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
Vvi4g1132 . . . . Bpe15g00476 Bpe13g00410 . . . . . Cma07g00417 Car03g00623 Car07g00367 Sed14g1201 Cpe19g00866 Cpe10g00673 Bhi03g00846 Tan03g2094 Cmetu04g2423 . Hepe04g1603 . . . . . . . . . Cone8ag0856 . Cone6ag1691 Cone9ag1613 Lsi01g00589 . . Cme08g00943 . . . . . . Bma03g00956 Bma06g00092 . Cmo03g00701 Cmo07g00415 . . . . . . . . . . . . . . . . . . . . Lsi07g01096 Csa06g03341 Chy02g00560 .
Vvi4g1133 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1134 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1135 Blo04g00880 . . . Bpe15g00477 . . . . . Cma03g00676 . Car03g00621 . Sed06g0591 . . Bhi03g00845 Tan03g2095 Cmetu04g0046 . Hepe04g1604 . . Cla01g01989 Cam01g2087 Cec04g1744 Cco04g1809 Clacu01g2105 Cmu01g1981 Cre04g1658 . . . Cone9ag1614 Lsi01g00588 . . . . . . . . . Bma03g00955 . . Cmo03g00700 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1136 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme08g00944 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa06g03342 Chy02g00559 .
Vvi4g1137 Blo04g00879 Blo16g00086 . . . Bpe13g00409 . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0857 Cone12ag0820 . . . . . . . . Bda11g01830 . . . . Bma06g00091 Sed02g0073 . . Cma16g01242 . . . . . Bhi10g01858 Tan05g1147 Cmetu11g2225 . Hepe08g0287 . . . . . . . . . Lsi07g01095 . . .
Vvi4g1138 Blo04g00878 Blo16g00087 . . Bpe15g00478 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0858 Cone12ag0821 . . . . . . . . . . . . Bma03g00954 . . . . Cma16g01243 . . . . . . . . . . . . . . . . . . . Lsi07g01094 . . .
Vvi4g1139 Blo04g00877 Blo16g00088 . . Bpe15g00479 Bpe13g00408 . . . . Cma03g00675 Cma07g00416 Car03g00620 Car07g00366 Sed14g1202 Cpe19g00867 Cpe10g00674 Bhi03g00844 Tan03g2096 Cmetu04g0205 . Hepe04g1605 . . Cla01g01990 Cam01g2088 Cec04g1745 Cco04g1810 Clacu01g2106 Cmu01g1982 Cre04g1659 Cone8ag0859 Cone12ag0822 . . Lsi01g00587 . . Cme08g00945 . . Bda11g01829 . . . . . . Cmo03g00699 Cmo07g00414 Cma16g01244 . . . . . . . . . . . . . . . . . . . Lsi07g01093 Csa06g03343 Chy02g00558 .
Vvi4g1140 . . . Bda10g00190 . . . . . . . . . Car07g00365 Sed10g1016 Cpe19g00868 . Bhi03g00843 Tan03g2098 Cmetu04g0501 . Hepe04g1606 . . Cla01g01991 Cam01g2090 Cec04g1747 Cco04g1812 Clacu01g2108 Cmu01g1984 Cre04g1661 . . . . Lsi01g00586 . . Cme08g00946 . Blo06g00291 . . Bpe10g00162 . . . . . Cmo07g00413 . . . . . . . . . . . . . . . . . . . . . Csa06g03344 Chy02g00557 .
Vvi4g1141 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma20g00756 . . . . Bhi10g01857 . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
10 6713608 6713942 + Bda033107 Bda10g00190 190
11 53533782 53535095 - Bda008765.1 Bda11g01829 1829
11 53535758 53546547 - Bda008766.1 Bda11g01830 1830
3 15416501 15419265 - XM_039026897.1 Bhi03g00843 843
3 15420469 15424385 - XM_039027370.1 Bhi03g00844 844
3 15425543 15433690 - XM_039027711.1 Bhi03g00845 845
3 15438893 15444659 - XM_039027768.1 Bhi03g00846 846
10 46169658 46171147 + XM_039044618.1 Bhi10g01857 1857
10 46224324 46228667 - XM_039045766.1 Bhi10g01858 1858
4 9850347 9851623 - BLOR13789 Blo04g00877 877
4 9852386 9857526 - BLOR13790 Blo04g00878 878
4 9876623 9878547 - BLOR13791 Blo04g00879 879
4 10006788 10012660 - BLOR13792 Blo04g00880 880
6 16090757 16091151 - BLOR16874 Blo06g00291 291
16 2240316 2242247 + BLOR07334 Blo16g00086 86
16 2245073 2250107 + BLOR07335 Blo16g00087 87
16 2251480 2255564 + BLOR07336 Blo16g00088 88
3 10148622 10159448 - Bma017293.1 Bma03g00954 954
3 10160804 10166695 - Bma017294.1 Bma03g00955 955
3 10168418 10170896 - Bma017295.1 Bma03g00956 956
6 1397987 1400018 - Bma022709.1 Bma06g00091 91
6 1401068 1404755 - Bma022710.1 Bma06g00092 92
10 4001458 4007639 + Bpe002473.1 Bpe10g00162 162
13 11789007 11790324 - Bpe006533.1 Bpe13g00408 408
13 11790896 11802085 - Bpe006534.1 Bpe13g00409 409
13 11803059 11806515 - Bpe006535.2 Bpe13g00410 410
15 16092662 16095327 + Bpe001410.1 Bpe15g00476 476
15 16097025 16102973 + Bpe001411.4 Bpe15g00477 477
15 16103551 16119122 + Bpe001412.1 Bpe15g00478 478
15 16119535 16120822 + Bpe001413.1 Bpe15g00479 479
1 33908394 33915440 + CaPI482276_01g020870.1 Cam01g2087 2087
1 33916760 33920040 + CaPI482276_01g020880.1 Cam01g2088 2088
1 33926885 33928640 + CaPI482276_01g020900.1 Cam01g2090 2090
3 5685593 5688951 - Carg00580-RA Car03g00620 620
3 5689860 5697833 - Carg00581-RA Car03g00621 621
3 5701438 5706049 - Carg00583-RA Car03g00623 623
7 1831056 1833508 - Carg07945-RA Car07g00365 365
7 1834158 1837136 - Carg07946-RA Car07g00366 366
7 1837956 1843454 - Carg07947-RA Car07g00367 367
4 32975579 32992273 + CcPI632755_04g018090.1 Cco04g1809 1809
4 32993576 32996906 + CcPI632755_04g018100.1 Cco04g1810 1810
4 33003641 33005396 + CcPI632755_04g018120.1 Cco04g1812 1812
4 36469228 36476243 + CePI673135_04g017440.1 Cec04g1744 1744
4 36477553 36480851 + CePI673135_04g017450.1 Cec04g1745 1745
4 36488763 36490518 + CePI673135_04g017470.1 Cec04g1747 1747
2 3343782 3345845 - Chy2G028240.1 Chy02g00557 557
2 3346711 3349913 - Chy2G028250.1 Chy02g00558 558
2 3350825 3357885 - Chy2G028260.1 Chy02g00559 559
2 3360365 3368210 - Chy2G028270.1 Chy02g00560 560
1 32742689 32767002 + ClG42_01g0210500.10 Clacu01g2105 2105
1 32768241 32771512 + ClG42_01g0210600.10 Clacu01g2106 2106
1 32778347 32780107 + ClG42_01g0210800.10 Clacu01g2108 2108
1 34551840 34559376 + ClCG01G020400.2 Cla01g01989 1989
1 34560339 34564177 + ClCG01G020410.1 Cla01g01990 1990
1 34565411 34573763 + ClCG01G020420.2 Cla01g01991 1991
3 5594321 5597716 - CmaCh03G006750.1 Cma03g00675 675
3 5598503 5608600 - CmaCh03G006760.1 Cma03g00676 676
7 1800742 1802617 - CmaCh07G004160.1 Cma07g00416 416
7 1803391 1807867 - CmaCh07G004170.1 Cma07g00417 417
16 9389659 9392716 + CmaCh16G012420.1 Cma16g01242 1242
16 9398969 9404815 + CmaCh16G012430.1 Cma16g01243 1243
16 9405592 9409337 + CmaCh16G012440.1 Cma16g01244 1244
20 3560838 3562536 + CmaCh20G007560.1 Cma20g00756 756
8 6201204 6206325 + MELO3C007918.2.1 Cme08g00943 943
8 6207674 6215361 + MELO3C007919.2.1 Cme08g00944 944
8 6216296 6220093 + MELO3C007920.2.1 Cme08g00945 945
8 6220727 6223096 + MELO3C007921.2.1 Cme08g00946 946
4 9061022 9068259 + PI0016152.1 Cmetu04g0046 46
4 3623730 3627327 - PI0024192.1 Cmetu04g0205 205
4 3620551 3623011 - PI0005575.1 Cmetu04g0501 501
4 3637488 3642781 - PI0025533.1 Cmetu04g2423 2423
11 28537348 28540909 + PI0018353.1 Cmetu11g2225 2225
3 6083070 6086459 - CmoCh03G006990.1 Cmo03g00699 699
3 6087097 6097291 - CmoCh03G007000.1 Cmo03g00700 700
3 6097507 6102625 - CmoCh03G007010.1 Cmo03g00701 701
7 1883178 1885646 - CmoCh07G004130.1 Cmo07g00413 413
7 1886279 1889277 - CmoCh07G004140.1 Cmo07g00414 414
7 1890147 1895225 - CmoCh07G004150.1 Cmo07g00415 415
1 33085447 33104536 + CmPI595203_01g019810.1 Cmu01g1981 1981
1 33105773 33109080 + CmPI595203_01g019820.1 Cmu01g1982 1982
1 33115913 33117672 + CmPI595203_01g019840.1 Cmu01g1984 1984
6 12795533 12798749 + Conep06aG0175600.1 Cone6ag1691 1691
8 8490009 8493926 + Conep08aG0088200.1 Cone8ag0856 856
8 8494188 8497747 + Conep08aG0088300.1 Cone8ag0857 857
8 8501919 8506443 + Conep08aG0088400.1 Cone8ag0858 858
8 8506994 8510096 + Conep08aG0088500.1 Cone8ag0859 859
9 11522602 11525886 + Conep09aG0166300.1 Cone9ag1613 1613
9 11526759 11532786 + Conep09aG0166400.1 Cone9ag1614 1614
12 7456432 7459523 + Conep12aG0084500.1 Cone12ag0820 820
12 7476353 7480803 + Conep12aG0084600.1 Cone12ag0821 821
12 7481376 7484527 + Conep12aG0084700.1 Cone12ag0822 822
10 3870589 3876012 + Cp4.1LG10g00330.1 Cpe10g00673 673
10 3876069 3889968 + Cp4.1LG10g00300.1 Cpe10g00674 674
19 6384764 6390236 + Cp4.1LG19g08740.1 Cpe19g00866 866
19 6390881 6394179 + Cp4.1LG19g08800.1 Cpe19g00867 867
19 6394551 6397118 + Cp4.1LG19g08820.1 Cpe19g00868 868
4 34947774 34954856 + CrPI670011_04g016580.1 Cre04g1658 1658
4 34956171 34959477 + CrPI670011_04g016590.1 Cre04g1659 1659
4 34966327 34968082 + CrPI670011_04g016610.1 Cre04g1661 1661
6 27899871 27905249 + CsaV3_6G047270.1 Csa06g03341 3341
6 27906553 27914406 + CsaV3_6G047280.1 Csa06g03342 3342
6 27914823 27918564 + CsaV3_6G047290.1 Csa06g03343 3343
6 27918965 27921395 + CsaV3_6G047300.1 Csa06g03344 3344
4 71498666 71503308 + Hsped.04g16030.1 Hepe04g1603 1603
4 71507089 71514604 + Hsped.04g16040.1 Hepe04g1604 1604
4 71515828 71519395 + Hsped.04g16050.1 Hepe04g1605 1605
4 71520827 71523794 + Hsped.04g16060.1 Hepe04g1606 1606
8 2596180 2598675 + Hsped.08g02870.1 Hepe08g0287 287
1 4663713 4665053 - Lsi01G005860.1 Lsi01g00586 586
1 4667053 4671001 - Lsi01G005870.1 Lsi01g00587 587
1 4671987 4679743 - Lsi01G005880.1 Lsi01g00588 588
1 4681807 4693514 - Lsi01G005890.1 Lsi01g00589 589
7 16321951 16324439 - Lsi07G010930.1 Lsi07g01093 1093
7 16326245 16332643 - Lsi07G010940.1 Lsi07g01094 1094
7 16340159 16344780 - Lsi07G010950.1 Lsi07g01095 1095
7 16345849 16350645 - Lsi07G010960.1 Lsi07g01096 1096
2 9023549 9028764 + Sed0013235.1 Sed02g0073 73
6 5176506 5185072 - Sed0005677.1 Sed06g0591 591
10 8838871 8841902 + Sed0007439.2 Sed10g1016 1016
14 21280083 21289117 + Sed0019164.1 Sed14g1201 1201
14 21291689 21295150 + Sed0024543.1 Sed14g1202 1202
3 75834590 75839781 + Tan0015087.1 Tan03g2094 2094
3 75850382 75857497 + Tan0013399.1 Tan03g2095 2095
3 75858667 75862668 + Tan0001001.1 Tan03g2096 2096
3 75865162 75867248 + Tan0000469.2 Tan03g2098 2098
5 10316444 10319283 - Tan0010980.2 Tan05g1147 1147
4 20147676 20163066 + Vvi4g1132 Vvi4g1132 1132
4 20165290 20169686 - Vvi4g1133 Vvi4g1133 1133
4 20178884 20189283 - Vvi4g1134 Vvi4g1134 1134
4 20192412 20209879 + Vvi4g1135 Vvi4g1135 1135
4 20212285 20219286 + Vvi4g1136 Vvi4g1136 1136
4 20219975 20223806 + Vvi4g1137 Vvi4g1137 1137
4 20226271 20236797 + Vvi4g1138 Vvi4g1138 1138
4 20238996 20242301 + Vvi4g1139 Vvi4g1139 1139
4 20243122 20247788 + Vvi4g1140 Vvi4g1140 1140
4 20251893 20253027 - Vvi4g1141 Vvi4g1141 1141
       

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