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
Vvi18g1710 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1711 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1712 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1713 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme09g00099 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi08g00135 . . .
Vvi18g1714 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1715 Blo01g01681 Blo12g00813 . Bda03g00359 . Bpe04g00319 Bma04g00336 . . . Cma01g00876 Cma09g01292 Car01g00801 . . Cpe06g00977 . Bhi04g02551 . . . . . . Cla08g00151 Cam08g0147 Cec08g0104 Cco08g0212 . Cmu08g0148 Cre08g0131 Cone4ag1155 . . . . . . Cme09g00106 . . Bda11g00923 . . . . . Sed01g3805 Cmo01g00919 Cmo09g01250 . . . Car09g01108 . Cpe02g00987 Bhi06g00145 Tan10g1859 Cmetu09g0015 . . . . Cla11g00801 Cam11g0837 Cec11g0822 Cco11g0824 Clacu11g1021 Cmu11g0883 Cre11g1281 Lsi08g00153 . . .
Vvi18g1716 Blo01g01682 Blo12g00812 . Bda03g00360 Bpe02g00260 Bpe04g00320 Bma04g00337 Bma01g02448 . . Cma01g00877 Cma09g01291 Car01g00802 . Sed03g0698 Cpe06g00975 . Bhi04g02550 Tan11g0043 Cmetu03g0129 . Hepe02g3468 . Lcy10g2361 Cla08g00152 Cam08g0148 Cec08g0103 Cco08g0213 . Cmu08g0149 Cre08g0132 Cone4ag1154 . . . . . . Cme09g00107 . . Bda11g00922 . . . . . Sed11g1774 Cmo01g00920 Cmo09g01249 . . . Car09g01106 . Cpe02g00986 Bhi06g00143 Tan10g1858 Cmetu09g1009 . . . . Cla11g00799 Cam11g0836 Cec11g0820 Cco11g0822 Clacu11g1022 Cmu11g0885 Cre11g1279 Lsi08g00154 . . .
Vvi18g1717 . Blo12g00811 . . . . . . . . . . . . . . . Bhi04g02549 Tan11g0045 . . Hepe02g3467 . Lcy10g2359 . . . . . . . Cone4ag1153 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla11g00797 Cam11g0833 Cec11g0819 Cco11g0821 Clacu11g1027 Cmu11g0888 Cre11g1275 . . . .
Vvi18g1718 . . . Bda03g00361 . Bpe04g00321 Bma04g00338 . . . . Cma09g01288 . . . Cpe06g00972 . . . . . . . . Cla08g00161 . Cec08g0097 Cco08g0221 . Cmu08g0153 Cre08g0140 . . . . . . . Cme09g00112 . . . . . . . . Sed10g1646 . Cmo09g01246 . . . Car09g01103 . . Bhi06g00128 Tan10g1852 Cmetu11g1682 . . . . Cla11g00796 Cam11g0832 Cec11g0818 Cco11g0820 Clacu11g1028 Cmu11g0889 . Lsi08g00162 . . .
Vvi18g1719 . . . . . . . . . . Cma01g00879 . Car01g00803 . . Cpe06g00949 . . . . . . . . Cla08g00168 . Cec08g0085 Cco08g0229 . Cmu08g0162 Cre08g0149 . . . . . . . Cme09g00114 . . . . . . . . Sed11g1771 Cmo01g00921 Cmo09g01210 . . . Car09g01079 . Cpe02g00985 Bhi06g00124 Tan10g1851 Cmetu09g1418 . . . . . . . . . . . Lsi08g00164 . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 3027531 3029667 + Bda016322.1 Bda03g00359 359
3 3030381 3041157 - Bda016323.1 Bda03g00360 360
3 3041942 3042982 - Bda016324.1 Bda03g00361 361
11 9022379 9033494 + Bda005677.1 Bda11g00922 922
11 9034348 9037401 - Bda005678.1 Bda11g00923 923
4 68521865 68542488 - XM_039030711.1 Bhi04g02549 2549
4 68627889 68640439 + XM_039029213.1 Bhi04g02550 2550
4 68670485 68680236 - XM_039030122.1 Bhi04g02551 2551
6 3243558 3246959 + XM_039034744.1 Bhi06g00124 124
6 3321554 3322949 + XM_039034434.1 Bhi06g00128 128
6 3502880 3512216 + XM_039033926.1 Bhi06g00143 143
6 3517037 3521139 - XM_039034813.1 Bhi06g00145 145
1 56527106 56529627 + BLOR01681 Blo01g01681 1681
1 56530144 56543083 - BLOR01682 Blo01g01682 1682
12 26486738 26488351 + BLOR04830 Blo12g00811 811
12 26489381 26502979 + BLOR04831 Blo12g00812 812
12 26503673 26505671 - BLOR04832 Blo12g00813 813
1 82100252 82111785 - Bma003318.1 Bma01g02448 2448
4 2743856 2745940 + Bma018795.1 Bma04g00336 336
4 2746541 2757236 - Bma018796.1 Bma04g00337 337
4 2758060 2759037 - Bma018797.1 Bma04g00338 338
2 1754665 1765663 + Bpe008105.1 Bpe02g00260 260
4 2040560 2042678 + Bpe015017.1 Bpe04g00319 319
4 2043307 2054339 - Bpe015018.1 Bpe04g00320 320
4 2055766 2056506 - Bpe015019.1 Bpe04g00321 321
8 2819203 2826565 + CaPI482276_08g001470.1 Cam08g0147 147
8 2827208 2840012 - CaPI482276_08g001480.1 Cam08g0148 148
11 10734091 10735101 - CaPI482276_11g008320.1 Cam11g0832 832
11 10769590 10780479 - CaPI482276_11g008330.1 Cam11g0833 833
11 10848559 10860790 + CaPI482276_11g008360.1 Cam11g0836 836
11 10876725 10881337 - CaPI482276_11g008370.1 Cam11g0837 837
1 5258804 5262030 + Carg26279-RA Car01g00801 801
1 5262943 5275169 - Carg26278-RA Car01g00802 802
1 5281109 5282137 + Carg26277-RA Car01g00803 803
9 10029348 10031898 - Carg27053-RA Car09g01079 1079
9 11207832 11208857 - Carg24112-RA Car09g01103 1103
9 11232037 11244707 + Carg24115-RA Car09g01106 1106
9 11249625 11254869 - Carg24117-RA Car09g01108 1108
8 3518005 3525346 + CcPI632755_08g002120.1 Cco08g0212 212
8 3525995 3538679 - CcPI632755_08g002130.1 Cco08g0213 213
8 3723365 3724375 + CcPI632755_08g002210.1 Cco08g0221 221
8 3954220 3955207 + CcPI632755_08g002290.1 Cco08g0229 229
11 9539712 9540700 - CcPI632755_11g008200.1 Cco11g0820 820
11 9568431 9586321 - CcPI632755_11g008210.1 Cco11g0821 821
11 9613883 9626321 + CcPI632755_11g008220.1 Cco11g0822 822
11 9644591 9647325 - CcPI632755_11g008240.1 Cco11g0824 824
8 1503279 1505848 - CePI673135_08g000850.1 Cec08g0085 85
8 1779495 1781555 - CePI673135_08g000970.1 Cec08g0097 97
8 1973434 1986504 + CePI673135_08g001030.1 Cec08g0103 103
8 1987157 1994342 - CePI673135_08g001040.1 Cec08g0104 104
11 9766692 9767696 - CePI673135_11g008180.1 Cec11g0818 818
11 9773965 9789811 - CePI673135_11g008190.1 Cec11g0819 819
11 9880560 9892647 + CePI673135_11g008200.1 Cec11g0820 820
11 9907980 9910701 - CePI673135_11g008220.1 Cec11g0822 822
11 12448022 12451715 + ClG42_11g0102100.10 Clacu11g1021 1021
11 12465942 12478128 - ClG42_11g0102200.10 Clacu11g1022 1022
11 12625859 12636968 + ClG42_11g0102700.10 Clacu11g1027 1027
11 12656330 12657334 + ClG42_11g0102800.10 Clacu11g1028 1028
8 2940551 2947790 + ClCG08G001500.2 Cla08g00151 151
8 2948058 2961952 - ClCG08G001510.1 Cla08g00152 152
8 3119737 3124557 + ClCG08G001600.1 Cla08g00161 161
8 3368973 3372555 + ClCG08G001680.2 Cla08g00168 168
11 11540745 11541749 - ClCG11G008330.1 Cla11g00796 796
11 11563136 11573634 - ClCG11G008340.2 Cla11g00797 797
11 11724972 11738052 + ClCG11G008360.2 Cla11g00799 799
11 11751676 11754409 - ClCG11G008380.2 Cla11g00801 801
1 4935735 4938341 + CmaCh01G008760.1 Cma01g00876 876
1 4939885 4952898 - CmaCh01G008770.1 Cma01g00877 877
1 4962173 4963201 + CmaCh01G008790.1 Cma01g00879 879
9 8886495 8887520 - CmaCh09G012880.1 Cma09g01288 1288
9 8913046 8929631 + CmaCh09G012910.1 Cma09g01291 1291
9 8927228 8936205 - CmaCh09G012920.1 Cma09g01292 1292
9 767040 775410 - MELO3C022144.2.1 Cme09g00099 99
9 804369 812373 + MELO3C022137.2.1 Cme09g00106 106
9 812640 823348 - MELO3C022135.2.1 Cme09g00107 107
9 849994 851074 + MELO3C022132.2.1 Cme09g00112 112
9 860050 861176 - MELO3C022130.2.1 Cme09g00114 114
3 26082720 26096613 + PI0015228.1 Cmetu03g0129 129
9 21026222 21030308 - PI0007900.1 Cmetu09g0015 15
9 21010568 21021664 + PI0007378.1 Cmetu09g1009 1009
9 20971092 20972202 + PI0000428.1 Cmetu09g1418 1418
11 30270629 30271795 + PI0022956.1 Cmetu11g1682 1682
1 5179022 5182369 + CmoCh01G009190.1 Cmo01g00919 919
1 5183766 5196471 - CmoCh01G009200.1 Cmo01g00920 920
1 5202966 5203997 + CmoCh01G009210.1 Cmo01g00921 921
9 9244864 9247927 - CmoCh09G012100.1 Cmo09g01210 1210
9 10725780 10726805 - CmoCh09G012460.1 Cmo09g01246 1246
9 10754876 10767857 + CmoCh09G012490.1 Cmo09g01249 1249
9 10767588 10777634 - CmoCh09G012500.1 Cmo09g01250 1250
8 2917370 2924609 + CmPI595203_08g001480.1 Cmu08g0148 148
8 2925251 2938019 - CmPI595203_08g001490.1 Cmu08g0149 149
8 3091420 3092430 + CmPI595203_08g001530.1 Cmu08g0153 153
8 3351964 3356601 + CmPI595203_08g001620.1 Cmu08g0162 162
11 11777487 11780960 + CmPI595203_11g008830.1 Cmu11g0883 883
11 11795190 11807367 - CmPI595203_11g008850.1 Cmu11g0885 885
11 11954973 11966090 + CmPI595203_11g008880.1 Cmu11g0888 888
11 11985387 11986391 + CmPI595203_11g008890.1 Cmu11g0889 889
4 9875890 9876413 - Conep04aG0119900.1 Cone4ag1153 1153
4 9877746 9888054 + Conep04aG0120000.1 Cone4ag1154 1154
4 9889480 9892745 - Conep04aG0120100.1 Cone4ag1155 1155
2 8921312 8922340 - Cp4.1LG02g11000.1 Cpe02g00985 985
2 8928722 8943198 + Cp4.1LG02g11060.1 Cpe02g00986 986
2 8943946 8947965 - Cp4.1LG02g11020.1 Cpe02g00987 987
6 8037575 8040748 - Cp4.1LG06g09690.1 Cpe06g00949 949
6 9203312 9204361 - Cp4.1LG06g09420.1 Cpe06g00972 972
6 9238425 9253862 + Cp4.1LG06g09470.1 Cpe06g00975 975
6 9259262 9264191 - Cp4.1LG06g09440.1 Cpe06g00977 977
8 2813012 2820324 + CrPI670011_08g001310.1 Cre08g0131 131
8 2821993 2833764 - CrPI670011_08g001320.1 Cre08g0132 132
8 3003479 3004489 + CrPI670011_08g001400.1 Cre08g0140 140
8 3251531 3255912 + CrPI670011_08g001490.1 Cre08g0149 149
11 11389003 11407303 - CrPI670011_11g012750.1 Cre11g1275 1275
11 11551908 11564400 + CrPI670011_11g012790.1 Cre11g1279 1279
11 11580852 11584324 - CrPI670011_11g012810.1 Cre11g1281 1281
2 83976143 83982419 - Hsped.02g34670.1 Hepe02g3467 3467
2 83989667 84003560 + Hsped.02g34680.1 Hepe02g3468 3468
10 47176957 47183264 - Maker00039506 Lcy10g2359 2359
10 47194246 47213498 + Maker00039314 Lcy10g2361 2361
8 2888915 2893059 + Lsi08G001350.1 Lsi08g00135 135
8 3178098 3185553 + Lsi08G001530.1 Lsi08g00153 153
8 3185579 3199209 - Lsi08G001540.1 Lsi08g00154 154
8 3342537 3343912 + Lsi08G001620.1 Lsi08g00162 162
8 3369661 3370710 - Lsi08G001640.1 Lsi08g00164 164
1 67209305 67213834 + Sed0017112.1 Sed01g3805 3805
3 4182663 4195968 + Sed0002348.1 Sed03g0698 698
10 33105708 33107942 + Sed0027875.1 Sed10g1646 1646
11 32691845 32694867 - Sed0002282.1 Sed11g1771 1771
11 32702616 32716892 + Sed0016992.2 Sed11g1774 1774
10 58428004 58429059 - Tan0001924.1 Tan10g1851 1851
10 58501353 58509501 - Tan0004853.1 Tan10g1852 1852
10 59011732 59029601 + Tan0009513.1 Tan10g1858 1858
10 59038199 59048442 - Tan0004285.1 Tan10g1859 1859
11 717430 731637 - Tan0020322.2 Tan11g0043 43
11 738074 743970 + Tan0004864.2 Tan11g0045 45
18 27975111 27979339 - Vvi18g1710 Vvi18g1710 1710
18 27982614 27983482 - Vvi18g1711 Vvi18g1711 1711
18 27983867 27985625 + Vvi18g1712 Vvi18g1712 1712
18 28012082 28015625 + Vvi18g1713 Vvi18g1713 1713
18 28030021 28034687 + Vvi18g1714 Vvi18g1714 1714
18 28113532 28119091 + Vvi18g1715 Vvi18g1715 1715
18 28120532 28137285 - Vvi18g1716 Vvi18g1716 1716
18 28144007 28159521 + Vvi18g1717 Vvi18g1717 1717
18 28161872 28162865 + Vvi18g1718 Vvi18g1718 1718
18 28167807 28168860 + Vvi18g1719 Vvi18g1719 1719
       

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