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
Vvi17g736 . . Bda06g00591 . . . . Bma12g01033 . . Cma10g00128 Cma11g00099 Car10g00120 Car11g00099 Sed08g0131 . Cpe04g01550 Bhi02g00436 Tan09g2239 Cmetu01g2583 . Hepe09g0196 . . Cla06g01658 Cam06g1843 Cec06g1894 Cco06g1899 . Cmu06g1744 Cre06g2562 . . Cone13ag0135 Cone19ag0137 . . . . . Blo15g00271 . . Bpe07g00833 . . . . Cmo10g00134 Cmo11g00099 . . . . . Cpe18g00842 . . . . . . . . . . . . . . Lsi06g01548 Csa01g00156 Chy02g02574 Cme02g01964
Vvi17g737 . . Bda06g00592 Bda15g00571 Bpe12g00594 . . Bma12g01034 . . Cma10g00127 Cma11g00098 Car10g00118 Car11g00098 Sed08g0128 . Cpe04g01551 Bhi02g00437 Tan09g2240 Cmetu09g0010 . Hepe09g0197 . . Cla06g01659 Cam06g1844 Cec06g1895 Cco06g1900 Clacu06g1803 . Cre06g2563 . . Cone13ag0136 . . . . . Blo13g00056 Blo15g00270 . . Bpe07g00834 . . Bma08g00168 . Cmo10g00133 Cmo11g00098 . . . . . . . . . . . . . . . . . . . . Lsi06g01549 Csa01g00155 Chy02g02575 Cme02g01965
Vvi17g738 Blo04g00738 . . . . . Bma06g00231 . Cmo13g00921 Cmo18g00125 . . . . . Cpe20g00236 . . . . . . . . . . . . . . . Cone2ag0904 Cone16ag0108 Cone13ag0137 Cone19ag0138 Lsi02g00366 Csa01g00844 Chy12g01272 Cme12g01699 . . . Bda14g00817 . . . . . . . Cma13g00893 Cma18g00163 Car13g00733 Car18g00156 Cpe09g01031 . Bhi08g01601 . . . . . . Cla01g01294 . . . . . . . . . .
Vvi17g739 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g740 . . Bda06g00593 . . . Bma06g00233 . . . Cma10g00126 Cma11g00097 Car10g00117 Car11g00097 . . Cpe04g01552 Bhi02g00439 Tan09g2242 . . Hepe09g0198 . . Cla06g01660 Cam06g1845 Cec06g1896 Cco06g1901 Clacu06g1804 Cmu06g1745 Cre06g2564 Cone2ag0905 Cone16ag0107 . . . . . . . Blo15g00269 Bda11g01660 . Bpe07g00835 . . . . Cmo10g00132 Cmo11g00097 . . . . . Cpe18g00843 . . . . . . . . . . . . . . Lsi06g01550 Csa01g00154 Chy02g02576 Cme02g01966
Vvi17g741 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g742 . . . . . . Bma06g00234 . . . . . . . . Cpe20g00240 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma18g00167 . . . . Bhi08g01605 Tan05g3313 Cmetu12g0829 Lac10g0894 Hepe07g1903 . . . . . . . . . . . . .
Vvi17g743 . . . . . . . . . . . . . . Sed12g2440 . Cpe04g01556 Bhi02g00449 Tan09g2251 Cmetu02g0993 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi06g01554 . . Cme02g01970
Vvi17g744 Blo04g00736 . . . . . . . Cmo13g00919 Cmo18g00126 . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00369 Csa01g00847 Chy12g01269 Cme12g01697 . . . Bda14g00813 . Bpe15g00636 Bma03g00783 . . . . Cma13g00890 . Car13g00730 Car18g00158 Cpe09g01028 . . . . . . . . Cla01g01297 Cam01g1433 Cec01g1467 Cco01g1458 Clacu01g1363 Cmu01g1268 Cre01g1268 . . . .
Vvi17g745 . . Bda06g00595 . . . . . . . Cma10g00125 . . . . . . . . . . . . . Cla06g01661 Cam06g1846 Cec06g1897 Cco06g1902 Clacu06g1805 Cmu06g1746 Cre06g2565 Cone2ag0907 Cone16ag0103 . . . . . . . . . . Bpe07g00836 . . . . Cmo10g00130 . . . . . . Cpe18g00844 . . . . . . . . . . . . . . . Csa01g00150 Chy02g02578 Cme02g01980
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 8135154 8140019 + Bda023855.2 Bda06g00591 591
6 8146990 8148633 + Bda023856.1 Bda06g00592 592
6 8152564 8154939 + Bda023857.1 Bda06g00593 593
6 8192265 8196711 + Bda023859.1 Bda06g00595 595
11 50705178 50707310 + Bda008553.1 Bda11g01660 1660
14 6266645 6267968 + Bda027583.1 Bda14g00813 813
14 6283031 6284572 - Bda027587.1 Bda14g00817 817
15 8892112 8893746 + Bda012413.1 Bda15g00571 571
2 8224531 8229579 + XM_039023507.1 Bhi02g00436 436
2 8231469 8234422 + XM_039022471.1 Bhi02g00437 437
2 8247017 8250781 + XM_039022963.1 Bhi02g00439 439
2 8427824 8573394 - XM_039022967.1 Bhi02g00449 449
8 45962937 45965884 + XM_039040095.1 Bhi08g01601 1601
8 46086408 46088480 + XM_039037972.1 Bhi08g01605 1605
4 6875790 6877620 + BLOR13648 Blo04g00736 736
4 6896254 6897849 - BLOR13650 Blo04g00738 738
13 836895 846048 + BLOR05337 Blo13g00056 56
15 2903256 2905951 - BLOR06663 Blo15g00269 269
15 2910446 2912724 - BLOR06664 Blo15g00270 270
15 2914082 2918392 - BLOR06665 Blo15g00271 271
3 7235857 7237185 + Bma017089.1 Bma03g00783 783
6 2860740 2861965 + Bma022855.1 Bma06g00231 231
6 2978589 2980865 + Bma022859.1 Bma06g00233 233
6 3023602 3024456 + Bma022860.1 Bma06g00234 234
8 2065971 2068768 - Bma027168.1 Bma08g00168 168
12 42415365 42419307 + Bma008381.1 Bma12g01033 1033
12 42420700 42422133 + Bma008382.1 Bma12g01034 1034
7 14549024 14553599 + Bpe021677.1 Bpe07g00833 833
7 14554983 14556849 + Bpe021678.1 Bpe07g00834 834
7 14559854 14562201 + Bpe021679.1 Bpe07g00835 835
7 14570954 14575368 + Bpe021680.1 Bpe07g00836 836
12 11682444 11685022 + Bpe005857.1 Bpe12g00594 594
15 17157220 17158544 - Bpe001568.1 Bpe15g00636 636
1 27877662 27879660 + CaPI482276_01g014330.1 Cam01g1433 1433
6 29451071 29455711 + CaPI482276_06g018430.1 Cam06g1843 1843
6 29458864 29461243 + CaPI482276_06g018440.1 Cam06g1844 1844
6 29470773 29485349 + CaPI482276_06g018450.1 Cam06g1845 1845
6 29492576 29497282 + CaPI482276_06g018460.1 Cam06g1846 1846
10 552566 556083 - Carg10349-RA Car10g00117 117
10 559818 562753 - Carg10350-RA Car10g00118 118
10 566322 567563 - Carg10352-RA Car10g00120 120
11 557067 560709 - Carg18133-RA Car11g00097 97
11 562693 564996 - Carg18134-RA Car11g00098 98
11 566688 571575 - Carg18135-RA Car11g00099 99
13 8430091 8432587 + Carg07680-RA Car13g00730 730
13 8442788 8444753 - Carg07683-RA Car13g00733 733
18 842274 845991 + Carg06722-RA Car18g00156 156
18 856701 859410 - Carg06724-RA Car18g00158 158
1 26348706 26350705 - CcPI632755_01g014580.1 Cco01g1458 1458
6 29181163 29185849 + CcPI632755_06g018990.1 Cco06g1899 1899
6 29189130 29191517 + CcPI632755_06g019000.1 Cco06g1900 1900
6 29201020 29215544 + CcPI632755_06g019010.1 Cco06g1901 1901
6 29223212 29227919 + CcPI632755_06g019020.1 Cco06g1902 1902
1 29334757 29336757 + CePI673135_01g014670.1 Cec01g1467 1467
6 32242754 32247360 + CePI673135_06g018940.1 Cec06g1894 1894
6 32250389 32252862 + CePI673135_06g018950.1 Cec06g1895 1895
6 32262495 32279090 + CePI673135_06g018960.1 Cec06g1896 1896
6 32281309 32291498 + CePI673135_06g018970.1 Cec06g1897 1897
2 28948188 28953021 + Chy2G048410.1 Chy02g02574 2574
2 28955906 28958422 + Chy2G048420.1 Chy02g02575 2575
2 28967162 28974896 + Chy2G048430.1 Chy02g02576 2576
2 28985651 28988917 + Chy2G048450.1 Chy02g02578 2578
12 17284252 17286279 + Chy12G218690.1 Chy12g01269 1269
12 17302183 17304319 - Chy12G218720.1 Chy12g01272 1272
1 24936976 24938975 - ClG42_01g0136300.10 Clacu01g1363 1363
6 28507622 28517847 + ClG42_06g0180300.10 Clacu06g1803 1803
6 28527479 28539983 + ClG42_06g0180400.10 Clacu06g1804 1804
6 28542651 28553884 + ClG42_06g0180500.10 Clacu06g1805 1805
1 26249281 26254959 + ClCG01G013090.1 Cla01g01294 1294
1 26286800 26290014 - ClCG01G013140.2 Cla01g01297 1297
6 30093776 30099479 + ClCG06G016950.2 Cla06g01658 1658
6 30102008 30104538 + ClCG06G016960.1 Cla06g01659 1659
6 30114025 30128836 + ClCG06G016980.2 Cla06g01660 1660
6 30135919 30141076 + ClCG06G017010.1 Cla06g01661 1661
10 551785 556934 - CmaCh10G001250.1 Cma10g00125 125
10 559786 569991 - CmaCh10G001260.1 Cma10g00126 126
10 574310 577849 - CmaCh10G001270.1 Cma10g00127 127
10 577868 582208 - CmaCh10G001280.1 Cma10g00128 128
11 522626 528994 - CmaCh11G000970.1 Cma11g00097 97
11 529010 534118 - CmaCh11G000980.1 Cma11g00098 98
11 535139 543163 - CmaCh11G000990.1 Cma11g00099 99
13 7191557 7194854 + CmaCh13G008900.1 Cma13g00890 890
13 7203622 7206019 - CmaCh13G008930.1 Cma13g00893 893
18 825651 829733 + CmaCh18G001630.1 Cma18g00163 163
18 848291 849890 + CmaCh18G001670.1 Cma18g00167 167
2 25893804 25901914 + MELO3C017096.2.1 Cme02g01964 1964
2 25903832 25906990 + MELO3C017095.2.1 Cme02g01965 1965
2 25916627 25920123 + MELO3C017093.2.1 Cme02g01966 1966
2 25940494 26002182 + MELO3C017087.2.1 Cme02g01970 1970
2 26073483 26077964 - MELO3C026292.2.1 Cme02g01980 1980
12 23860484 23863378 + MELO3C002263.2.1 Cme12g01697 1697
12 23877706 23879666 - MELO3C002261.2.1 Cme12g01699 1699
1 1671811 1680490 + PI0023807.4 Cmetu01g2583 2583
2 24284891 24326831 - PI0026527.1 Cmetu02g0993 993
9 18283216 18284777 + PI0022050.1 Cmetu09g0010 10
12 5208364 5209324 + PI0021658.1 Cmetu12g0829 829
10 589213 593930 - CmoCh10G001300.1 Cmo10g00130 130
10 597207 608021 - CmoCh10G001320.1 Cmo10g00132 132
10 613002 615795 - CmoCh10G001330.1 Cmo10g00133 133
10 617038 620715 - CmoCh10G001340.1 Cmo10g00134 134
11 516889 524262 - CmoCh11G000970.1 Cmo11g00097 97
11 525909 528705 - CmoCh11G000980.1 Cmo11g00098 98
11 530167 535279 - CmoCh11G000990.1 Cmo11g00099 99
13 8126647 8129334 + CmoCh13G009190.1 Cmo13g00919 919
13 8137683 8141838 - CmoCh13G009210.1 Cmo13g00921 921
18 888021 893283 + CmoCh18G001250.1 Cmo18g00125 125
18 901979 905135 - CmoCh18G001260.1 Cmo18g00126 126
1 25276554 25278553 - CmPI595203_01g012680.1 Cmu01g1268 1268
6 28402161 28420853 + CmPI595203_06g017440.1 Cmu06g1744 1744
6 28430426 28444896 + CmPI595203_06g017450.1 Cmu06g1745 1745
6 28452435 28457144 + CmPI595203_06g017460.1 Cmu06g1746 1746
2 34854307 34856725 + Conep02aG0193400.1 Cone2ag0904 904
2 34859692 34862893 + Conep02aG0193500.1 Cone2ag0905 905
2 34873291 34877544 + Conep02aG0193700.1 Cone2ag0907 907
13 781387 787121 + Conep13aG0014000.1 Cone13ag0135 135
13 787908 790042 + Conep13aG0014100.1 Cone13ag0136 136
13 792263 794646 + Conep13aG0014200.1 Cone13ag0137 137
16 607976 612308 - Conep16aG0010500.1 Cone16ag0103 103
16 622001 625159 - Conep16aG0010900.1 Cone16ag0107 107
16 632936 635519 - Conep16aG0011000.1 Cone16ag0108 108
19 737859 742756 + Conep19aG0014300.1 Cone19ag0137 137
19 746743 749070 + Conep19aG0014400.1 Cone19ag0138 138
4 12140471 12153662 + Cp4.1LG04g15430.1 Cpe04g01550 1550
4 12155091 12157986 + Cp4.1LG04g15410.1 Cpe04g01551 1551
4 12159244 12163228 + Cp4.1LG04g15380.1 Cpe04g01552 1552
4 12177814 12180372 - Cp4.1LG04g15580.1 Cpe04g01556 1556
9 9049888 9053095 + Cp4.1LG09g10160.1 Cpe09g01028 1028
9 9064342 9069912 - Cp4.1LG09g10400.1 Cpe09g01031 1031
18 7762179 7770276 + Cp4.1LG18g08380.1 Cpe18g00842 842
18 7774285 7785494 + Cp4.1LG18g08390.1 Cpe18g00843 843
18 7788713 7793533 + Cp4.1LG18g08360.1 Cpe18g00844 844
20 1347646 1349619 + Cp4.1LG20g02350.1 Cpe20g00236 236
20 1367964 1368428 + Cp4.1LG20g02360.1 Cpe20g00240 240
1 25909450 25911449 + CrPI670011_01g012680.1 Cre01g1268 1268
6 33231106 33235785 + CrPI670011_06g025620.1 Cre06g2562 2562
6 33238926 33241304 + CrPI670011_06g025630.1 Cre06g2563 2563
6 33251088 33265772 + CrPI670011_06g025640.1 Cre06g2564 2564
6 33273369 33278080 + CrPI670011_06g025650.1 Cre06g2565 2565
1 965346 972606 - CsaV3_1G001500.1 Csa01g00150 150
1 986550 990279 - CsaV3_1G001540.1 Csa01g00154 154
1 998651 1001364 - CsaV3_1G001550.1 Csa01g00155 155
1 1004426 1009311 - CsaV3_1G001560.1 Csa01g00156 156
1 5290383 5293511 + CsaV3_1G008440.1 Csa01g00844 844
1 5306606 5309761 - CsaV3_1G008470.1 Csa01g00847 847
7 62718910 62720796 + Hsped.07g19030.1 Hepe07g1903 1903
9 1557158 1562391 + Hsped.09g01960.1 Hepe09g0196 196
9 1565416 1568925 + Hsped.09g01970.1 Hepe09g0197 197
9 1578449 1582229 + Hsped.09g01980.1 Hepe09g0198 198
10 7148683 7149360 + Lag0024939.1 Lac10g0894 894
2 3140797 3148528 + Lsi02G003660.1 Lsi02g00366 366
2 3177279 3180578 - Lsi02G003690.1 Lsi02g00369 369
6 25837499 25843302 + Lsi06G015480.1 Lsi06g01548 1548
6 25844549 25847397 + Lsi06G015490.1 Lsi06g01549 1549
6 25857697 25874301 + Lsi06G015500.1 Lsi06g01550 1550
6 25902237 25948571 - Lsi06G015540.1 Lsi06g01554 1554
8 730348 733285 - Sed0026305.2 Sed08g0128 128
8 734482 740394 - Sed0011264.3 Sed08g0131 131
12 34072292 34129062 - Sed0023277.1 Sed12g2440 2440
5 85015573 85016753 + Tan0018148.1 Tan05g3313 3313
9 72361375 72367370 + Tan0015792.1 Tan09g2239 2239
9 72369790 72372588 + Tan0005290.1 Tan09g2240 2240
9 72381571 72385571 + Tan0019282.1 Tan09g2242 2242
9 72471666 72546376 - Tan0006726.1 Tan09g2251 2251
17 9281673 9297710 + Vvi17g736 Vvi17g736 736
17 9300910 9306438 + Vvi17g737 Vvi17g737 737
17 9308907 9314007 + Vvi17g738 Vvi17g738 738
17 9334983 9343747 - Vvi17g739 Vvi17g739 739
17 9345960 9349253 + Vvi17g740 Vvi17g740 740
17 9350737 9350923 - Vvi17g741 Vvi17g741 741
17 9360727 9362879 - Vvi17g742 Vvi17g742 742
17 9403895 9557083 + Vvi17g743 Vvi17g743 743
17 9558481 9562161 + Vvi17g744 Vvi17g744 744
17 9583250 9590379 - Vvi17g745 Vvi17g745 745
       

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