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
Vvi18g900 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1894 Cone7ag1806 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla11g00426 Cam11g0477 Cec11g0472 Cco11g0466 Clacu11g0600 Cmu11g0459 Cre11g0941 . . . .
Vvi18g901 . . . . . . . . . Cmo12g00434 . . . Car12g00459 Sed02g1607 . Cpe07g00437 Bhi04g00270 Tan02g1939 Cmetu06g0284 . Hepe10g0662 . Lcy13g2003 Cla08g01509 Cam08g1998 Cec08g1573 Cco08g1710 Clacu08g1688 . Cre08g1471 . . . . . . . Cme03g01974 Blo17g00812 . Bda08g01296 . . . . . . . . Cma12g00488 Cma05g00226 Car05g00188 . . . . . . . . . . . . . . . . . Lsi08g01413 . Chy03g01480 .
Vvi18g902 . . . . . . . . Cmo05g00235 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe05g00079 . Bma05g00109 . . . . . . . Cpe11g00188 . . . . . . . . . . . . . . . . Csa02g02033 . .
Vvi18g903 . . . . . . . . Cmo05g00236 Cmo12g00433 . . . Car12g00457 Sed11g1018 . Cpe07g00436 Bhi04g00268 Tan02g1940 Cmetu03g1115 . Hepe10g0661 . Lcy13g2002 Cla08g01508 Cam08g1996 Cec08g1571 Cco08g1708 Clacu08g1686 . Cre08g1469 Cone4ag1895 Cone7ag1807 . . . . . Cme03g01973 Blo17g00811 Blo18g00823 Bda08g01295 Bda01g01487 Bpe02g01683 Bpe05g00081 Bma01g00769 Bma05g00110 . . . Cma12g00486 Cma05g00227 Car05g00189 . Cpe11g00189 . . . . . . . . . . . . . . . Lsi08g01412 Csa02g02034 Chy03g01479 .
Vvi18g904 . . . . . . . . . . . . . Car12g00456 Sed04g3587 . Cpe07g00435 Bhi04g00266 Tan02g0834 Cmetu01g1929 . Hepe02g0532 . Lcy13g2001 Cla08g01507 Cam08g1995 Cec08g1570 Cco08g1707 Clacu08g1685 . Cre08g1468 Cone4ag1896 Cone7ag1808 Cone17ag1325 Cone20ag0151 . . . Cme03g01972 Blo17g00810 Blo18g00822 Bda08g01294 Bda01g01488 Bpe02g01684 Bpe05g00082 Bma01g00768 . . . . Cma12g00485 . . . . . . . . . . . . . . . . . . . Lsi08g01411 Csa02g02035 Chy03g01478 .
Vvi18g905 . . Bda01g00541 . . Bpe04g00208 Bma04g00202 Bma01g02308 . . Cma01g01891 Cma09g00172 Car01g01475 . . . . . . . . . . . . . . . . . . Cone4ag1897 . Cone17ag1326 . Lsi04g01642 Csa03g04186 Chy04g00532 . . . . . . . . . . Cmo01g01954 Cmo09g00167 . . . Car09g00152 . Cpe02g00141 . . . . . . . Cla05g01961 Cam05g2110 Cec05g2121 Cco05g2174 Clacu05g2099 Cmu05g1976 Cre05g2095 . . . Cme04g00612
Vvi18g906 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g907 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g908 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag1138 Cone8ag1186 . . Lsi04g01643 Csa03g04187 Chy04g00531 . Blo17g00809 . Bda08g01292 . . Bpe05g00083 . Bma05g00111 . . . . . . Car09g00151 . . . . . . . . . Cla05g01960 Cam05g2108 Cec05g2119 Cco05g2172 Clacu05g2097 Cmu05g1974 Cre05g2093 . . . Cme04g00611
Vvi18g909 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 32360312 32363562 + Bda002553.2 Bda01g00541 541
1 50767920 50771359 + Bda003742.1 Bda01g01487 1487
1 50772478 50773619 - Bda003743.1 Bda01g01488 1488
8 52598442 52603337 + Bda030325.1 Bda08g01292 1292
8 52613966 52616314 + Bda030327.1 Bda08g01294 1294
8 52617356 52620403 - Bda030328.1 Bda08g01295 1295
8 52636076 52636855 - Bda030329.1 Bda08g01296 1296
4 6439422 6443349 + XM_039028121.1 Bhi04g00266 266
4 6445817 6453250 - XM_039029401.1 Bhi04g00268 268
4 6457314 6458571 - XM_039029477.1 Bhi04g00270 270
17 26061501 26063283 + BLOR08355 Blo17g00809 809
17 26067385 26069530 + BLOR08356 Blo17g00810 810
17 26069997 26077178 - BLOR08357 Blo17g00811 811
17 26109499 26110401 - BLOR08358 Blo17g00812 812
18 24257999 24259191 + BLOR09310 Blo18g00822 822
18 24259857 24263230 - BLOR09311 Blo18g00823 823
1 7089176 7090320 + Bma000989.1 Bma01g00768 768
1 7091273 7095549 - Bma000990.1 Bma01g00769 769
1 80624404 80627692 - Bma003170.1 Bma01g02308 2308
4 1777269 1780644 - Bma018651.1 Bma04g00202 202
5 3366787 3367566 + Bma020805.1 Bma05g00109 109
5 3371533 3374425 + Bma020806.2 Bma05g00110 110
5 3381371 3383104 - Bma020807.1 Bma05g00111 111
2 19433467 19436638 + Bpe009518.5 Bpe02g01683 1683
2 19437671 19438805 - Bpe025172 Bpe02g01684 1684
4 1423371 1427178 - Bpe014926.1 Bpe04g00208 208
5 1391226 1392008 + Bpe017468.1 Bpe05g00079 79
5 1420755 1424129 + Bpe017470.1 Bpe05g00081 81
5 1424863 1427128 - Bpe025781 Bpe05g00082 82
5 1431859 1433592 - Bpe017471.1 Bpe05g00083 83
5 29576725 29584283 + CaPI482276_05g021080.1 Cam05g2108 2108
5 29589554 29593752 + CaPI482276_05g021100.1 Cam05g2110 2110
8 25737911 25741598 + CaPI482276_08g019950.1 Cam08g1995 1995
8 25744027 25749665 - CaPI482276_08g019960.1 Cam08g1996 1996
8 25759890 25760633 - CaPI482276_08g019980.1 Cam08g1998 1998
11 6272911 6274576 - CaPI482276_11g004770.1 Cam11g0477 477
1 12601805 12604739 - Carg17130-RA Car01g01475 1475
5 988134 994005 + Carg11815-RA Car05g00188 188
5 994898 997858 + Carg11814-RA Car05g00189 189
9 729697 732518 + Carg08735-RA Car09g00151 151
9 732557 735448 + Carg08736-RA Car09g00152 152
12 2884509 2890094 + Carg04064-RA Car12g00456 456
12 2889728 2893659 - Carg04065-RA Car12g00457 457
12 2896964 2899399 - Carg04067-RA Car12g00459 459
5 30543446 30550993 + CcPI632755_05g021720.1 Cco05g2172 2172
5 30557899 30560672 + CcPI632755_05g021740.1 Cco05g2174 2174
8 28424821 28428545 + CcPI632755_08g017070.1 Cco08g1707 1707
8 28430919 28436558 - CcPI632755_08g017080.1 Cco08g1708 1708
8 28446858 28447601 - CcPI632755_08g017100.1 Cco08g1710 1710
11 4936617 4938279 - CcPI632755_11g004660.1 Cco11g0466 466
5 32916940 32924447 + CePI673135_05g021190.1 Cec05g2119 2119
5 32931330 32934110 + CePI673135_05g021210.1 Cec05g2121 2121
8 27289560 27293272 + CePI673135_08g015700.1 Cec08g1570 1570
8 27295762 27301383 - CePI673135_08g015710.1 Cec08g1571 1571
8 27311674 27312417 - CePI673135_08g015730.1 Cec08g1573 1573
11 5065833 5067496 - CePI673135_11g004720.1 Cec11g0472 472
3 17246088 17247169 + Chy3G064580.1 Chy03g01478 1478
3 17249315 17253684 - Chy3G064590.1 Chy03g01479 1479
3 17257563 17258306 - Chy3G064600.1 Chy03g01480 1480
4 5293795 5296126 + Chy4G072490.1 Chy04g00531 531
4 5296910 5300406 + Chy4G072500.1 Chy04g00532 532
5 29787180 29794826 + ClG42_05g0209700.10 Clacu05g2097 2097
5 29801599 29804387 + ClG42_05g0209900.10 Clacu05g2099 2099
8 26482616 26486283 + ClG42_08g0168500.10 Clacu08g1685 1685
8 26488772 26494394 - ClG42_08g0168600.10 Clacu08g1686 1686
8 26504619 26505362 - ClG42_08g0168800.10 Clacu08g1688 1688
11 5754547 5756209 - ClG42_11g0060000.10 Clacu11g0600 600
5 31401441 31410330 + ClCG05G019160.2 Cla05g01960 1960
5 31410887 31420074 + ClCG05G019180.1 Cla05g01961 1961
8 27869358 27873274 + ClCG08G015270.1 Cla08g01507 1507
8 27875649 27882062 - ClCG08G015280.2 Cla08g01508 1508
8 27886711 27893198 - ClCG08G015290.1 Cla08g01509 1509
11 4887120 4888801 - ClCG11G004540.1 Cla11g00426 426
1 12384256 12387374 - CmaCh01G018910.1 Cma01g01891 1891
5 963953 967163 + CmaCh05G002260.1 Cma05g00226 226
5 967933 971927 + CmaCh05G002270.1 Cma05g00227 227
9 730445 740479 + CmaCh09G001720.1 Cma09g00172 172
12 2526463 2529148 + CmaCh12G004850.1 Cma12g00485 485
12 2529116 2535289 - CmaCh12G004860.1 Cma12g00486 486
12 2538169 2538912 - CmaCh12G004880.1 Cma12g00488 488
3 27597781 27601088 + MELO3C010928.2.1 Cme03g01972 1972
3 27602097 27606885 - MELO3C010927.2.1 Cme03g01973 1973
3 27610121 27611135 - MELO3C010926.2.1 Cme03g01974 1974
4 5885025 5887810 + MELO3C003877.2.1 Cme04g00611 611
4 5888584 5891022 + MELO3C003878.2.1 Cme04g00612 612
1 6775644 6780471 + PI0004545.1 Cmetu01g1929 1929
3 1738929 1744983 + PI0002443.2 Cmetu03g1115 1115
6 1458947 1462813 - PI0023511.1 Cmetu06g0284 284
1 13899900 13902986 - CmoCh01G019540.1 Cmo01g01954 1954
5 1005033 1005776 + CmoCh05G002350.1 Cmo05g00235 235
5 1006549 1009614 + CmoCh05G002360.1 Cmo05g00236 236
9 755161 758484 + CmoCh09G001670.1 Cmo09g00167 167
12 2661900 2667243 - CmoCh12G004330.1 Cmo12g00433 433
12 2670123 2670866 - CmoCh12G004340.1 Cmo12g00434 434
5 29514177 29521844 + CmPI595203_05g019740.1 Cmu05g1974 1974
5 29526239 29531405 + CmPI595203_05g019760.1 Cmu05g1976 1976
11 5066376 5068038 - CmPI595203_11g004590.1 Cmu11g0459 459
4 13502004 13503452 + Conep04aG0195500.1 Cone4ag1894 1894
4 13504443 13508201 + Conep04aG0195600.1 Cone4ag1895 1895
4 13508440 13510711 - Conep04aG0195700.1 Cone4ag1896 1896
4 13510843 13514432 - Conep04aG0195800.1 Cone4ag1897 1897
7 11810173 11811552 + Conep07aG0186000.1 Cone7ag1806 1806
7 11812149 11815997 + Conep07aG0186100.1 Cone7ag1807 1807
7 11817172 11818061 - Conep07aG0186200.1 Cone7ag1808 1808
8 10160027 10161655 - Conep08aG0122000.1 Cone8ag1186 1186
12 9120342 9122036 - Conep12aG0117400.1 Cone12ag1138 1138
17 9361594 9363785 - Conep17aG0135700.1 Cone17ag1325 1325
17 9364257 9366882 - Conep17aG0135800.1 Cone17ag1326 1326
20 663697 665552 + Conep20aG0015900.1 Cone20ag0151 151
2 701610 707733 + Cp4.1LG02g07380.1 Cpe02g00141 141
7 2795539 2802033 + Cp4.1LG07g04300.1 Cpe07g00435 435
7 2799821 2806880 - Cp4.1LG07g04390.1 Cpe07g00436 436
7 2810074 2810955 - Cp4.1LG07g04410.1 Cpe07g00437 437
11 1023307 1024050 + Cp4.1LG11g01870.1 Cpe11g00188 188
11 1024844 1029192 + Cp4.1LG11g01860.1 Cpe11g00189 189
5 32829033 32836651 + CrPI670011_05g020930.1 Cre05g2093 2093
5 32843443 32846236 + CrPI670011_05g020950.1 Cre05g2095 2095
8 27551360 27555072 + CrPI670011_08g014680.1 Cre08g1468 1468
8 27557173 27563170 - CrPI670011_08g014690.1 Cre08g1469 1469
8 27573679 27574422 - CrPI670011_08g014710.1 Cre08g1471 1471
11 6702835 6704497 - CrPI670011_11g009410.1 Cre11g0941 941
2 18748069 18750549 + CsaV3_2G028520.1 Csa02g02033 2033
2 18752410 18758425 + CsaV3_2G028530.1 Csa02g02034 2034
2 18758814 18762010 - CsaV3_2G028540.1 Csa02g02035 2035
3 36728775 36732227 - CsaV3_3G044920.1 Csa03g04186 4186
3 36733057 36735481 - CsaV3_3G044930.1 Csa03g04187 4187
2 5338862 5340390 + Hsped.02g05320.1 Hepe02g0532 532
10 8763406 8769312 - Hsped.10g06610.1 Hepe10g0661 661
10 8774287 8775717 - Hsped.10g06620.1 Hepe10g0662 662
13 38992622 38998334 + Maker00033741 Lcy13g2001 2001
13 39000631 39006722 - Maker00033634 Lcy13g2002 2002
13 39010933 39011676 - Maker00033648 Lcy13g2003 2003
4 23897160 23901273 - Lsi04G016420.1 Lsi04g01642 1642
4 23902021 23904948 - Lsi04G016430.1 Lsi04g01643 1643
8 22357588 22361467 + Lsi08G014110.1 Lsi08g01411 1411
8 22363137 22370118 - Lsi08G014120.1 Lsi08g01412 1412
8 22373655 22374398 - Lsi08G014130.1 Lsi08g01413 1413
2 51555241 51559897 - Sed0005299.1 Sed02g1607 1607
4 45180796 45184724 + Sed0006188.1 Sed04g3587 3587
11 25292853 25301221 + Sed0006776.1 Sed11g1018 1018
2 8871414 8875037 + Tan0021336.1 Tan02g0834 834
2 87974895 87976377 + Tan0014449.1 Tan02g1939 1939
2 87984225 87990315 + Tan0009905.1 Tan02g1940 1940
18 10250571 10252002 + Vvi18g900 Vvi18g900 900
18 10260452 10262103 + Vvi18g901 Vvi18g901 901
18 10271070 10272232 + Vvi18g902 Vvi18g902 902
18 10276322 10286829 + Vvi18g903 Vvi18g903 903
18 10288252 10294905 - Vvi18g904 Vvi18g904 904
18 10298370 10306754 - Vvi18g905 Vvi18g905 905
18 10308209 10309560 + Vvi18g906 Vvi18g906 906
18 10309575 10313870 + Vvi18g907 Vvi18g907 907
18 10314904 10317391 - Vvi18g908 Vvi18g908 908
18 10333850 10334042 + Vvi18g909 Vvi18g909 909
       

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