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
Vvi17g556 . . . . . . Bma06g00170 . . . Cma10g00190 Cma11g00144 Car10g00180 Car11g00150 Sed08g0214 . Cpe04g01500 Bhi02g00326 Tan09g2124 Cmetu02g0201 . Hepe09g0121 . . Cla06g01592 Cam06g1765 Cec06g1818 Cco06g1824 Clacu06g1728 Cmu06g1672 Cre06g2488 Cone2ag0844 Cone16ag0171 . . . . . . . . . Bda14g00853 . . . . . Cmo10g00207 Cmo11g00165 . . . . . Cpe18g00795 . . . . . . . . . . . . . . Lsi06g01465 Csa01g00233 Chy02g02499 Cme02g01885
Vvi17g557 . . . Bda15g00603 Bpe12g00547 . . . . . Cma10g00191 Cma11g00143 Car10g00182 Car11g00151 . . . Bhi02g00318 . . . . . . Cla06g01591 . . . . . . Cone2ag0843 . . . . . . . Blo13g00009 . . . . . . Bma08g00221 . Cmo10g00208 Cmo11g00166 . . . . . Cpe18g00794 . . . . . . . . . . . . . . Lsi06g01463 Csa01g00234 Chy02g02498 Cme02g01884
Vvi17g558 . . Bda06g00544 . Bpe12g00545 . . Bma12g00996 . . Cma10g00192 Cma11g00142 Car10g00183 Car11g00152 . . . Bhi02g00315 Tan09g2120 . . Hepe09g0117 . . Cla06g01590 Cam06g1762 Cec06g1815 Cco06g1821 Clacu06g1725 Cmu06g1669 Cre06g2485 . . . . . . . . Blo13g00007 Blo15g00310 . . Bpe07g00781 . . Bma08g00222 . . Cmo11g00167 . . . . . . . . . . . . . . . . . . . . Lsi06g01462 Csa01g00236 Chy02g02496 Cme02g01883
Vvi17g559 Blo04g00772 . . . . . . . . . Cma10g00194 . Car10g00184 Car11g00153 Sed08g0217 . Cpe04g01498 Bhi02g00313 Tan09g2119 Cmetu02g1781 . Hepe09g0116 . . . . . . . . . Cone2ag0842 . . . . . . . . . . Bda14g00854 . Bpe15g00600 . . . Cmo10g00209 Cmo11g00168 . . . . . Cpe18g00792 . . . . . . . . . . . . . . . Csa01g00237 Chy02g02495 Cme02g01881
Vvi17g560 . . . Bda15g00606 Bpe12g00544 . . . . . Cma10g00195 . Car10g00185 . Sed08g0218 . . Bhi02g00312 Tan09g2118 Cmetu06g2001 . Hepe09g0115 . . Cla06g01589 Cam06g1758 Cec06g1814 Cco06g1817 Clacu06g1724 Cmu06g1667 Cre06g2481 . . Cone13ag0068 Cone19ag0069 . . . . Blo13g00006 . . . . . . Bma08g00223 . Cmo10g00210 . . . . . . Cpe18g00790 . . . . . . . . . . . . . . Lsi06g01461 Csa01g00238 Chy02g02494 Cme02g01880
Vvi17g561 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g562 . . . . Bpe12g00543 . . . Cmo13g01192 . Cma10g00196 Cma11g00141 Car10g00186 Car11g00154 . Cpe20g00016 Cpe04g01497 . . . . . . . Cla06g01588 Cam06g1757 Cec06g1813 Cco06g1816 Clacu06g1723 Cmu06g1666 Cre06g2480 . . . . Lsi02g00077 Csa01g00554 Chy12g01536 Cme12g01987 . . . . . . . Bma08g00224 Sed02g0836 Cmo10g00211 Cmo11g00169 Cma13g01138 . Car13g00968 . . Cpe18g00789 Bhi08g01160 Tan05g2435 Cmetu12g0332 Lac10g0082 Hepe07g2505 . . Cla04g01194 Cam04g1252 Cec01g1763 Cco01g1810 Clacu04g1282 Cmu04g1258 Cre01g1552 Lsi06g01460 Csa01g00239 Chy02g02493 Cme02g01879
Vvi17g563 . . . Bda15g00607 Bpe12g00542 . . . . . . Cma11g00140 . Car11g00155 . . Cpe04g01496 . . . . . . . Cla06g01587 Cam06g1756 Cec06g1812 Cco06g1815 Clacu06g1722 Cmu06g1665 Cre06g2479 . . . . . . . . Blo13g00005 . . . . . . Bma08g00225 . . Cmo11g00171 . . . . . . . . . . . . . . . . . . . . . Csa01g00240 Chy02g02492 Cme02g01878
Vvi17g564 . . . . . Bpe13g00296 Bma06g00169 . . . . . . . . . . . . . . . . . . . . . . . . Cone2ag0841 . . . Lsi02g00079 Csa01g00557 Chy12g01535 Cme12g01985 . . Bda11g01704 . . . . . Sed08g2077 . . . . . . . . Bhi08g01153 Tan05g2433 Cmetu12g0183 . Hepe07g2503 . . Cla04g01192 Cam04g1249 Cec01g1760 Cco01g1807 Clacu04g1279 Cmu04g1256 Cre01g1549 . . . .
Vvi17g565 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00080 Csa01g00558 Chy12g01534 Cme12g01984 . . . . . . . . Sed01g2340 . . . . Car13g00970 . . . Bhi08g01149 Tan05g2432 Cmetu12g1892 . Hepe07g2502 . . Cla04g01191 . . Cco01g1805 Clacu04g1277 . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 7717519 7718757 + Bda023802.1 Bda06g00544 544
11 51272494 51274566 + Bda008602.1 Bda11g01704 1704
14 6571257 6573017 + Bda027626.1 Bda14g00853 853
14 6573385 6575336 - Bda027627.1 Bda14g00854 854
15 9246653 9247271 + Bda012447.1 Bda15g00603 603
15 9252428 9263751 + Bda033305 Bda15g00606 606
15 9262375 9266067 - Bda012449.1 Bda15g00607 607
2 5914978 5919147 - XM_039024316.1 Bhi02g00312 312
2 5939550 5941309 + XM_039023666.1 Bhi02g00313 313
2 5942549 5945339 + XM_039023934.1 Bhi02g00315 315
2 5949099 5955458 - XM_039023679.1 Bhi02g00318 318
2 5979750 5982603 - XM_039024680.1 Bhi02g00326 326
8 36269152 36273942 - XM_039038892.1 Bhi08g01149 1149
8 36275895 36280912 - XM_039039307.1 Bhi08g01153 1153
8 36498204 36500492 - XM_039039680.1 Bhi08g01160 1160
4 7585181 7587994 - BLOR13684 Blo04g00772 772
13 50985 54460 + BLOR05286 Blo13g00005 5
13 63456 65463 - BLOR05287 Blo13g00006 6
13 71954 73180 + BLOR05288 Blo13g00007 7
13 92272 93490 - BLOR05290 Blo13g00009 9
15 3529421 3530659 - BLOR06704 Blo15g00310 310
6 2165909 2167903 - Bma022784.1 Bma06g00169 169
6 2170744 2174832 - Bma022785.1 Bma06g00170 170
8 2768687 2770204 + Bma031429 Bma08g00221 221
8 2770457 2771683 - Bma027232.1 Bma08g00222 222
8 2774113 2776268 + Bma031430 Bma08g00223 223
8 2777739 2779363 + Bma027233.1 Bma08g00224 224
8 2782055 2785869 - Bma027234.1 Bma08g00225 225
12 42032798 42034018 + Bma008343.1 Bma12g00996 996
7 14263812 14265050 + Bpe021626.1 Bpe07g00781 781
12 11284229 11288019 + Bpe005808.1 Bpe12g00542 542
12 11292910 11294534 - Bpe005809.1 Bpe12g00543 543
12 11296367 11298597 - Bpe024896 Bpe12g00544 544
12 11301039 11302265 + Bpe005810.2 Bpe12g00545 545
12 11306859 11307567 - Bpe005811.1 Bpe12g00547 547
13 10811459 10814690 + Bpe006422.1 Bpe13g00296 296
15 16912378 16914337 + Bpe001534.1 Bpe15g00600 600
4 26467728 26477421 - CaPI482276_04g012490.1 Cam04g1249 1249
4 26493488 26495253 - CaPI482276_04g012520.1 Cam04g1252 1252
6 28796807 28799423 + CaPI482276_06g017560.1 Cam06g1756 1756
6 28802845 28805010 - CaPI482276_06g017570.1 Cam06g1757 1757
6 28809024 28811299 - CaPI482276_06g017580.1 Cam06g1758 1758
6 28820411 28825804 + CaPI482276_06g017620.1 Cam06g1762 1762
6 28834061 28836283 - CaPI482276_06g017650.1 Cam06g1765 1765
10 878468 880836 + Carg17964-RA Car10g00180 180
10 883472 885358 + Carg17962-RA Car10g00182 182
10 886479 887717 - Carg17961-RA Car10g00183 183
10 888731 890550 - Carg17960-RA Car10g00184 184
10 891543 893059 + Carg17959-RA Car10g00185 185
10 895188 898035 + Carg17958-RA Car10g00186 186
11 847936 849592 + Carg18187-RA Car11g00150 150
11 850641 851519 + Carg18188-RA Car11g00151 151
11 851954 855084 - Carg18189-RA Car11g00152 152
11 855730 857299 - Carg18190-RA Car11g00153 153
11 858029 860039 + Carg18191-RA Car11g00154 154
11 862175 866132 - Carg18192-RA Car11g00155 155
13 9709734 9711401 + Carg04703-RA Car13g00968 968
13 9716248 9720215 + Carg04701-RA Car13g00970 970
1 30724035 30727504 - CcPI632755_01g018050.1 Cco01g1805 1805
1 30730226 30734238 - CcPI632755_01g018070.1 Cco01g1807 1807
1 30753520 30755341 - CcPI632755_01g018100.1 Cco01g1810 1810
6 28502607 28505637 + CcPI632755_06g018150.1 Cco06g1815 1815
6 28508718 28510881 - CcPI632755_06g018160.1 Cco06g1816 1816
6 28514935 28517191 - CcPI632755_06g018170.1 Cco06g1817 1817
6 28529441 28530679 + CcPI632755_06g018210.1 Cco06g1821 1821
6 28539103 28541259 - CcPI632755_06g018240.1 Cco06g1824 1824
1 32147733 32157616 - CePI673135_01g017600.1 Cec01g1760 1760
1 32174997 32176815 - CePI673135_01g017630.1 Cec01g1763 1763
6 31571525 31574579 + CePI673135_06g018120.1 Cec06g1812 1812
6 31577676 31579842 - CePI673135_06g018130.1 Cec06g1813 1813
6 31583740 31586098 - CePI673135_06g018140.1 Cec06g1814 1814
6 31592642 31598079 + CePI673135_06g018150.1 Cec06g1815 1815
6 31606472 31608696 - CePI673135_06g018180.1 Cec06g1818 1818
2 28423387 28426036 + Chy2G047590.1 Chy02g02492 2492
2 28429186 28431128 - Chy2G047600.1 Chy02g02493 2493
2 28434143 28436400 - Chy2G047610.1 Chy02g02494 2494
2 28438123 28439616 + Chy2G047620.1 Chy02g02495 2495
2 28441289 28442524 + Chy2G047630.1 Chy02g02496 2496
2 28445422 28447337 - Chy2G047650.1 Chy02g02498 2498
2 28448336 28451537 - Chy2G047660.1 Chy02g02499 2499
12 19058921 19062037 - Chy12G221340.1 Chy12g01534 1534
12 19063862 19070100 - Chy12G221350.1 Chy12g01535 1535
12 19078147 19079989 - Chy12G221360.1 Chy12g01536 1536
4 26822837 26826305 - ClG42_04g0127700.10 Clacu04g1277 1277
4 26829178 26832860 - ClG42_04g0127900.10 Clacu04g1279 1279
4 26848490 26850296 - ClG42_04g0128200.10 Clacu04g1282 1282
6 27850488 27853192 + ClG42_06g0172200.10 Clacu06g1722 1722
6 27856622 27858785 - ClG42_06g0172300.10 Clacu06g1723 1723
6 27862730 27865033 - ClG42_06g0172400.10 Clacu06g1724 1724
6 27875534 27880892 + ClG42_06g0172500.10 Clacu06g1725 1725
6 27889397 27891591 - ClG42_06g0172800.10 Clacu06g1728 1728
4 27065147 27070793 - ClCG04G012180.2 Cla04g01191 1191
4 27072862 27076822 - ClCG04G012190.2 Cla04g01192 1192
4 27094213 27096896 - ClCG04G012210.2 Cla04g01194 1194
6 29411422 29414458 + ClCG06G016150.1 Cla06g01587 1587
6 29416844 29419756 - ClCG06G016160.2 Cla06g01588 1588
6 29423673 29425976 - ClCG06G016170.2 Cla06g01589 1589
6 29436422 29442496 + ClCG06G016180.2 Cla06g01590 1590
6 29442749 29448243 - ClCG06G016200.1 Cla06g01591 1591
6 29450031 29452605 - ClCG06G016210.1 Cla06g01592 1592
10 865735 870638 + CmaCh10G001900.1 Cma10g00190 190
10 870899 872785 + CmaCh10G001910.1 Cma10g00191 191
10 873816 875054 - CmaCh10G001920.1 Cma10g00192 192
10 876448 878285 - CmaCh10G001940.1 Cma10g00194 194
10 878836 880553 + CmaCh10G001950.1 Cma10g00195 195
10 882611 885624 + CmaCh10G001960.1 Cma10g00196 196
11 752212 756501 + CmaCh11G001400.1 Cma11g00140 140
11 757756 760782 - CmaCh11G001410.1 Cma11g00141 141
11 761504 766838 + CmaCh11G001420.1 Cma11g00142 142
11 765229 768191 - CmaCh11G001430.1 Cma11g00143 143
11 769297 770944 - CmaCh11G001440.1 Cma11g00144 144
13 8406675 8408886 + CmaCh13G011380.1 Cma13g01138 1138
2 25350691 25353739 + MELO3C017179.2.1 Cme02g01878 1878
2 25356039 25358685 - MELO3C017178.2.1 Cme02g01879 1879
2 25361569 25363302 - MELO3C017177.2.1 Cme02g01880 1880
2 25364310 25366427 + MELO3C017176.2.1 Cme02g01881 1881
2 25367975 25369297 + MELO3C017175.2.1 Cme02g01883 1883
2 25372623 25373898 - MELO3C017174.2.1 Cme02g01884 1884
2 25375740 25378458 - MELO3C017173.2.1 Cme02g01885 1885
12 25598671 25603234 - MELO3C001991.2.1 Cme12g01984 1984
12 25604424 25608124 - MELO3C001989.2.1 Cme12g01985 1985
12 25615555 25617940 - MELO3C001987.2.1 Cme12g01987 1987
2 23688616 23690863 + PI0023725.1 Cmetu02g0201 201
2 23702746 23704232 - PI0012758.1 Cmetu02g1781 1781
6 14818677 14823782 - PI0015386.1 Cmetu06g2001 2001
12 511638 516201 + PI0017177.1 Cmetu12g0183 183
12 498870 501876 + PI0014555.1 Cmetu12g0332 332
12 516900 521913 + PI0000350.1 Cmetu12g1892 1892
10 926403 931319 + CmoCh10G002070.1 Cmo10g00207 207
10 931570 933456 + CmoCh10G002080.1 Cmo10g00208 208
10 934166 938659 - CmoCh10G002090.1 Cmo10g00209 209
10 939620 941108 + CmoCh10G002100.1 Cmo10g00210 210
10 943198 945710 + CmoCh10G002110.1 Cmo10g00211 211
11 817216 818317 + CmoCh11G001650.1 Cmo11g00165 165
11 818859 819737 + CmoCh11G001660.1 Cmo11g00166 166
11 820460 821698 - CmoCh11G001670.1 Cmo11g00167 167
11 823871 825700 - CmoCh11G001680.1 Cmo11g00168 168
11 826368 829467 + CmoCh11G001690.1 Cmo11g00169 169
11 830781 834409 - CmoCh11G001710.1 Cmo11g00171 171
13 9426937 9429111 + CmoCh13G011920.1 Cmo13g01192 1192
4 27004751 27014444 - CmPI595203_04g012560.1 Cmu04g1256 1256
4 27030053 27031859 - CmPI595203_04g012580.1 Cmu04g1258 1258
6 27758787 27761491 + CmPI595203_06g016650.1 Cmu06g1665 1665
6 27764825 27766988 - CmPI595203_06g016660.1 Cmu06g1666 1666
6 27770933 27773238 - CmPI595203_06g016670.1 Cmu06g1667 1667
6 27783743 27789102 + CmPI595203_06g016690.1 Cmu06g1669 1669
6 27797609 27799803 - CmPI595203_06g016720.1 Cmu06g1672 1672
2 34405217 34407557 - Conep02aG0187100.1 Cone2ag0841 841
2 34427363 34429379 + Conep02aG0187200.1 Cone2ag0842 842
2 34429850 34431383 - Conep02aG0187300.1 Cone2ag0843 843
2 34432196 34434076 - Conep02aG0187400.1 Cone2ag0844 844
13 422286 424015 - Conep13aG0007200.1 Cone13ag0068 68
16 1087585 1089459 + Conep16aG0017500.1 Cone16ag0171 171
19 430049 431791 - Conep19aG0007400.1 Cone19ag0069 69
4 11846726 11851094 + Cp4.1LG04g14880.1 Cpe04g01496 1496
4 11852184 11855292 - Cp4.1LG04g14900.1 Cpe04g01497 1497
4 11855921 11857433 + Cp4.1LG04g14890.1 Cpe04g01498 1498
4 11863618 11867305 - Cp4.1LG04g14960.1 Cpe04g01500 1500
18 7448845 7451853 - Cp4.1LG18g07900.1 Cpe18g00789 789
18 7453350 7455274 - Cp4.1LG18g07950.1 Cpe18g00790 790
18 7455695 7463132 + Cp4.1LG18g07800.1 Cpe18g00792 792
18 7463360 7464581 - Cp4.1LG18g07970.1 Cpe18g00794 794
18 7465716 7468178 - Cp4.1LG18g07910.1 Cpe18g00795 795
20 95532 98013 - Cp4.1LG20g00260.1 Cpe20g00016 16
1 28671527 28680966 - CrPI670011_01g015490.1 Cre01g1549 1549
1 28699040 28700852 - CrPI670011_01g015520.1 Cre01g1552 1552
6 32569303 32572037 + CrPI670011_06g024790.1 Cre06g2479 2479
6 32575422 32577587 - CrPI670011_06g024800.1 Cre06g2480 2480
6 32581670 32583794 - CrPI670011_06g024810.1 Cre06g2481 2481
6 32596331 32597569 + CrPI670011_06g024850.1 Cre06g2485 2485
6 32606079 32608297 - CrPI670011_06g024880.1 Cre06g2488 2488
1 1494695 1497065 + CsaV3_1G002330.1 Csa01g00233 233
1 1500865 1503209 + CsaV3_1G002340.1 Csa01g00234 234
1 1503785 1506265 - CsaV3_1G002350.1 Csa01g00236 236
1 1506718 1509062 - CsaV3_1G002370.1 Csa01g00237 237
1 1510045 1512624 + CsaV3_1G002380.1 Csa01g00238 238
1 1515388 1518837 + CsaV3_1G002390.1 Csa01g00239 239
1 1520624 1523912 - CsaV3_1G002400.1 Csa01g00240 240
1 3605166 3608682 + CsaV3_1G005540.1 Csa01g00554 554
1 3617749 3620792 + CsaV3_1G005570.1 Csa01g00557 557
1 3621937 3626203 + CsaV3_1G005580.1 Csa01g00558 558
7 69351187 69356293 - Hsped.07g25020.1 Hepe07g2502 2502
7 69359253 69370276 - Hsped.07g25030.1 Hepe07g2503 2503
7 69383785 69385438 - Hsped.07g25050.1 Hepe07g2505 2505
9 914913 917607 - Hsped.09g01150.1 Hepe09g0115 115
9 920619 922377 + Hsped.09g01160.1 Hepe09g0116 116
9 924451 927369 + Hsped.09g01170.1 Hepe09g0117 117
9 938414 941103 - Hsped.09g01210.1 Hepe09g0121 121
10 647831 649610 + Lag0024127.1 Lac10g0082 82
2 668006 670737 + Lsi02G000770.1 Lsi02g00077 77
2 682832 687574 + Lsi02G000790.1 Lsi02g00079 79
2 690558 693797 + Lsi02G000800.1 Lsi02g00080 80
6 25140536 25143251 - Lsi06G014600.1 Lsi06g01460 1460
6 25148195 25152936 - Lsi06G014610.1 Lsi06g01461 1461
6 25154672 25165106 + Lsi06G014620.1 Lsi06g01462 1462
6 25165708 25167573 - Lsi06G014630.1 Lsi06g01463 1463
6 25171703 25175674 - Lsi06G014650.1 Lsi06g01465 1465
1 17653766 17659224 - Sed0017917.1 Sed01g2340 2340
2 45968421 45970992 - Sed0004715.1 Sed02g0836 836
8 1252526 1255327 + Sed0006743.1 Sed08g0214 214
8 1265119 1267380 - Sed0020269.1 Sed08g0217 217
8 1269594 1272673 + Sed0012156.1 Sed08g0218 218
8 34958255 34961118 + Sed0011950.2 Sed08g2077 2077
5 75465033 75468680 - Tan0021044.1 Tan05g2432 2432
5 75475478 75480108 - Tan0002410.1 Tan05g2433 2433
5 75498270 75500570 - Tan0005445.1 Tan05g2435 2435
9 71484012 71485939 - Tan0015640.1 Tan09g2118 2118
9 71494800 71496813 + Tan0019951.1 Tan09g2119 2119
9 71497208 71500391 + Tan0017304.1 Tan09g2120 2120
9 71508051 71511343 - Tan0005345.1 Tan09g2124 2124
17 6795548 6797879 + Vvi17g556 Vvi17g556 556
17 6799122 6802702 + Vvi17g557 Vvi17g557 557
17 6803426 6806485 - Vvi17g558 Vvi17g558 558
17 6820942 6822833 + Vvi17g559 Vvi17g559 559
17 6825920 6827723 + Vvi17g560 Vvi17g560 560
17 6831713 6832614 - Vvi17g561 Vvi17g561 561
17 6845878 6853538 + Vvi17g562 Vvi17g562 562
17 6854109 6859764 - Vvi17g563 Vvi17g563 563
17 6871144 6878292 + Vvi17g564 Vvi17g564 564
17 6879839 6886156 + Vvi17g565 Vvi17g565 565
       

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