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
Vvi2g112 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g113 . . . Bda08g00480 . . . . . . . . . . . Cpe14g00470 . . . . . . . . . . . . . . . . . Cone6ag0841 Cone9ag0838 . . . Cme07g01578 . . . . . . Bma05g00859 . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00644 Chy07g01166 .
Vvi2g114 . . . . . . . Bma14g00628 . Cmo16g00607 . Cma15g01272 . Car15g01146 . Cpe14g00469 . . . . . . . . Cla07g01415 Cam07g1516 Cec07g1612 Cco07g1572 Clacu07g1504 Cmu07g1474 Cre07g1851 Cone8ag0252 Cone12ag0259 . . . Csa05g00213 Chy09g01286 Cme07g01576 . . Bda07g00464 . . Bpe11g00640 . . . . Cmo15g01341 . Cma16g00554 . . . Cpe13g00117 Bhi12g00158 . . . . . . Cla01g00197 Cam01g0203 Cec01g0197 Cco01g0202 Clacu01g0199 Cmu01g0195 Cre09g2312 Lsi09g00185 Csa04g00645 Chy07g01165 Cme09g01830
Vvi2g115 . . . . . . . . Cmo06g01051 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g116 Blo02g01142 . . Bda08g00478 Bpe05g00684 . . . . . . . . . . . . . . . . . . . Cla07g01417 Cam07g1518 Cec07g1614 Cco07g1574 Clacu07g1506 Cmu07g1476 Cre07g1853 Cone8ag0251 Cone12ag0258 . . . . . . . . . . . . Bma05g00861 . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00647 Chy07g01163 .
Vvi2g117 Blo02g01143 . . Bda08g00477 Bpe05g00685 . . Bma14g00556 . . . Cma15g01274 . Car15g01148 . . . . . . . . . . . . . . . . . . Cone12ag0602 . . . Csa05g00211 Chy09g01288 . . . Bda07g00462 . . Bpe11g00712 Bma05g00866 . . . Cmo15g01343 . . . . . Cpe13g00115 Bhi12g00156 . . Lac11g2008 . . Lcy12g1577 Cla01g00195 Cam01g0201 Cec01g0195 Cco01g0200 Clacu01g0197 Cmu01g0193 Cre09g2314 Lsi09g00183 . . Cme09g01832
Vvi2g118 Blo02g01144 . . Bda08g00475 Bpe05g00686 Bpe07g00075 . Bma14g00630 Cmo06g01049 Cmo16g00604 . . . . . Cpe14g00467 . . . . . . . . Cla07g01418 Cam07g1519 Cec07g1615 Cco07g1575 Clacu07g1507 Cmu07g1477 Cre07g1854 . . Cone6ag0843 Cone9ag0840 . . . . . . Bda07g00461 . . . Bma05g00868 Bma12g00606 . . . . Cma16g00553 Car06g00866 . . . . . . . . . . . . . . . . . . Csa04g00648 Chy07g01162 .
Vvi2g119 . . . . . . Bma07g01682 . . . . Cma15g01275 Car02g00655 Car15g01149 . . Cpe05g00804 . . . . . . . . . . . . . . . . Cone6ag0845 Cone9ag0842 . Csa05g00209 Chy09g01289 . . Blo19g00364 . Bda09g00017 . . . . . Cmo02g00912 Cmo15g01344 . . . . . Cpe13g00114 Bhi12g00152 . . Lac11g2004 Hepe06g1483 . Lcy12g1574 . . . . . . . . . . Cme09g01834
Vvi2g120 Blo02g01146 . . Bda08g00471 Bpe05g00689 . . . . Cmo16g00602 . . . . . Cpe14g00466 . . . . . . . . Cla07g01419 Cam07g1520 Cec07g1616 Cco07g1576 Clacu07g1508 Cmu07g1478 Cre07g1855 . . Cone6ag0846 Cone9ag0843 . . . . . . . . . . Bma05g00871 . . . . . Cma16g00551 . . . . . . . . . . . . . . . . . . . Csa04g00649 Chy07g01161 .
Vvi2g121 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 5918731 5920008 + Bda025562.1 Bda07g00461 461
7 5920369 5921298 - Bda025563.1 Bda07g00462 462
7 5923462 5925365 - Bda025565.1 Bda07g00464 464
8 4904202 4904720 + Bda024923.1 Bda08g00471 471
8 4925010 4926198 + Bda024926.1 Bda08g00475 475
8 4932746 4934363 - Bda024928.1 Bda08g00477 477
8 4935466 4940064 - Bda024929.1 Bda08g00478 478
8 4943171 4945476 - Bda024931.1 Bda08g00480 480
9 314918 316968 + Bda034070 Bda09g00017 17
12 4611964 4614736 + XM_039019446.1 Bhi12g00152 152
12 4623868 4626014 - XM_039020333.1 Bhi12g00156 156
12 4702596 4709719 - XM_039050777.1 Bhi12g00158 158
2 42857589 42870039 + BLOR10872 Blo02g01142 1142
2 42873047 42880556 + BLOR10873 Blo02g01143 1143
2 42881613 42882844 - BLOR10874 Blo02g01144 1144
2 42950773 42951274 - BLOR10876 Blo02g01146 1146
19 23352264 23355009 - BLOR09707 Blo19g00364 364
5 46131362 46133608 + Bma021978.1 Bma05g00859 859
5 46155237 46164571 + Bma021980.1 Bma05g00861 861
5 46208805 46211067 + Bma021985.1 Bma05g00866 866
5 46286951 46288135 - Bma021988.2 Bma05g00868 868
5 46325312 46325794 - Bma031212 Bma05g00871 871
7 52385057 52387345 - Bma031417 Bma07g01682 1682
12 27387142 27388300 + Bma007782.1 Bma12g00606 606
14 5985010 5987046 - Bma010987.1 Bma14g00556 556
14 6766560 6768749 + Bma011070.1 Bma14g00628 628
14 6773024 6774295 - Bma011072.4 Bma14g00630 630
5 20468127 20472664 + Bpe018097.1 Bpe05g00684 684
5 20479480 20481125 + Bpe018098.1 Bpe05g00685 685
5 20483289 20484543 - Bpe018099.1 Bpe05g00686 686
5 20513603 20514088 - Bpe018102.1 Bpe05g00689 689
7 549080 550236 - Bpe020887.2 Bpe07g00075 75
11 4935938 4937810 - Bpe003998.5 Bpe11g00640 640
11 5492428 5494641 + Bpe004069.1 Bpe11g00712 712
1 2314295 2316067 - CaPI482276_01g002010.1 Cam01g0201 201
1 2325131 2330705 - CaPI482276_01g002030.1 Cam01g0203 203
7 29770550 29780657 + CaPI482276_07g015160.1 Cam07g1516 1516
7 29789095 29796666 + CaPI482276_07g015180.1 Cam07g1518 1518
7 29797360 29799108 - CaPI482276_07g015190.1 Cam07g1519 1519
7 29808520 29809809 - CaPI482276_07g015200.1 Cam07g1520 1520
2 4919653 4921850 - Carg08568-RA Car02g00655 655
6 6752759 6753897 + Carg20884-RA Car06g00866 866
15 9028798 9032048 + Carg21270-RA Car15g01146 1146
15 9037609 9038779 + Carg21272-RA Car15g01148 1148
15 9039463 9041928 - Carg21273-RA Car15g01149 1149
1 1903203 1904979 - CcPI632755_01g002000.1 Cco01g0200 200
1 1915953 1921819 - CcPI632755_01g002020.1 Cco01g0202 202
7 29714869 29725124 + CcPI632755_07g015720.1 Cco07g1572 1572
7 29733502 29741189 + CcPI632755_07g015740.1 Cco07g1574 1574
7 29741805 29743541 - CcPI632755_07g015750.1 Cco07g1575 1575
7 29753633 29755486 - CcPI632755_07g015760.1 Cco07g1576 1576
1 1895214 1898175 - CePI673135_01g001950.1 Cec01g0195 195
1 1908796 1914312 - CePI673135_01g001970.1 Cec01g0197 197
7 31629464 31639125 + CePI673135_07g016120.1 Cec07g1612 1612
7 31647394 31654985 + CePI673135_07g016140.1 Cec07g1614 1614
7 31655679 31657436 - CePI673135_07g016150.1 Cec07g1615 1615
7 31667818 31669109 - CePI673135_07g016160.1 Cec07g1616 1616
7 16515840 16516724 + Chy7G139910.1 Chy07g01161 1161
7 16523191 16524920 + Chy7G139920.1 Chy07g01162 1162
7 16527708 16531956 - Chy7G139930.1 Chy07g01163 1163
7 16538336 16544616 - Chy7G139950.1 Chy07g01165 1165
7 16547901 16550153 - Chy7G139960.1 Chy07g01166 1166
9 14848406 14853135 + Chy9G170020.1 Chy09g01286 1286
9 14859790 14864488 + Chy9G170040.1 Chy09g01288 1288
9 14865450 14867732 - Chy9G170050.1 Chy09g01289 1289
1 1933682 1935453 - ClG42_01g0019700.10 Clacu01g0197 197
1 1944666 1950150 - ClG42_01g0019900.10 Clacu01g0199 199
7 29628449 29638552 + ClG42_07g0150400.10 Clacu07g1504 1504
7 29646976 29654512 + ClG42_07g0150600.10 Clacu07g1506 1506
7 29654990 29656737 - ClG42_07g0150700.10 Clacu07g1507 1507
7 29667255 29668592 - ClG42_07g0150800.10 Clacu07g1508 1508
1 1944317 1947253 - ClCG01G001980.2 Cla01g00195 195
1 1957470 1963222 - ClCG01G002000.1 Cla01g00197 197
7 31340208 31345433 + ClCG07G014920.1 Cla07g01415 1415
7 31353402 31359023 + ClCG07G014940.2 Cla07g01417 1417
7 31361479 31363226 - ClCG07G014950.1 Cla07g01418 1418
7 31373748 31375157 - ClCG07G014960.1 Cla07g01419 1419
15 8069893 8071737 + CmaCh15G012720.1 Cma15g01272 1272
15 8076264 8077535 + CmaCh15G012740.1 Cma15g01274 1274
15 8077974 8081335 - CmaCh15G012750.1 Cma15g01275 1275
16 2835858 2836454 + CmaCh16G005510.1 Cma16g00551 551
16 2839755 2841702 + CmaCh16G005530.1 Cma16g00553 553
16 2844942 2851531 - CmaCh16G005540.1 Cma16g00554 554
7 21564350 21570534 - MELO3C016305.2.1 Cme07g01576 1576
7 21597180 21599822 - MELO3C016306.2.1 Cme07g01578 1578
9 22586779 22591881 + MELO3C005741.2.1 Cme09g01830 1830
9 22596985 22599275 + MELO3C005743.2.1 Cme09g01832 1832
9 22602634 22605297 - MELO3C005745.2.1 Cme09g01834 1834
2 5613586 5617107 - CmoCh02G009120.1 Cmo02g00912 912
6 8163263 8164782 + CmoCh06G010490.1 Cmo06g01049 1049
6 8175871 8177340 - CmoCh06G010510.1 Cmo06g01051 1051
15 9180623 9183979 + CmoCh15G013410.1 Cmo15g01341 1341
15 9198736 9199980 + CmoCh15G013430.1 Cmo15g01343 1343
15 9200550 9203013 - CmoCh15G013440.1 Cmo15g01344 1344
16 2939824 2940667 + CmoCh16G006020.1 Cmo16g00602 602
16 2944189 2946378 + CmoCh16G006040.1 Cmo16g00604 604
16 2949630 2968808 - CmoCh16G006070.1 Cmo16g00607 607
1 1885649 1888582 - CmPI595203_01g001930.1 Cmu01g0193 193
1 1897818 1903300 - CmPI595203_01g001950.1 Cmu01g0195 195
7 29880232 29890363 + CmPI595203_07g014740.1 Cmu07g1474 1474
7 29898785 29906106 + CmPI595203_07g014760.1 Cmu07g1476 1476
7 29906799 29908546 - CmPI595203_07g014770.1 Cmu07g1477 1477
7 29918998 29920335 - CmPI595203_07g014780.1 Cmu07g1478 1478
6 4298018 4299963 - Conep06aG0086700.1 Cone6ag0841 841
6 4302580 4304243 - Conep06aG0086900.1 Cone6ag0843 843
6 4310842 4313863 - Conep06aG0087100.1 Cone6ag0845 845
6 4320807 4321728 - Conep06aG0087200.1 Cone6ag0846 846
8 1436305 1438196 - Conep08aG0026100.1 Cone8ag0251 251
8 1441460 1444101 - Conep08aG0026200.1 Cone8ag0252 252
9 4108447 4109155 - Conep09aG0085800.1 Cone9ag0838 838
9 4112644 4114122 - Conep09aG0086000.1 Cone9ag0840 840
9 4116127 4117943 - Conep09aG0086200.1 Cone9ag0842 842
9 4120168 4120764 - Conep09aG0086300.1 Cone9ag0843 843
12 1363560 1366592 - Conep12aG0026300.1 Cone12ag0258 258
12 1367915 1371949 - Conep12aG0026400.1 Cone12ag0259 259
12 5344233 5349567 + Conep12aG0062300.1 Cone12ag0602 602
5 4986967 4990496 + Cp4.1LG05g08000.1 Cpe05g00804 804
13 822107 824539 + Cp4.1LG13g01120.1 Cpe13g00114 114
13 825295 826212 - Cp4.1LG13g01210.1 Cpe13g00115 115
13 831889 835230 - Cp4.1LG13g01180.1 Cpe13g00117 117
14 2944284 2944633 + Cp4.1LG14g02540.1 Cpe14g00466 466
14 2948856 2950335 + Cp4.1LG14g02520.1 Cpe14g00467 467
14 2953668 2958655 - Cp4.1LG14g02500.1 Cpe14g00469 469
14 2959119 2962362 - Cp4.1LG14g02460.1 Cpe14g00470 470
7 33876765 33887030 + CrPI670011_07g018510.1 Cre07g1851 1851
7 33895622 33903440 + CrPI670011_07g018530.1 Cre07g1853 1853
7 33903920 33905664 - CrPI670011_07g018540.1 Cre07g1854 1854
7 33916003 33917415 - CrPI670011_07g018550.1 Cre07g1855 1855
9 42406741 42412379 + CrPI670011_09g023120.1 Cre09g2312 2312
9 42423071 42426018 + CrPI670011_09g023140.1 Cre09g2314 2314
4 4306307 4309079 + CsaV3_4G006440.1 Csa04g00644 644
4 4311522 4318077 + CsaV3_4G006450.1 Csa04g00645 645
4 4322551 4332383 + CsaV3_4G006470.1 Csa04g00647 647
4 4328507 4332383 - CsaV3_4G006480.1 Csa04g00648 648
4 4337274 4338943 - CsaV3_4G006490.1 Csa04g00649 649
5 1264617 1267363 + CsaV3_5G002090.1 Csa05g00209 209
5 1270718 1272824 - CsaV3_5G002110.1 Csa05g00211 211
5 1279383 1284646 - CsaV3_5G002130.1 Csa05g00213 213
6 65421822 65424661 + Hsped.06g14830.1 Hepe06g1483 1483
11 35575276 35577994 + Lag0032642.1 Lac11g2004 2004
11 35594078 35595689 - Lag0032646.1 Lac11g2008 2008
12 35823659 35826789 + Maker00029468 Lcy12g1574 1574
12 35836890 35839019 - Maker00029412 Lcy12g1577 1577
9 1908517 1910691 - Lsi09G001830.1 Lsi09g00183 183
9 1925184 1932148 - Lsi09G001850.1 Lsi09g00185 185
2 1168948 1169486 - Vvi2g112 Vvi2g112 112
2 1184187 1187119 + Vvi2g113 Vvi2g113 113
2 1193760 1198827 + Vvi2g114 Vvi2g114 114
2 1208152 1209559 + Vvi2g115 Vvi2g115 115
2 1211764 1218586 + Vvi2g116 Vvi2g116 116
2 1219224 1228009 + Vvi2g117 Vvi2g117 117
2 1228313 1229702 - Vvi2g118 Vvi2g118 118
2 1230450 1235851 - Vvi2g119 Vvi2g119 119
2 1239609 1240527 - Vvi2g120 Vvi2g120 120
2 1244908 1246172 - Vvi2g121 Vvi2g121 121
       

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