7189862 7220111 - Vvi18g617 Vvi18g617 617
18 7253934 7254270 - Vvi18g618 Vvi18g618 618
18 7260113 7260686 + Vvi18g619 Vvi18g619 619
       

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