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
Vvi17g566 Blo04g00773 . Bda06g00542 Bda15g00608 Bpe12g00541 . . Bma12g00994 . . . Cma11g00139 Car10g00187 Car11g00156 . . Cpe04g01495 . . . . . . . Cla06g01586 Cam06g1755 Cec06g1811 Cco06g1814 Clacu06g1721 Cmu06g1664 Cre06g2478 Cone2ag0840 Cone16ag0175 . . Lsi02g00081 Csa01g00560 Chy12g01533 Cme12g01983 Blo13g00003 Blo15g00312 . . Bpe07g00779 . . Bma08g00227 Sed08g2078 Cmo10g00213 Cmo11g00172 . . . . . Cpe18g00788 Bhi08g01147 Tan05g2431 Cmetu02g0368 Lac10g0087 Hepe07g2501 . . Cla04g01190 Cam04g1247 Cec01g1758 Cco01g1804 Clacu04g1276 Cmu04g1254 Cre01g1547 . Csa01g00241 Chy02g02491 Cme02g01877
Vvi17g567 . . Bda06g00541 . . . . . . . Cma10g00197 Cma11g00138 Car10g00188 Car11g00157 . . Cpe04g01494 Bhi02g00307 . . . Hepe09g0111 . . . . . . . . . . . . . . . . . . Blo15g00315 . . Bpe07g00778 . . . . Cmo10g00214 Cmo11g00173 . . . . . . . . . . . . . . . . . . . . Lsi06g01458 Csa01g00242 . Cme02g01876
Vvi17g568 Blo04g00776 Blo16g00183 . . . Bpe13g00297 . . Cmo13g01195 . . . . . . Cpe20g00014 . . . . . . . . . . . . . . . Cone2ag0839 Cone16ag0176 . . Lsi02g00083 Csa01g00562 Chy12g01531 Cme12g01980 . . . . . . . . Sed08g2081 . . Cma13g01140 . Car13g00971 . . . Bhi08g01145 Tan05g2429 . . Hepe07g2500 . . Cla04g01189 Cam04g1246 Cec01g1757 Cco01g1802 Clacu04g1274 Cmu04g1253 Cre01g1546 . . . .
Vvi17g569 . . . . . . . . Cmo13g01196 . Cma10g00199 Cma11g00136 Car10g00190 Car11g00159 . . Cpe04g01492 . . . . . . . Cla06g01584 Cam06g1752 Cec06g1808 Cco06g1811 Clacu06g1718 Cmu06g1661 Cre06g2475 Cone2ag0837 Cone16ag0177 Cone13ag0064 Cone19ag0066 Lsi02g00084 Csa01g00563 Chy12g01530 Cme12g01979 . . . . . . . Bma08g00231 Sed08g2082 Cmo10g00217 Cmo11g00175 Cma13g01141 . Car13g00972 . . Cpe18g00785 Bhi08g01143 Tan05g2427 Cmetu02g1502 Lac10g0091 Hepe07g2499 . . Cla04g01188 Cam04g1245 Cec01g1756 . Clacu04g1273 Cmu04g1252 Cre01g1545 Lsi06g01456 Csa01g00243 Chy02g02489 Cme02g01873
Vvi17g570 . . . . . . . . . . Cma10g00200 . Car10g00191 . . . . . . . . . . . Cla06g01583 . . . . . . Cone2ag0836 . . . . . . . . . . . . . . . . Cmo10g00218 . . . . . . . . . . . . . . . . . . . . . Lsi06g01455 Csa01g00245 Chy02g02488 .
Vvi17g571 . . . . . . . . Cmo13g01198 . Cma10g00201 Cma11g00135 Car10g00192 Car11g00161 . Cpe20g00013 Cpe04g01490 . . . . . . . Cla06g01580 . . . . . . Cone2ag0835 Cone16ag0179 Cone13ag0063 Cone19ag0065 Lsi02g00085 Csa01g00564 . Cme12g01978 . . . . . Bpe15g00598 Bma03g00836 . . Cmo10g00219 Cmo11g00176 Cma13g01143 . Car13g00973 . . Cpe18g00784 Bhi08g01142 . . . . . . Cla04g01187 . . . . . . Lsi06g01454 Csa01g00247 . Cme02g01871
Vvi17g572 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g573 . . . Bda15g00611 . . . . . . . Cma11g00134 . Car11g00162 Sed12g1961 . Cpe04g01489 Bhi02g00302 Tan09g2101 Cmetu10g1617 . Hepe09g0105 . . Cla06g01579 Cam06g1747 Cec06g1805 Cco06g1807 Clacu06g1713 Cmu06g1657 Cre06g2470 . . . Cone19ag0064 . . . . . . . . . . . . . . Cmo11g00178 . . . . . . . . . . . . . . . . . . . . Lsi06g01453 Csa01g00250 Chy02g02484 Cme02g01870
Vvi17g574 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g575 . . . . . . . . Cmo13g01199 . . . . . . Cpe20g00012 . . . . . . . . . . . . . . . Cone2ag0834 Cone16ag0180 . . Lsi02g00086 Csa01g00565 Chy12g01529 Cme12g01977 . . . . . . . . . . . Cma13g01145 . Car13g00974 . . . . . . . . . . Cla04g01186 Cam04g1243 Cec01g1754 Cco01g1800 Clacu04g1271 Cmu04g1250 Cre01g1543 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 7696263 7697165 + Bda023799.1 Bda06g00541 541
6 7698513 7699410 + Bda023800.1 Bda06g00542 542
15 9272694 9273616 - Bda012450.1 Bda15g00608 608
15 9286800 9293276 - Bda012453.1 Bda15g00611 611
2 5658433 5686019 - XM_039023062.1 Bhi02g00302 302
2 5816495 5818030 - XM_039022564.1 Bhi02g00307 307
8 36140027 36141760 - XM_039037824.1 Bhi08g01142 1142
8 36143339 36146621 - XM_039039522.1 Bhi08g01143 1143
8 36227187 36228977 - XM_039037744.1 Bhi08g01145 1145
8 36268098 36269329 + XM_039038897.1 Bhi08g01147 1147
4 7617799 7618859 - BLOR13685 Blo04g00773 773
4 7670317 7674105 - BLOR13688 Blo04g00776 776
13 29525 30677 + BLOR05284 Blo13g00003 3
15 3585189 3586160 - BLOR06706 Blo15g00312 312
15 3642505 3643438 - BLOR06709 Blo15g00315 315
16 4058913 4060063 + BLOR07431 Blo16g00183 183
3 7941254 7942430 - Bma017151.1 Bma03g00836 836
8 2793852 2794773 - Bma027236.1 Bma08g00227 227
8 2823396 2824993 - Bma027240.1 Bma08g00231 231
12 42023138 42026867 + Bma008341.1 Bma12g00994 994
7 14251584 14252498 + Bpe021623.1 Bpe07g00778 778
7 14254429 14255054 + Bpe021624.1 Bpe07g00779 779
12 11278473 11279391 + Bpe005807.1 Bpe12g00541 541
13 10817959 10819108 - Bpe006423.1 Bpe13g00297 297
15 16898607 16899798 + Bpe001532.1 Bpe15g00598 598
4 26432944 26435472 + CaPI482276_04g012430.1 Cam04g1243 1243
4 26443798 26446563 - CaPI482276_04g012450.1 Cam04g1245 1245
4 26454885 26456049 - CaPI482276_04g012460.1 Cam04g1246 1246
4 26462635 26465203 + CaPI482276_04g012470.1 Cam04g1247 1247
6 28717727 28730470 - CaPI482276_06g017470.1 Cam06g1747 1747
6 28774174 28775238 - CaPI482276_06g017520.1 Cam06g1752 1752
6 28793862 28795050 + CaPI482276_06g017550.1 Cam06g1755 1755
10 901163 902103 - Carg17957-RA Car10g00187 187
10 902985 904563 - Carg17956-RA Car10g00188 188
10 908671 910094 + Carg17954-RA Car10g00190 190
10 910115 911686 - Carg17953-RA Car10g00191 191
10 914955 916203 + Carg17952-RA Car10g00192 192
11 866857 868131 - Carg18193-RA Car11g00156 156
11 869855 870879 - Carg18194-RA Car11g00157 157
11 876574 878253 + Carg18196-RA Car11g00159 159
11 882718 883903 + Carg18198-RA Car11g00161 161
11 885843 898474 + Carg18199-RA Car11g00162 162
13 9721342 9723102 + Carg04700-RA Car13g00971 971
13 9723529 9726230 + Carg04699-RA Car13g00972 972
13 9726888 9728256 + Carg04698-RA Car13g00973 973
13 9728584 9731251 - Carg04697-RA Car13g00974 974
1 30687078 30689672 + CcPI632755_01g018000.1 Cco01g1800 1800
1 30710954 30712118 - CcPI632755_01g018020.1 Cco01g1802 1802
1 30722571 30723503 + CcPI632755_01g018040.1 Cco01g1804 1804
6 28422879 28435802 - CcPI632755_06g018070.1 Cco06g1807 1807
6 28478422 28479490 - CcPI632755_06g018110.1 Cco06g1811 1811
6 28499730 28500913 + CcPI632755_06g018140.1 Cco06g1814 1814
1 32111396 32113940 + CePI673135_01g017540.1 Cec01g1754 1754
1 32122126 32124882 - CePI673135_01g017560.1 Cec01g1756 1756
1 32133642 32134807 - CePI673135_01g017570.1 Cec01g1757 1757
1 32142637 32145200 + CePI673135_01g017580.1 Cec01g1758 1758
6 31502314 31515166 - CePI673135_06g018050.1 Cec06g1805 1805
6 31547442 31548516 - CePI673135_06g018080.1 Cec06g1808 1808
6 31568582 31569768 + CePI673135_06g018110.1 Cec06g1811 1811
2 28371592 28383869 - Chy2G047510.1 Chy02g02484 2484
2 28407265 28408785 + Chy2G047550.1 Chy02g02488 2488
2 28409060 28410147 - Chy2G047560.1 Chy02g02489 2489
2 28417130 28421364 + Chy2G047580.1 Chy02g02491 2491
12 19032616 19035241 + Chy12G221290.1 Chy12g01529 1529
12 19038395 19043900 - Chy12G221300.1 Chy12g01530 1530
12 19046861 19048026 - Chy12G221310.1 Chy12g01531 1531
12 19057148 19058077 + Chy12G221330.1 Chy12g01533 1533
4 26788639 26791224 + ClG42_04g0127100.10 Clacu04g1271 1271
4 26799432 26802196 - ClG42_04g0127300.10 Clacu04g1273 1273
4 26810287 26811451 - ClG42_04g0127400.10 Clacu04g1274 1274
4 26821382 26822314 + ClG42_04g0127600.10 Clacu04g1276 1276
6 27776449 27788809 - ClG42_06g0171300.10 Clacu06g1713 1713
6 27826580 27827644 - ClG42_06g0171800.10 Clacu06g1718 1718
6 27847543 27848729 + ClG42_06g0172100.10 Clacu06g1721 1721
4 27032300 27035174 + ClCG04G012120.2 Cla04g01186 1186
4 27039800 27040997 - ClCG04G012130.2 Cla04g01187 1187
4 27042823 27046143 - ClCG04G012140.1 Cla04g01188 1188
4 27053695 27055434 - ClCG04G012150.1 Cla04g01189 1189
4 27061578 27066086 + ClCG04G012160.2 Cla04g01190 1190
6 29336146 29349289 - ClCG06G016050.2 Cla06g01579 1579
6 29369941 29371827 - ClCG06G016060.1 Cla06g01580 1580
6 29385777 29387297 + ClCG06G016090.1 Cla06g01583 1583
6 29387330 29388771 - ClCG06G016100.1 Cla06g01584 1584
6 29404223 29410247 + ClCG06G016130.2 Cla06g01586 1586
10 888640 892358 - CmaCh10G001970.1 Cma10g00197 197
10 896488 898051 + CmaCh10G001990.1 Cma10g00199 199
10 898195 899778 - CmaCh10G002000.1 Cma10g00200 200
10 902752 904237 + CmaCh10G002010.1 Cma10g00201 201
11 720087 733902 - CmaCh11G001340.1 Cma11g00134 134
11 735487 737007 - CmaCh11G001350.1 Cma11g00135 135
11 741082 742328 - CmaCh11G001360.1 Cma11g00136 136
11 744009 749261 + CmaCh11G001380.1 Cma11g00138 138
11 750299 751773 + CmaCh11G001390.1 Cma11g00139 139
13 8413237 8420458 + CmaCh13G011400.1 Cma13g01140 1140
13 8421124 8423804 + CmaCh13G011410.1 Cma13g01141 1141
13 8424732 8425885 + CmaCh13G011430.1 Cma13g01143 1143
13 8426670 8430577 - CmaCh13G011450.1 Cma13g01145 1145
2 25300775 25313336 - MELO3C017186.2.1 Cme02g01870 1870
2 25323802 25325467 - MELO3C017185.2.1 Cme02g01871 1871
2 25335515 25337690 - MELO3C017183.2.1 Cme02g01873 1873
2 25344916 25346661 + MELO3C017181.2.1 Cme02g01876 1876
2 25348203 25349722 + MELO3C017180.2.1 Cme02g01877 1877
12 25573140 25576483 + MELO3C001997.2.1 Cme12g01977 1977
12 25579387 25580777 - MELO3C001996.2.1 Cme12g01978 1978
12 25582205 25585554 - MELO3C001995.2.1 Cme12g01979 1979
12 25588365 25590108 - MELO3C001994.2.1 Cme12g01980 1980
12 25597998 25598553 + MELO3C001992.2.1 Cme12g01983 1983
2 23721506 23723130 - PI0024353.1 Cmetu02g0368 368
2 23735274 23736988 + PI0011539.1 Cmetu02g1502 1502
10 12030960 12033399 - PI0027368.1 Cmetu10g1617 1617
10 948889 950839 - CmoCh10G002130.1 Cmo10g00213 213
10 951009 952446 - CmoCh10G002140.1 Cmo10g00214 214
10 956719 958027 + CmoCh10G002170.1 Cmo10g00217 217
10 958170 959741 - CmoCh10G002180.1 Cmo10g00218 218
10 962768 964327 + CmoCh10G002190.1 Cmo10g00219 219
11 834931 836675 - CmoCh11G001720.1 Cmo11g00172 172
11 837883 839593 - CmoCh11G001730.1 Cmo11g00173 173
11 844750 846683 + CmoCh11G001750.1 Cmo11g00175 175
11 851075 852562 + CmoCh11G001760.1 Cmo11g00176 176
11 854334 867114 + CmoCh11G001780.1 Cmo11g00178 178
13 9434322 9441106 + CmoCh13G011950.1 Cmo13g01195 1195
13 9441324 9443928 + CmoCh13G011960.1 Cmo13g01196 1196
13 9444807 9445960 + CmoCh13G011980.1 Cmo13g01198 1198
13 9446633 9448774 - CmoCh13G011990.1 Cmo13g01199 1199
4 26970510 26973095 + CmPI595203_04g012500.1 Cmu04g1250 1250
4 26981329 26984093 - CmPI595203_04g012520.1 Cmu04g1252 1252
4 26992182 26993346 - CmPI595203_04g012530.1 Cmu04g1253 1253
4 26999717 27002226 + CmPI595203_04g012540.1 Cmu04g1254 1254
6 27684983 27697328 - CmPI595203_06g016570.1 Cmu06g1657 1657
6 27735056 27736120 - CmPI595203_06g016610.1 Cmu06g1661 1661
6 27755842 27757028 + CmPI595203_06g016640.1 Cmu06g1664 1664
2 34356174 34359050 + Conep02aG0186200.1 Cone2ag0834 834
2 34364146 34365369 - Conep02aG0186300.1 Cone2ag0835 835
2 34375726 34377102 + Conep02aG0186400.1 Cone2ag0836 836
2 34377471 34379740 - Conep02aG0186500.1 Cone2ag0837 837
2 34386484 34388218 - Conep02aG0186700.1 Cone2ag0839 839
2 34403965 34405602 + Conep02aG0187000.1 Cone2ag0840 840
13 388885 390171 - Conep13aG0006600.1 Cone13ag0063 63
13 391892 393877 - Conep13aG0006700.1 Cone13ag0064 64
16 1117713 1119547 - Conep16aG0017900.1 Cone16ag0175 175
16 1128713 1130193 + Conep16aG0018000.1 Cone16ag0176 176
16 1142747 1144635 + Conep16aG0018100.1 Cone16ag0177 177
16 1157936 1159147 + Conep16aG0018300.1 Cone16ag0179 179
16 1166158 1168973 - Conep16aG0018400.1 Cone16ag0180 180
19 399974 404858 - Conep19aG0006800.1 Cone19ag0064 64
19 407679 408978 - Conep19aG0006900.1 Cone19ag0065 65
19 411084 412452 - Conep19aG0007000.1 Cone19ag0066 66
4 11814248 11827468 - Cp4.1LG04g14950.1 Cpe04g01489 1489
4 11828940 11830658 - Cp4.1LG04g14910.1 Cpe04g01490 1490
4 11835397 11837148 - Cp4.1LG04g14940.1 Cpe04g01492 1492
4 11841897 11843935 + Cp4.1LG04g14850.1 Cpe04g01494 1494
4 11844811 11846348 + Cp4.1LG04g14870.1 Cpe04g01495 1495
18 7429793 7431616 - Cp4.1LG18g07920.1 Cpe18g00784 784
18 7434536 7438149 - Cp4.1LG18g07940.1 Cpe18g00785 785
18 7444269 7445828 + Cp4.1LG18g07870.1 Cpe18g00788 788
20 76697 79208 + Cp4.1LG20g00010.1 Cpe20g00012 12
20 79516 81343 - Cp4.1LG20g00380.1 Cpe20g00013 13
20 81473 92628 - Cp4.1LG20g00360.1 Cpe20g00014 14
1 28633401 28635915 + CrPI670011_01g015430.1 Cre01g1543 1543
1 28644284 28647044 - CrPI670011_01g015450.1 Cre01g1545 1545
1 28659289 28660454 - CrPI670011_01g015460.1 Cre01g1546 1546
1 28666400 28668993 + CrPI670011_01g015470.1 Cre01g1547 1547
6 32480348 32493226 - CrPI670011_06g024700.1 Cre06g2470 2470
6 32539426 32540494 - CrPI670011_06g024750.1 Cre06g2475 2475
6 32560685 32561871 + CrPI670011_06g024780.1 Cre06g2478 2478
1 1525225 1527210 - CsaV3_1G002410.1 Csa01g00241 241
1 1529037 1529941 - CsaV3_1G002420.1 Csa01g00242 242
1 1533454 1540327 + CsaV3_1G002430.1 Csa01g00243 243
1 1538580 1540100 - CsaV3_1G002450.1 Csa01g00245 245
1 1548860 1551112 + CsaV3_1G002470.1 Csa01g00247 247
1 1562532 1573789 + CsaV3_1G002500.1 Csa01g00250 250
1 3626647 3627932 - CsaV3_1G005600.1 Csa01g00560 560
1 3635301 3637281 + CsaV3_1G005620.1 Csa01g00562 562
1 3639759 3642489 + CsaV3_1G005630.1 Csa01g00563 563
1 3644029 3645213 + CsaV3_1G005640.1 Csa01g00564 564
1 3648040 3651515 - CsaV3_1G005650.1 Csa01g00565 565
7 69326876 69329984 - Hsped.07g24990.1 Hepe07g2499 2499
7 69338454 69339622 - Hsped.07g25000.1 Hepe07g2500 2500
7 69346219 69350959 + Hsped.07g25010.1 Hepe07g2501 2501
9 836868 851951 - Hsped.09g01050.1 Hepe09g0105 105
9 892173 893602 + Hsped.09g01110.1 Hepe09g0111 111
10 677428 678349 - Lag0024132.1 Lac10g0087 87
10 719611 722033 + Lag0024136.1 Lac10g0091 91
2 694390 698036 - Lsi02G000810.1 Lsi02g00081 81
2 704574 707262 + Lsi02G000830.1 Lsi02g00083 83
2 712422 715393 + Lsi02G000840.1 Lsi02g00084 84
2 716855 718361 + Lsi02G000850.1 Lsi02g00085 85
2 722278 725396 - Lsi02G000860.1 Lsi02g00086 86
6 25068946 25083405 - Lsi06G014530.1 Lsi06g01453 1453
6 25102113 25103748 - Lsi06G014540.1 Lsi06g01454 1454
6 25113414 25114934 + Lsi06G014550.1 Lsi06g01455 1455
6 25114916 25116575 - Lsi06G014560.1 Lsi06g01456 1456
6 25126453 25132632 + Lsi06G014580.1 Lsi06g01458 1458
8 34963279 34964755 - Sed0020579.1 Sed08g2078 2078
8 34977421 34979721 + Sed0011442.2 Sed08g2081 2081
8 34980857 34984204 + Sed0026463.1 Sed08g2082 2082
12 30649686 30676181 + Sed0001989.1 Sed12g1961 1961
5 75422612 75425755 - Tan0009436.1 Tan05g2427 2427
5 75442237 75444248 - Tan0015571.2 Tan05g2429 2429
5 75463232 75464150 + Tan0022228.1 Tan05g2431 2431
9 71387864 71411413 - Tan0016325.1 Tan09g2101 2101
17 6886159 6887564 - Vvi17g566 Vvi17g566 566
17 6888372 6890086 - Vvi17g567 Vvi17g567 567
17 6914851 6916706 - Vvi17g568 Vvi17g568 568
17 6967306 6971068 + Vvi17g569 Vvi17g569 569
17 6971151 6972402 - Vvi17g570 Vvi17g570 570
17 6977308 6979211 + Vvi17g571 Vvi17g571 571
17 6993892 6995184 + Vvi17g572 Vvi17g572 572
17 6996559 7022145 + Vvi17g573 Vvi17g573 573
17 7023613 7027080 + Vvi17g574 Vvi17g574 574
17 7027584 7031512 - Vvi17g575 Vvi17g575 575
       

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