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
Vvi2g662 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0458 . . . . . . . . . . . . . Bma12g00203 . . . . . . . . . . . . . . . . Cla09g01145 Cam09g1204 Cec09g1218 Cco09g1245 . . Cre09g1165 . . . .
Vvi2g663 Blo02g00996 . . . . Bpe07g00206 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi07g01212 . . . . . . . . . Bma05g00384 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g664 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g665 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g666 Blo02g00995 . . Bda08g00627 Bpe05g00531 . . . Cmo06g00661 Cmo16g01204 Cma02g01610 . Car02g01369 . Sed08g2255 Cpe14g00957 Cpe05g00181 Bhi11g00152 Tan01g2183 Cmetu12g1582 . . . . Cla10g00163 Cam10g0164 Cec10g0174 Cco10g0173 Clacu10g0165 Cmu10g1014 Cre10g0424 . . . . Lsi07g01202 . Chy04g00087 Cme06g02477 . . . . . . Bma05g00714 Bma12g00205 Sed01g4104 Cmo02g01653 Cmo19g00255 Cma06g00653 Cma16g01153 Car06g00583 Car16g01093 . Cpe15g00218 Bhi05g00507 Tan07g1971 Cmetu04g3079 Lac11g2408 Hepe06g1025 . Lcy12g1942 Cla09g01136 Cam09g1193 Cec09g1207 Cco09g1228 . . Cre09g1153 . Csa03g04616 Chy06g02139 Cme04g00111
Vvi2g667 . . . . . . . . . . Cma02g01611 . Car02g01370 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo02g01654 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g668 . . . . . . . Bma14g00150 Cmo06g00660 Cmo16g01205 Cma02g01612 . Car02g01371 . Sed04g0833 Cpe14g00958 Cpe05g00179 Bhi11g00153 Tan01g2184 Cmetu06g1142 . . Mch10g1649 . Cla10g00162 Cam10g0163 Cec10g0173 Cco10g0172 Clacu10g0164 Cmu10g1013 Cre10g0423 . . . . Lsi07g01201 . Chy04g00088 Cme06g02476 Blo03g00855 Blo19g00186 Bda07g00102 Bda09g00718 Bpe08g00837 Bpe11g00339 . Bma12g00209 . Cmo02g01656 Cmo19g00254 Cma06g00652 Cma16g01154 Car06g00582 Car16g01094 . Cpe15g00217 Bhi05g00505 . . . Hepe06g1024 . . Cla09g01132 Cam09g1188 Cec09g1202 Cco09g1223 . . Cre09g1149 . Csa03g04613 Chy06g02140 Cme04g00113
Vvi2g669 . . . . . . . Bma14g00151 Cmo06g00659 . . . . . Sed02g0116 . . Bhi11g00154 Tan01g2186 Cmetu06g2320 . . Mch10g1650 . Cla10g00161 Cam10g0162 Cec10g0172 Cco10g0171 Clacu10g0163 Cmu10g1012 Cre10g0422 . . . . Lsi07g01200 . Chy04g00089 Cme06g02475 Blo03g00856 Blo19g00187 Bda07g00101 Bda09g00719 Bpe08g00836 Bpe11g00338 . . Sed01g4106 . . Cma06g00651 Cma16g01155 Car06g00581 . . . Bhi05g00503 Tan07g1974 Cmetu04g0986 Lac11g2411 Hepe06g1023 . Lcy12g1945 Cla09g01131 Cam09g1187 Cec09g1199 Cco09g1222 . . Cre09g1148 . Csa03g04612 Chy06g02141 Cme04g00114
Vvi2g670 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g671 Blo02g00993 . . . . . Bma07g00930 Bma14g00153 Cmo06g00657 Cmo16g01208 Cma02g01614 . Car02g01373 . Sed08g1916 Cpe14g00960 Cpe05g00176 Bhi11g00156 Tan01g2188 Cmetu06g1892 . Hepe06g1772 Mch10g1654 . Cla10g00159 Cam10g0160 Cec10g0170 Cco10g0168 Clacu10g0161 Cmu10g1010 Cre10g0420 Cone8ag0471 Cone12ag0465 . . Lsi07g01198 . Chy04g00093 Cme06g02473 Blo03g00858 Blo19g00189 Bda07g00099 Bda09g00724 Bpe08g00833 Bpe11g00336 . . Sed01g4108 Cmo02g01657 Cmo19g00251 Cma06g00648 Cma16g01157 Car06g00579 Car16g01097 . Cpe15g00214 Bhi05g00500 Tan07g1978 Cmetu04g2523 Lac11g2414 Hepe06g1020 . Lcy12g1947 Cla09g01129 Cam09g1183 Cec09g1195 Cco09g1216 . . Cre09g1145 . Csa03g04609 Chy06g02143 Cme04g00117
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 1167675 1169576 + Bda025157.1 Bda07g00099 99
7 1176089 1177048 + Bda025159.1 Bda07g00101 101
7 1180774 1181433 - Bda025160.1 Bda07g00102 102
8 6428359 6429618 + Bda029091.1 Bda08g00627 627
9 12140449 12141105 + Bda031396.1 Bda09g00718 718
9 12155298 12156944 - Bda031397.2 Bda09g00719 719
9 12230570 12232528 - Bda031405.1 Bda09g00724 724
5 11051778 11054520 + XM_039031803.1 Bhi05g00500 500
5 11281719 11283839 + XM_039032688.1 Bhi05g00503 503
5 11322504 11325679 - XM_039032983.1 Bhi05g00505 505
5 11351810 11355241 - XM_039031564.1 Bhi05g00507 507
11 3548547 3552003 + XM_039049561.1 Bhi11g00152 152
11 3560054 3561190 + XM_039050349.1 Bhi11g00153 153
11 3569756 3571090 - XM_039049756.1 Bhi11g00154 154
11 3623455 3625825 - XM_039048241.1 Bhi11g00156 156
2 38538853 38540613 + BLOR10723 Blo02g00993 993
2 38567728 38574086 - BLOR10725 Blo02g00995 995
2 38637462 38648916 - BLOR10726 Blo02g00996 996
3 34378808 34379467 + BLOR12036 Blo03g00855 855
3 34384154 34385122 - BLOR12037 Blo03g00856 856
3 34406074 34407978 + BLOR12039 Blo03g00858 858
19 8292120 8292755 + BLOR09529 Blo19g00186 186
19 8308746 8309561 - BLOR09530 Blo19g00187 187
19 8412187 8414145 - BLOR09532 Blo19g00189 189
5 12139914 12142346 - Bma021209.1 Bma05g00384 384
5 41359524 41360751 - Bma021790.1 Bma05g00714 714
7 34124281 34126239 + Bma026040.1 Bma07g00930 930
12 2697773 2704955 - Bma007090.1 Bma12g00203 203
12 2735852 2737115 + Bma007093.1 Bma12g00205 205
12 2752007 2752642 + Bma007097.1 Bma12g00209 209
14 2116513 2117172 + Bma010557.1 Bma14g00150 150
14 2123347 2124312 - Bma010558.1 Bma14g00151 151
14 2131378 2133228 - Bma010560.1 Bma14g00153 153
5 19489721 19490946 - Bpe017948.1 Bpe05g00531 531
7 1436188 1438776 + Bpe021017.1 Bpe07g00206 206
8 10483940 10485898 + Bpe022955.1 Bpe08g00833 833
8 10520402 10521193 + Bpe022958.1 Bpe08g00836 836
8 10532453 10533082 - Bpe022959.1 Bpe08g00837 837
11 2441302 2443206 + Bpe003710.1 Bpe11g00336 336
11 2449093 2450061 + Bpe003712.1 Bpe11g00338 338
11 2454040 2454699 - Bpe003713.1 Bpe11g00339 339
9 12860593 12862635 + CaPI482276_09g011830.1 Cam09g1183 1183
9 12943093 12944055 + CaPI482276_09g011870.1 Cam09g1187 1187
9 12984130 12984834 - CaPI482276_09g011880.1 Cam09g1188 1188
9 13029986 13033005 - CaPI482276_09g011930.1 Cam09g1193 1193
9 13312576 13320217 + CaPI482276_09g012040.1 Cam09g1204 1204
10 3229778 3231748 + CaPI482276_10g001600.1 Cam10g0160 160
10 3239390 3240307 + CaPI482276_10g001620.1 Cam10g0162 162
10 3246713 3247663 - CaPI482276_10g001630.1 Cam10g0163 163
10 3252668 3253620 - CaPI482276_10g001640.1 Cam10g0164 164
2 9060325 9061321 + Carg08836-RA Car02g01369 1369
2 9062268 9063405 + Carg08837-RA Car02g01370 1370
2 9066341 9067024 + Carg08838-RA Car02g01371 1371
2 9070511 9072595 - Carg08840-RA Car02g01373 1373
6 3330995 3332860 + Carg23384-RA Car06g00579 579
6 3337770 3338720 + Carg23382-RA Car06g00581 581
6 3341128 3341784 - Carg23381-RA Car06g00582 582
6 3343194 3347093 - Carg23380-RA Car06g00583 583
16 9384902 9387586 + Carg26193-RA Car16g01093 1093
16 9388912 9389963 + Carg26194-RA Car16g01094 1094
16 9398140 9400053 - Carg26197-RA Car16g01097 1097
9 12304360 12306396 + CcPI632755_09g012160.1 Cco09g1216 1216
9 12410868 12411830 + CcPI632755_09g012220.1 Cco09g1222 1222
9 12448402 12449094 - CcPI632755_09g012230.1 Cco09g1223 1223
9 12497437 12500230 - CcPI632755_09g012280.1 Cco09g1228 1228
9 12960028 12981291 + CcPI632755_09g012450.1 Cco09g1245 1245
10 1645807 1647774 + CcPI632755_10g001680.1 Cco10g0168 168
10 1656670 1657983 + CcPI632755_10g001710.1 Cco10g0171 171
10 1663995 1664933 - CcPI632755_10g001720.1 Cco10g0172 172
10 1669990 1671089 - CcPI632755_10g001730.1 Cco10g0173 173
9 12378250 12380286 + CePI673135_09g011950.1 Cec09g1195 1195
9 12486937 12487899 + CePI673135_09g011990.1 Cec09g1199 1199
9 12541025 12541717 - CePI673135_09g012020.1 Cec09g1202 1202
9 12590371 12591709 - CePI673135_09g012070.1 Cec09g1207 1207
9 12841443 12851658 - CePI673135_09g012180.1 Cec09g1218 1218
10 1673160 1675127 + CePI673135_10g001700.1 Cec10g0170 170
10 1682751 1683668 + CePI673135_10g001720.1 Cec10g0172 172
10 1690028 1690973 - CePI673135_10g001730.1 Cec10g0173 173
10 1696166 1697109 - CePI673135_10g001740.1 Cec10g0174 174
4 873483 878212 + Chy4G068050.1 Chy04g00087 87
4 882354 884922 + Chy4G068060.1 Chy04g00088 88
4 890840 891826 - Chy4G068070.1 Chy04g00089 89
4 902982 905021 - Chy4G068110.1 Chy04g00093 93
6 25728631 25729726 + Chy6G126670.1 Chy06g02139 2139
6 25731685 25732603 + Chy6G126680.1 Chy06g02140 2140
6 25739642 25740613 - Chy6G126690.1 Chy06g02141 2141
6 25749137 25751122 - Chy6G126710.1 Chy06g02143 2143
10 1951009 1952979 + ClG42_10g0016100.10 Clacu10g0161 161
10 1960741 1961658 + ClG42_10g0016300.10 Clacu10g0163 163
10 1967974 1968942 - ClG42_10g0016400.10 Clacu10g0164 164
10 1974042 1974994 - ClG42_10g0016500.10 Clacu10g0165 165
9 12559892 12562104 + ClCG09G011922.1 Cla09g01129 1129
9 12637860 12638822 + ClCG09G011926.1 Cla09g01131 1131
9 12675331 12676023 - ClCG09G011928.1 Cla09g01132 1132
9 12725180 12728515 - ClCG09G011960.1 Cla09g01136 1136
9 13196386 13215833 + ClCG09G012040.2 Cla09g01145 1145
10 1703280 1705364 + ClCG10G001590.2 Cla10g00159 159
10 1712351 1714642 + ClCG10G001610.1 Cla10g00161 161
10 1720720 1722499 - ClCG10G001620.2 Cla10g00162 162
10 1729068 1732309 - ClCG10G001630.1 Cla10g00163 163
2 9161100 9163394 + CmaCh02G016100.1 Cma02g01610 1610
2 9164156 9165742 + CmaCh02G016110.1 Cma02g01611 1611
2 9167938 9169217 + CmaCh02G016120.1 Cma02g01612 1612
2 9172765 9174807 - CmaCh02G016140.1 Cma02g01614 1614
6 3215044 3216885 + CmaCh06G006480.1 Cma06g00648 648
6 3220470 3221378 + CmaCh06G006510.1 Cma06g00651 651
6 3223761 3224417 - CmaCh06G006520.1 Cma06g00652 652
6 3225620 3227011 - CmaCh06G006530.1 Cma06g00653 653
16 8867734 8870936 + CmaCh16G011530.1 Cma16g01153 1153
16 8872184 8872852 + CmaCh16G011540.1 Cma16g01154 1154
16 8877074 8878021 - CmaCh16G011550.1 Cma16g01155 1155
16 8881798 8883705 - CmaCh16G011570.1 Cma16g01157 1157
4 871905 874601 + MELO3C003407.2.1 Cme04g00111 111
4 883389 884682 + MELO3C003408.2.1 Cme04g00113 113
4 891361 892955 - MELO3C003409.2.1 Cme04g00114 114
4 902979 905666 - MELO3C003412.2.1 Cme04g00117 117
6 31713059 31715361 + MELO3C013851.2.1 Cme06g02473 2473
6 31720775 31722924 + MELO3C013853.2.1 Cme06g02475 2475
6 31728857 31730173 - MELO3C013854.2.1 Cme06g02476 2476
6 31733791 31737419 - MELO3C013855.2.1 Cme06g02477 2477
4 32584142 32586388 + PI0023777.1 Cmetu04g0986 986
4 32568187 32571225 + PI0007112.1 Cmetu04g2523 2523
4 32606613 32607611 - PI0016797.1 Cmetu04g3079 3079
6 29654355 29656324 + PI0001953.1 Cmetu06g1142 1142
6 29670885 29672860 - PI0025176.1 Cmetu06g1892 1892
6 29662087 29664295 - PI0015619.1 Cmetu06g2320 2320
12 5239273 5243106 - PI0026129.1 Cmetu12g1582 1582
2 9533475 9536080 + CmoCh02G016530.1 Cmo02g01653 1653
2 9537094 9538554 + CmoCh02G016540.1 Cmo02g01654 1654
2 9541943 9542626 + CmoCh02G016560.1 Cmo02g01656 1656
2 9546095 9548179 - CmoCh02G016570.1 Cmo02g01657 1657
6 3318070 3319935 + CmoCh06G006570.1 Cmo06g00657 657
6 3324405 3325340 + CmoCh06G006590.1 Cmo06g00659 659
6 3326763 3328114 - CmoCh06G006600.1 Cmo06g00660 660
6 3329251 3333443 - CmoCh06G006610.1 Cmo06g00661 661
16 8616424 8619529 + CmoCh16G012040.1 Cmo16g01204 1204
16 8620838 8621503 + CmoCh16G012050.1 Cmo16g01205 1205
16 8631197 8633101 - CmoCh16G012080.1 Cmo16g01208 1208
19 1832010 1833863 + CmoCh19G002510.1 Cmo19g00251 251
19 1850342 1851070 - CmoCh19G002540.1 Cmo19g00254 254
19 1855240 1859517 - CmoCh19G002550.1 Cmo19g00255 255
10 2101974 2103944 + CmPI595203_10g010100.1 Cmu10g1010 1010
10 2111691 2112608 + CmPI595203_10g010120.1 Cmu10g1012 1012
10 2118938 2119897 - CmPI595203_10g010130.1 Cmu10g1013 1013
10 2124994 2125946 - CmPI595203_10g010140.1 Cmu10g1014 1014
8 3119283 3121785 - Conep08aG0049200.1 Cone8ag0471 471
12 2828600 2833427 - Conep12aG0047600.1 Cone12ag0458 458
12 2953872 2956356 - Conep12aG0048400.1 Cone12ag0465 465
5 929089 931170 + Cp4.1LG05g00100.1 Cpe05g00176 176
5 948188 948871 - Cp4.1LG05g00020.1 Cpe05g00179 179
5 952949 953945 - Cp4.1LG05g00030.1 Cpe05g00181 181
14 8076058 8079269 + Cp4.1LG14g09570.1 Cpe14g00957 957
14 8080259 8081490 + Cp4.1LG14g09560.1 Cpe14g00958 958
14 8090753 8092669 - Cp4.1LG14g09600.1 Cpe14g00960 960
15 1833374 1835251 + Cp4.1LG15g02130.1 Cpe15g00214 214
15 1874353 1875779 - Cp4.1LG15g02150.1 Cpe15g00217 217
15 1885214 1887534 - Cp4.1LG15g02160.1 Cpe15g00218 218
9 12527079 12529115 + CrPI670011_09g011450.1 Cre09g1145 1145
9 12640085 12641047 + CrPI670011_09g011480.1 Cre09g1148 1148
9 12676515 12677207 - CrPI670011_09g011490.1 Cre09g1149 1149
9 12717343 12724164 - CrPI670011_09g011530.1 Cre09g1153 1153
9 13202105 13226318 + CrPI670011_09g011650.1 Cre09g1165 1165
10 3081178 3083148 + CrPI670011_10g004200.1 Cre10g0420 420
10 3090928 3091845 + CrPI670011_10g004220.1 Cre10g0422 422
10 3097848 3098790 - CrPI670011_10g004230.1 Cre10g0423 423
10 3103829 3104914 - CrPI670011_10g004240.1 Cre10g0424 424
3 40071324 40074834 + CsaV3_3G049150.1 Csa03g04609 4609
3 40081840 40084240 + CsaV3_3G049180.1 Csa03g04612 4612
3 40090988 40092469 - CsaV3_3G049190.1 Csa03g04613 4613
3 40103772 40110187 - CsaV3_3G049220.1 Csa03g04616 4616
6 58162673 58164661 + Hsped.06g10200.1 Hepe06g1020 1020
6 58178615 58180854 + Hsped.06g10230.1 Hepe06g1023 1023
6 58200634 58201884 - Hsped.06g10240.1 Hepe06g1024 1024
6 58210943 58215277 + Hsped.06g10250.1 Hepe06g1025 1025
6 68801441 68804118 - Hsped.06g17720.1 Hepe06g1772 1772
11 40340593 40341940 + Lag0033046.1 Lac11g2408 2408
11 40365680 40366644 - Lag0033049.1 Lac11g2411 2411
11 40380498 40382585 - Lag0033052.1 Lac11g2414 2414
12 40775651 40784626 + Maker00038214 Lcy12g1942 1942
12 40806959 40807873 - Maker00038064 Lcy12g1945 1945
12 40825210 40832258 - Maker00038145 Lcy12g1947 1947
7 17487021 17489000 + Lsi07G011980.1 Lsi07g01198 1198
7 17495852 17496814 + Lsi07G012000.1 Lsi07g01200 1200
7 17506030 17506695 - Lsi07G012010.1 Lsi07g01201 1201
7 17509569 17513464 - Lsi07G012020.1 Lsi07g01202 1202
7 17682121 17685962 - Lsi07G012120.1 Lsi07g01212 1212
10 16640092 16640724 + MC10g1312 Mch10g1649 1649
10 16647551 16648495 - MC10g1313 Mch10g1650 1650
10 16658991 16661619 - MC10g1316 Mch10g1654 1654
1 69914558 69918883 + Sed0010416.3 Sed01g4104 4104
1 69934284 69936632 - Sed0021104.1 Sed01g4106 4106
1 69950923 69953567 - Sed0018501.1 Sed01g4108 4108
2 23405057 23406705 + Sed0014879.1 Sed02g0116 116
4 7079350 7080493 + Sed0004825.1 Sed04g0833 833
8 33575049 33576470 + Sed0004944.1 Sed08g1916 1916
8 36188797 36192565 + Sed0024308.2 Sed08g2255 2255
1 25663636 25664701 + Tan0021896.1 Tan01g2183 2183
1 25674226 25675431 + Tan0018255.1 Tan01g2184 2184
1 25731177 25733372 - Tan0001135.1 Tan01g2186 2186
1 25750967 25753756 - Tan0015748.1 Tan01g2188 2188
7 71468760 71471876 + Tan0022171.3 Tan07g1971 1971
7 71490104 71492520 - Tan0011968.1 Tan07g1974 1974
7 71506523 71509344 - Tan0021071.1 Tan07g1978 1978
2 7296722 7304697 + Vvi2g662 Vvi2g662 662
2 7304808 7308522 - Vvi2g663 Vvi2g663 663
2 7320725 7320902 - Vvi2g664 Vvi2g664 664
2 7322916 7339488 + Vvi2g665 Vvi2g665 665
2 7360571 7365558 + Vvi2g666 Vvi2g666 666
2 7366545 7368528 + Vvi2g667 Vvi2g667 667
2 7370113 7372531 + Vvi2g668 Vvi2g668 668
2 7389083 7392295 - Vvi2g669 Vvi2g669 669
2 7397009 7400572 + Vvi2g670 Vvi2g670 670
2 7426477 7428895 - Vvi2g671 Vvi2g671 671
       

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