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
Vvi4g602 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g603 . . Bda01g00655 Bda03g00111 . Bpe02g00527 . . . . . . Car09g00344 . . . Cpe06g00283 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe04g00095 . . Sed13g1949 . Cmo09g00397 Cma09g00396 . . . . . Bhi09g03040 Tan01g3532 Cmetu07g2214 . Hepe01g1947 Mch11g0482 . . . . . . . . . . . Cme07g00142
Vvi4g604 . . . . . . . . . . . . Car09g00343 . . . Cpe06g00282 . . . . . . . . . . . . . . Cone4ag1732 . . . . . . . . . . . . . . . . . Cmo09g00396 Cma09g00394 . . . . . Bhi09g03041 . . . Hepe01g1946 Mch11g0481 . . . . . . . . . . . .
Vvi4g605 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g606 . . . . . . Bma04g00103 . . . . . . . . . . . . . . . . . Cla05g01661 Cam05g1772 Cec05g1780 Cco05g1839 Clacu05g1762 Cmu05g1648 Cre05g1776 . . . . Lsi04g01355 . . . . . . . . Bpe04g00096 . . Sed13g1948 . . . . . . . . Bhi09g03042 Tan01g3530 Cmetu07g1663 . . . . . . . . . . . . . . Cme07g00143
Vvi4g607 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g608 . Blo12g01042 . Bda03g00112 . . Bma04g00104 . Cmo05g00345 Cmo12g00324 . . . Car12g00354 Sed03g1654 Cpe07g00329 . Bhi04g00065 Tan02g2778 Cmetu03g2063 . Hepe10g0207 . Lcy13g1843 . . . . . . . . . . Cone20ag0311 . . . Cme03g01563 . . . . . . . . . . . . Cma12g00371 . Car05g00287 Cpe11g00287 . . . . . . . . Cla08g01377 Cam08g1847 Cec08g1425 Cco08g1558 Clacu08g1542 . Cre08g1325 Lsi08g01259 . Chy03g01073 .
Vvi4g609 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g610 Blo01g01424 Blo12g01041 Bda01g00654 . . Bpe02g00226 . Bma01g02181 . . . . Car09g00342 . . . Cpe06g00281 . . . . . . . Cla05g01660 Cam05g1771 Cec05g1779 Cco05g1838 Clacu05g1761 Cmu05g1647 Cre05g1775 Cone4ag1731 Cone7ag1650 . . Lsi04g01356 . . . . . . . . Bpe04g00097 . . Sed13g1947 . Cmo09g00395 Cma09g00393 . . . . . Bhi09g03043 Tan01g3529 Cmetu07g0445 . Hepe01g1944 Mch11g0480 . . . . . . . . . . . Cme07g00144
Vvi4g611 . . . . . . . . . . Cma01g01679 . Car09g00341 . . . Cpe06g00280 . . . . . . . Cla05g01659 . . . . . . . . . Cone20ag0309 Lsi04g01357 . . . . . . . . . . . . Cmo01g01729 Cmo09g00394 Cma09g00392 . Car01g01294 . . . Bhi09g03044 . . . Hepe01g1943 Mch11g0479 . . . . . . . . . . . Cme07g00146
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 33528371 33530244 + Bda002681.1 Bda01g00654 654
1 33576890 33578496 - Bda002683.1 Bda01g00655 655
3 986579 987879 + Bda016050.1 Bda03g00111 111
3 990075 992397 + Bda016051.1 Bda03g00112 112
4 1777797 1781244 + XM_039030329.1 Bhi04g00065 65
9 78649289 78651947 + XM_039042257.1 Bhi09g03040 3040
9 78651916 78661421 - XM_039042256.1 Bhi09g03041 3041
9 78654292 78661421 - XM_039042255.1 Bhi09g03042 3042
9 78675611 78680158 - XM_039041732.1 Bhi09g03043 3043
9 78714677 78719401 + XM_039041264.1 Bhi09g03044 3044
1 53038210 53040958 - BLOR01424 Blo01g01424 1424
12 28255029 28257104 + BLOR05060 Blo12g01041 1041
12 28257350 28259688 - BLOR05061 Blo12g01042 1042
1 78705257 78707442 - Bma003027.1 Bma01g02181 2181
4 820407 821843 - Bma031084 Bma04g00103 103
4 822121 824398 + Bma018550.3 Bma04g00104 104
2 1559948 1571752 + Bpe008072.1 Bpe02g00226 226
2 3428745 3430560 - Bpe025080 Bpe02g00527 527
4 689509 690821 + Bpe014817.1 Bpe04g00095 95
4 691790 692781 - Bpe014818.1 Bpe04g00096 96
4 695747 698043 - Bpe014819.2 Bpe04g00097 97
5 26560507 26563637 + CaPI482276_05g017710.1 Cam05g1771 1771
5 26564727 26568443 + CaPI482276_05g017720.1 Cam05g1772 1772
8 24554027 24557990 + CaPI482276_08g018470.1 Cam08g1847 1847
1 11658306 11660093 + Carg10743-RA Car01g01294 1294
5 1585138 1588563 - Carg09372-RA Car05g00287 287
9 1886758 1888125 - Carg02821-RA Car09g00341 341
9 1889490 1891781 + Carg02822-RA Car09g00342 342
9 1892830 1896399 + Carg02823-RA Car09g00343 343
9 1896876 1900625 - Carg02824-RA Car09g00344 344
12 2254103 2257488 + Carg03961-RA Car12g00354 354
5 27358079 27361199 + CcPI632755_05g018380.1 Cco05g1838 1838
5 27362332 27366060 + CcPI632755_05g018390.1 Cco05g1839 1839
8 27217939 27221842 + CcPI632755_08g015580.1 Cco08g1558 1558
5 29695523 29698643 + CePI673135_05g017790.1 Cec05g1779 1779
5 29699790 29703493 + CePI673135_05g017800.1 Cec05g1780 1780
8 26072622 26076591 + CePI673135_08g014250.1 Cec08g1425 1425
3 14139510 14142531 - Chy3G060530.1 Chy03g01073 1073
5 26764458 26767577 + ClG42_05g0176100.10 Clacu05g1761 1761
5 26768698 26772449 + ClG42_05g0176200.10 Clacu05g1762 1762
8 25294752 25298716 + ClG42_08g0154200.10 Clacu08g1542 1542
5 28252564 28256171 - ClCG05G016080.1 Cla05g01659 1659
5 28268933 28272060 + ClCG05G016090.2 Cla05g01660 1660
5 28273181 28279952 + ClCG05G016110.2 Cla05g01661 1661
8 26636360 26645293 + ClCG08G013800.2 Cla08g01377 1377
1 11455528 11457370 + CmaCh01G016790.1 Cma01g01679 1679
9 1659169 1661801 - CmaCh09G003920.1 Cma09g00392 392
9 1662920 1665348 + CmaCh09G003930.1 Cma09g00393 393
9 1667985 1672207 + CmaCh09G003940.1 Cma09g00394 394
9 1672266 1675200 - CmaCh09G003960.1 Cma09g00396 396
12 1917064 1920685 + CmaCh12G003710.1 Cma12g00371 371
3 24702831 24706171 - MELO3C011312.2.1 Cme03g01563 1563
7 913243 918591 + MELO3C016946.2.1 Cme07g00142 142
7 921570 923367 - MELO3C032323.2.1 Cme07g00143 143
7 924229 926656 - MELO3C016944.2.1 Cme07g00144 144
7 928884 931921 + MELO3C016943.2.1 Cme07g00146 146
3 4710450 4713901 + PI0026911.1 Cmetu03g2063 2063
7 23830069 23836590 + PI0010271.1 Cmetu07g0445 445
7 23836961 23841097 + PI0004962.1 Cmetu07g1663 1663
7 23842074 23846345 - PI0024241.1 Cmetu07g2214 2214
1 12933561 12935278 + CmoCh01G017290.1 Cmo01g01729 1729
5 1539959 1544131 - CmoCh05G003450.1 Cmo05g00345 345
9 1738150 1739617 - CmoCh09G003940.1 Cmo09g00394 394
9 1741055 1743055 + CmoCh09G003950.1 Cmo09g00395 395
9 1744306 1749220 + CmoCh09G003960.1 Cmo09g00396 396
9 1748787 1752641 - CmoCh09G003970.1 Cmo09g00397 397
12 2022380 2026155 + CmoCh12G003240.1 Cmo12g00324 324
5 26483306 26486428 + CmPI595203_05g016470.1 Cmu05g1647 1647
5 26487549 26491310 + CmPI595203_05g016480.1 Cmu05g1648 1648
4 12796808 12797587 + Conep04aG0178600.1 Cone4ag1731 1731
4 12798137 12799787 + Conep04aG0178700.1 Cone4ag1732 1732
7 11123510 11125905 + Conep07aG0169900.1 Cone7ag1650 1650
20 1381179 1382544 - Conep20aG0032200.1 Cone20ag0309 309
20 1386205 1388801 - Conep20aG0032400.1 Cone20ag0311 311
6 1540883 1542926 - Cp4.1LG06g02840.1 Cpe06g00280 280
6 1544403 1546576 + Cp4.1LG06g02790.1 Cpe06g00281 281
6 1547420 1554061 + Cp4.1LG06g02730.1 Cpe06g00282 282
6 1552014 1555289 - Cp4.1LG06g02830.1 Cpe06g00283 283
7 2136488 2140385 + Cp4.1LG07g03300.1 Cpe07g00329 329
11 1554713 1558228 - Cp4.1LG11g02840.1 Cpe11g00287 287
5 29735262 29738416 + CrPI670011_05g017750.1 Cre05g1775 1775
5 29739564 29743310 + CrPI670011_05g017760.1 Cre05g1776 1776
8 26356400 26360364 + CrPI670011_08g013250.1 Cre08g1325 1325
1 84288469 84292207 - Hsped.01g19430.1 Hepe01g1943 1943
1 84299339 84302280 + Hsped.01g19440.1 Hepe01g1944 1944
1 84308832 84313326 + Hsped.01g19460.1 Hepe01g1946 1946
1 84315216 84318857 - Hsped.01g19470.1 Hepe01g1947 1947
10 2102385 2105886 - Hsped.10g02070.1 Hepe10g0207 207
13 37388256 37392012 + Maker00033814 Lcy13g1843 1843
4 21292386 21297143 - Lsi04G013550.1 Lsi04g01355 1355
4 21297238 21300352 - Lsi04G013560.1 Lsi04g01356 1356
4 21304352 21308234 + Lsi04G013570.1 Lsi04g01357 1357
8 21036313 21039369 + Lsi08G012590.1 Lsi08g01259 1259
11 3065920 3068504 - MC11g0386 Mch11g0479 479
11 3071421 3073872 + MC11g0387 Mch11g0480 480
11 3074985 3080796 + MC11g0388 Mch11g0481 481
11 3079970 3083357 - MC11g0389 Mch11g0482 482
3 10629279 10632789 + Sed0002524.1 Sed03g1654 1654
13 24387388 24390369 + Sed0027737.1 Sed13g1947 1947
13 24393335 24399710 + Sed0006692.1 Sed13g1948 1948
13 24399825 24404000 - Sed0002011.1 Sed13g1949 1949
1 100467865 100471017 + Tan0012776.1 Tan01g3529 3529
1 100472605 100476409 + Tan0007061.1 Tan01g3530 3530
1 100481264 100482925 - Tan0011549.2 Tan01g3532 3532
2 96083042 96086652 + Tan0012643.1 Tan02g2778 2778
4 6981230 6982155 + Vvi4g602 Vvi4g602 602
4 6999685 7004075 + Vvi4g603 Vvi4g603 603
4 7004529 7007066 - Vvi4g604 Vvi4g604 604
4 7007088 7008322 - Vvi4g605 Vvi4g605 605
4 7008325 7009119 - Vvi4g606 Vvi4g606 606
4 7009416 7013238 + Vvi4g607 Vvi4g607 607
4 7015911 7025331 + Vvi4g608 Vvi4g608 608
4 7027360 7101962 + Vvi4g609 Vvi4g609 609
4 7106562 7110294 - Vvi4g610 Vvi4g610 610
4 7134441 7137026 + Vvi4g611 Vvi4g611 611
       

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