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
Vvi5g799 . . . Bda08g00007 . . . Bma05g01258 Cmo08g01026 . . . . . . . . . . . . . . . Cla06g00703 Cam06g0754 Cec06g0760 Cco06g0772 Clacu06g0745 Cmu06g0728 Cre06g1505 . . . . . Csa02g01020 Chy05g00284 . . . . . Bpe05g01112 . . . . . . Cma08g01055 . . . . Cpe17g00222 . . . . . . . . . . . . . . Lsi09g01190 . . Cme05g00625
Vvi5g800 . . . . . Bpe14g01288 . . . . Cma06g01287 Cma14g01850 Car06g01105 Car14g01658 . . Cpe03g01550 . . . . . . . . . . . . . . Cone14ag0189 . Cone7ag0355 Cone4ag0368 Lsi05g01779 . . Cme06g00442 Blo02g00682 . . Bda13g00032 . . Bma02g00745 . . Cmo06g01292 Cmo14g01895 . . . . . . . . . . . . . Cla05g00401 Cam05g0437 Cec05g0443 Cco05g0442 Clacu05g0432 Cmu05g0413 Cre05g0474 . Csa03g01158 Chy06g00421 .
Vvi5g801 . . . Bda08g00008 Bpe04g00979 . . Bma05g01259 . Cmo17g00133 . . . . . . . . . . . . . . Cla06g00705 Cam06g0755 Cec06g0761 Cco06g0773 Clacu06g0746 Cmu06g0729 Cre06g1506 . . . . . Csa02g01019 Chy05g00283 . . . . . Bpe05g01113 . . . . . . . Cma17g00130 . Car17g00116 Cpe12g00114 . . . . . . . . . . . . . . . Lsi09g01188 . . Cme05g00626
Vvi5g802 Blo01g00305 . . Bda08g00009 Bpe04g00978 . Bma04g01025 Bma05g01260 . Cmo17g00131 . . . . . . . . . . . . . . Cla06g00706 Cam06g0756 Cec06g0762 Cco06g0774 Clacu06g0747 Cmu06g0730 Cre06g1507 Cone14ag0191 Cone15ag0201 . . . Csa02g01018 Chy05g00282 . . . . . Bpe05g01114 . . . . . . . Cma17g00129 . Car17g00115 Cpe12g00113 . . . . . . . . . . . . . . . Lsi09g01186 . . Cme05g00627
Vvi5g803 . . Bda03g01100 . . . Bma04g01026 . Cmo08g01024 . . Cma14g01852 . Car14g01659 . . Cpe03g01551 . . . . . . . Cla06g00707 . . . . . . Cone14ag0192 Cone15ag0202 Cone7ag0357 Cone4ag0369 Lsi05g01780 Csa02g01017 Chy05g00281 Cme06g00441 . . . . . . . . . . Cmo14g01897 Cma08g01053 . Car08g00930 . . Cpe17g00223 . . . . . . . Cla05g00400 . . . . . . . Csa03g01157 Chy06g00420 Cme05g00629
Vvi5g804 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g805 . . Bda03g01102 . Bpe04g00977 . Bma04g01027 . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0193 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g806 . . . . . . . . . . . Cma14g01853 . Car14g01660 . . Cpe03g01552 . . . . . . . . . . . . . . . . Cone7ag0358 Cone4ag0370 Lsi05g01781 . . Cme06g00440 . Blo07g00290 Bda11g00652 . . Bpe13g00535 . . . . Cmo14g01898 . . . . . . . . . . . . . Cla05g00399 Cam05g0435 Cec05g0441 Cco05g0440 Clacu05g0430 Cmu05g0411 Cre05g0472 . Csa03g01156 Chy06g00419 .
Vvi5g807 . . . Bda08g00010 . . . Bma05g01261 . . Cma06g01286 Cma14g01854 Car06g01104 Car14g01661 . Cpe08g00364 Cpe03g01553 . . . . . . . . . . . . . . . . Cone7ag0359 Cone4ag0371 Lsi05g01782 . . Cme06g00439 . . . . Bpe05g01116 . . . . Cmo06g01291 Cmo14g01899 . . . . . . . . . . . . . Cla05g00398 Cam05g0434 Cec05g0440 Cco05g0439 Clacu05g0429 Cmu05g0410 Cre05g0471 . Csa03g01154 Chy06g00418 .
Vvi5g808 Blo01g00306 . . Bda08g00011 . . . Bma05g01262 Cmo08g01023 . . . . . . . . . . . . . . . Cla06g00708 Cam06g0758 Cec06g0764 Cco06g0776 Clacu06g0749 Cmu06g0732 Cre06g1509 . . . . . Csa02g01016 Chy05g00280 . . . . . Bpe05g01117 . . . . . . Cma08g01052 . Car08g00929 . . Cpe17g00224 . . . . . . . . . . . . . . Lsi09g01183 . . Cme05g00630
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 11068465 11069379 + Bda017144.1 Bda03g01100 1100
3 11078172 11080037 + Bda017146.1 Bda03g01102 1102
8 99545 101053 + Bda024397.2 Bda08g00007 7
8 108646 109377 + Bda024399.1 Bda08g00008 8
8 109815 110849 - Bda024400.1 Bda08g00009 9
8 114970 116777 - Bda024401.1 Bda08g00010 10
8 117464 123265 + Bda024402.1 Bda08g00011 11
11 6453724 6455478 - Bda005398.1 Bda11g00652 652
13 524843 526963 + Bda000874.2 Bda13g00032 32
1 3756529 3761343 - BLOR00305 Blo01g00305 305
1 3761681 3773772 + BLOR00306 Blo01g00306 306
2 19776486 19778606 + BLOR10412 Blo02g00682 682
7 3378868 3380487 - BLOR18222 Blo07g00290 290
2 38490212 38492332 + Bma015447.1 Bma02g00745 745
4 17997797 17998711 - Bma019640.1 Bma04g01025 1025
4 18003216 18004115 + Bma019641.1 Bma04g01026 1026
4 18004808 18006670 + Bma019642.1 Bma04g01027 1027
5 51949473 51951017 + Bma022450.2 Bma05g01258 1258
5 51951597 51952323 + Bma022451.1 Bma05g01259 1259
5 51952928 51953962 - Bma022452.1 Bma05g01260 1260
5 51958179 51959831 - Bma022453.1 Bma05g01261 1261
5 51961320 51966951 + Bma022454.1 Bma05g01262 1262
4 6761963 6763525 - Bpe015643.1 Bpe04g00977 977
4 6782294 6782824 + Bpe015644.1 Bpe04g00978 978
4 6784908 6788613 - Bpe015645.1 Bpe04g00979 979
5 23503368 23504891 + Bpe018529.1 Bpe05g01112 1112
5 23505583 23506304 + Bpe018530.1 Bpe05g01113 1113
5 23506936 23507967 - Bpe018531.1 Bpe05g01114 1114
5 23512989 23514743 - Bpe018533.1 Bpe05g01116 1116
5 23515564 23521282 + Bpe018534.1 Bpe05g01117 1117
13 12674202 12675954 + Bpe010239.1 Bpe13g00535 535
14 9798260 9799741 - Bpe014645.1 Bpe14g01288 1288
5 3931724 3934972 + CaPI482276_05g004340.1 Cam05g0434 434
5 3941819 3943916 + CaPI482276_05g004350.1 Cam05g0435 435
5 3964712 3966790 + CaPI482276_05g004370.1 Cam05g0437 437
6 10137004 10142500 + CaPI482276_06g007540.1 Cam06g0754 754
6 10148524 10149656 + CaPI482276_06g007550.1 Cam06g0755 755
6 10150535 10153055 - CaPI482276_06g007560.1 Cam06g0756 756
6 10178552 10188613 - CaPI482276_06g007580.1 Cam06g0758 758
6 8292595 8296626 + Carg06254-RA Car06g01104 1104
6 8299720 8301795 + Carg06253-RA Car06g01105 1105
8 6230717 6241903 + Carg10995-RA Car08g00929 929
8 6243165 6244361 - Carg10994-RA Car08g00930 930
14 13235930 13238005 - Carg16529-RA Car14g01658 1658
14 13245078 13245987 + Carg16528-RA Car14g01659 1659
14 13246829 13249171 - Carg16527-RA Car14g01660 1660
14 13251622 13254746 - Carg16526-RA Car14g01661 1661
17 730971 734955 + Carg10117-RA Car17g00115 115
17 734283 735561 - Carg10116-RA Car17g00116 116
5 3588060 3591288 + CcPI632755_05g004390.1 Cco05g0439 439
5 3598208 3600301 + CcPI632755_05g004400.1 Cco05g0440 440
5 3620892 3622970 + CcPI632755_05g004420.1 Cco05g0442 442
6 8850463 8855925 + CcPI632755_06g007720.1 Cco06g0772 772
6 8861955 8863093 + CcPI632755_06g007730.1 Cco06g0773 773
6 8863980 8867867 - CcPI632755_06g007740.1 Cco06g0774 774
6 8885404 8893073 - CcPI632755_06g007760.1 Cco06g0776 776
5 3586711 3589916 + CePI673135_05g004400.1 Cec05g0440 440
5 3594578 3596673 + CePI673135_05g004410.1 Cec05g0441 441
5 3617849 3619927 + CePI673135_05g004430.1 Cec05g0443 443
6 8880543 8886031 + CePI673135_06g007600.1 Cec06g0760 760
6 8896680 8897729 + CePI673135_06g007610.1 Cec06g0761 761
6 8898623 8901144 - CePI673135_06g007620.1 Cec06g0762 762
6 8926406 8942151 - CePI673135_06g007640.1 Cec06g0764 764
5 2732586 2753667 + Chy5G093260.1 Chy05g00280 280
5 2755500 2756978 - Chy5G093270.1 Chy05g00281 281
5 2785854 2788318 + Chy5G093280.1 Chy05g00282 282
5 2789077 2789581 - Chy5G093290.1 Chy05g00283 283
5 2791582 2795163 - Chy5G093300.1 Chy05g00284 284
6 2839601 2842484 + Chy6G109460.1 Chy06g00418 418
6 2848816 2850918 + Chy6G109470.1 Chy06g00419 419
6 2854098 2855100 - Chy6G109480.1 Chy06g00420 420
6 2864922 2867009 + Chy6G109490.1 Chy06g00421 421
5 3644779 3648031 + ClG42_05g0042900.10 Clacu05g0429 429
5 3654762 3656859 + ClG42_05g0043000.10 Clacu05g0430 430
5 3677355 3679433 + ClG42_05g0043200.10 Clacu05g0432 432
6 8700878 8706287 + ClG42_06g0074500.10 Clacu06g0745 745
6 8711340 8712482 + ClG42_06g0074600.10 Clacu06g0746 746
6 8713378 8715884 - ClG42_06g0074700.10 Clacu06g0747 747
6 8741744 8762340 - ClG42_06g0074900.10 Clacu06g0749 749
5 3611122 3614706 + ClCG05G003860.1 Cla05g00398 398
5 3620944 3623712 + ClCG05G003880.1 Cla05g00399 399
5 3625776 3627245 - ClCG05G003890.2 Cla05g00400 400
5 3643977 3646055 + ClCG05G003910.1 Cla05g00401 401
6 8928380 8932284 + ClCG06G007300.1 Cla06g00703 703
6 8937849 8938991 + ClCG06G007320.1 Cla06g00705 705
6 8939887 8942393 - ClCG06G007330.2 Cla06g00706 706
6 8964820 8966417 + ClCG06G007340.2 Cla06g00707 707
6 8967896 8987258 - ClCG06G007350.2 Cla06g00708 708
6 8553299 8557493 + CmaCh06G012860.1 Cma06g01286 1286
6 8560075 8562150 + CmaCh06G012870.1 Cma06g01287 1287
8 6591167 6603515 + CmaCh08G010520.1 Cma08g01052 1052
8 6604701 6606168 - CmaCh08G010530.1 Cma08g01053 1053
8 6614040 6617839 - CmaCh08G010550.1 Cma08g01055 1055
14 13168601 13170676 - CmaCh14G018500.1 Cma14g01850 1850
14 13177579 13178659 + CmaCh14G018520.1 Cma14g01852 1852
14 13179392 13181976 - CmaCh14G018530.1 Cma14g01853 1853
14 13184100 13187778 - CmaCh14G018540.1 Cma14g01854 1854
17 675270 678435 + CmaCh17G001290.1 Cma17g00129 129
17 678312 680152 - CmaCh17G001300.1 Cma17g00130 130
5 6494810 6498928 + MELO3C023048.2.1 Cme05g00625 625
5 6499963 6501684 + MELO3C023049.2.1 Cme05g00626 626
5 6501377 6503142 - MELO3C023050.2.1 Cme05g00627 627
5 6554668 6556011 + MELO3C023051.2.1 Cme05g00629 629
5 6580078 6598704 - MELO3C023052.2.1 Cme05g00630 630
6 2786388 2789438 + MELO3C006364.2.1 Cme06g00439 439
6 2795756 2798830 + MELO3C006365.2.1 Cme06g00440 440
6 2799829 2801359 - MELO3C006366.2.1 Cme06g00441 441
6 2811188 2814624 + MELO3C006367.2.1 Cme06g00442 442
6 9741585 9745349 + CmoCh06G012910.1 Cmo06g01291 1291
6 9748567 9750642 + CmoCh06G012920.1 Cmo06g01292 1292
8 6660219 6671472 + CmoCh08G010230.1 Cmo08g01023 1023
8 6672474 6673985 - CmoCh08G010240.1 Cmo08g01024 1024
8 6682212 6686052 - CmoCh08G010260.1 Cmo08g01026 1026
14 14151102 14156541 - CmoCh14G018950.1 Cmo14g01895 1895
14 14163879 14164946 + CmoCh14G018970.1 Cmo14g01897 1897
14 14165672 14168238 - CmoCh14G018980.1 Cmo14g01898 1898
14 14170217 14173371 - CmoCh14G018990.1 Cmo14g01899 1899
17 767319 770174 + CmoCh17G001310.1 Cmo17g00131 131
17 770701 772340 - CmoCh17G001330.1 Cmo17g00133 133
5 3481366 3484617 + CmPI595203_05g004100.1 Cmu05g0410 410
5 3491329 3493426 + CmPI595203_05g004110.1 Cmu05g0411 411
5 3514005 3516083 + CmPI595203_05g004130.1 Cmu05g0413 413
6 8519130 8524540 + CmPI595203_06g007280.1 Cmu06g0728 728
6 8529622 8530764 + CmPI595203_06g007290.1 Cmu06g0729 729
6 8531660 8534166 - CmPI595203_06g007300.1 Cmu06g0730 730
6 8560062 8570392 - CmPI595203_06g007320.1 Cmu06g0732 732
4 1667169 1670277 - Conep04aG0038100.1 Cone4ag0368 368
4 1678350 1679426 + Conep04aG0038200.1 Cone4ag0369 369
4 1679604 1682308 - Conep04aG0038300.1 Cone4ag0370 370
4 1683034 1685256 - Conep04aG0038400.1 Cone4ag0371 371
7 1542641 1545716 - Conep07aG0036400.1 Cone7ag0355 355
7 1555178 1556280 + Conep07aG0036600.1 Cone7ag0357 357
7 1556662 1558520 - Conep07aG0036700.1 Cone7ag0358 358
7 1559655 1561941 - Conep07aG0036800.1 Cone7ag0359 359
14 864936 866321 - Conep14aG0019300.1 Cone14ag0189 189
14 868318 870061 - Conep14aG0019500.1 Cone14ag0191 191
14 875270 876288 + Conep14aG0019600.1 Cone14ag0192 192
14 877023 879347 + Conep14aG0019700.1 Cone14ag0193 193
15 952976 954960 - Conep15aG0020500.1 Cone15ag0201 201
15 960309 961352 + Conep15aG0020600.1 Cone15ag0202 202
3 12047798 12049873 - Cp4.1LG03g09610.1 Cpe03g01550 1550
3 12057261 12058165 + Cp4.1LG03g09700.1 Cpe03g01551 1551
3 12058599 12061665 - Cp4.1LG03g09570.1 Cpe03g01552 1552
3 12063496 12068398 - Cp4.1LG03g09600.1 Cpe03g01553 1553
8 2256328 2260202 - Cp4.1LG08g03130.1 Cpe08g00364 364
12 728912 732126 + Cp4.1LG12g01080.1 Cpe12g00113 113
12 732304 733910 - Cp4.1LG12g01210.1 Cpe12g00114 114
17 1406239 1412533 + Cp4.1LG17g02030.1 Cpe17g00222 222
17 1419485 1421381 + Cp4.1LG17g02110.1 Cpe17g00223 223
17 1422709 1431805 - Cp4.1LG17g02190.1 Cpe17g00224 224
5 4269885 4273103 + CrPI670011_05g004710.1 Cre05g0471 471
5 4280106 4282188 + CrPI670011_05g004720.1 Cre05g0472 472
5 4302914 4304992 + CrPI670011_05g004740.1 Cre05g0474 474
6 9686355 9691828 + CrPI670011_06g015050.1 Cre06g1505 1505
6 9697912 9699071 + CrPI670011_06g015060.1 Cre06g1506 1506
6 9699964 9702484 - CrPI670011_06g015070.1 Cre06g1507 1507
6 9727177 9733622 - CrPI670011_06g015090.1 Cre06g1509 1509
2 9883211 9911154 + CsaV3_2G012320.1 Csa02g01016 1016
2 9909483 9911911 - CsaV3_2G012330.1 Csa02g01017 1017
2 9928305 9931417 + CsaV3_2G012340.1 Csa02g01018 1018
2 9930653 9933082 - CsaV3_2G012350.1 Csa02g01019 1019
2 9933868 9937820 - CsaV3_2G012360.1 Csa02g01020 1020
3 9041698 9045188 + CsaV3_3G011540.1 Csa03g01154 1154
3 9048617 9051007 + CsaV3_3G011560.1 Csa03g01156 1156
3 9052564 9053881 - CsaV3_3G011570.1 Csa03g01157 1157
3 9063113 9065200 + CsaV3_3G011580.1 Csa03g01158 1158
5 25106515 25108593 - Lsi05G017790.1 Lsi05g01779 1779
5 25135486 25136222 + Lsi05G017800.1 Lsi05g01780 1780
5 25138492 25140915 - Lsi05G017810.1 Lsi05g01781 1781
5 25146601 25150225 - Lsi05G017820.1 Lsi05g01782 1782
9 19105902 19118539 + Lsi09G011830.1 Lsi09g01183 1183
9 19140846 19143290 + Lsi09G011860.1 Lsi09g01186 1186
9 19143860 19145833 - Lsi09G011880.1 Lsi09g01188 1188
9 19146833 19150990 - Lsi09G011900.1 Lsi09g01190 1190
5 9803722 9808509 + Vvi5g799 Vvi5g799 799
5 9819373 9821392 - Vvi5g800 Vvi5g800 800
5 9849940 9851116 + Vvi5g801 Vvi5g801 801
5 9854038 9862925 - Vvi5g802 Vvi5g802 802
5 9921389 9922390 + Vvi5g803 Vvi5g803 803
5 9935077 9953608 + Vvi5g804 Vvi5g804 804
5 9961042 9963031 + Vvi5g805 Vvi5g805 805
5 9996137 10002158 - Vvi5g806 Vvi5g806 806
5 10014086 10062107 - Vvi5g807 Vvi5g807 807
5 10088504 10130208 + Vvi5g808 Vvi5g808 808
       

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