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
Vvi17g546 . Blo16g00186 . . . . . . Cmo13g01185 . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00069 Csa01g00542 Chy12g01546 Cme12g01997 . . . . . . . . . . . Cma13g01130 . . . . . Bhi08g01176 . . Lac10g0072 . . . . . . . . . . . . . .
Vvi17g547 . . . . . . . . Cmo13g01183 . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa01g00544 Chy12g01545 . . . . Bda14g00849 . . Bma03g00824 . Sed08g2065 . . Cma13g01129 . . . . . Bhi08g01175 Tan05g2447 Cmetu10g1222 Lac10g0073 Hepe07g2513 . . Cla04g01202 Cam04g1264 Cec01g1774 Cco01g1822 Clacu04g1293 Cmu04g1269 Cre01g1562 . . . .
Vvi17g548 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g549 . . . . . . . . Cmo13g01185 . . . . . . . . . . . . . . . . . . . . . . Cone2ag0848 . . . Lsi02g00070 Csa01g00546 Chy12g01543 Cme12g01996 . . . . . . Bma03g00827 . . . . Cma13g01131 . . . . . Bhi08g01172 . . . Hepe07g2512 . . Cla04g01201 . . . . . . . . . .
Vvi17g550 . Blo16g00185 . . . Bpe13g00291 Bma06g00173 . . . . . . . . . . . . . . . . . . . . . . . . . Cone16ag0166 . . . Csa01g00547 Chy12g01542 Cme12g01995 . . . . . . . . Sed08g2066 . . . . . . . . Bhi08g01170 Tan05g2445 Cmetu12g1137 Lac10g0074 Hepe07g2511 . . . . . . . . . . . . .
Vvi17g551 . . Bda06g00546 Bda15g00601 Bpe12g00549 Bpe13g00292 . Bma12g00997 . . . Cma11g00147 . Car11g00149 . . . Bhi02g00328 . . . . . . Cla06g01594 . . . . . . Cone2ag0847 Cone16ag0167 Cone13ag0071 Cone19ag0072 Lsi02g00071 Csa01g00548 Chy12g01541 Cme12g01994 Blo13g00010 Blo15g00308 . . Bpe07g00784 . Bma03g00828 Bma08g00218 . . Cmo11g00161 Cma13g01132 . Car13g00964 . . . Bhi08g01169 . . . . . . Cla04g01200 . . . . . . Lsi06g01470 Csa01g00230 Chy02g02502 Cme02g01888
Vvi17g552 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g553 . . . . . Bpe13g00294 Bma06g00171 . Cmo13g01186 . . . . . . Cpe20g00018 . . . . . . . . . . . . . . . . Cone16ag0169 . . Lsi02g00073 Csa01g00550 Chy12g01540 Cme12g01992 . . Bda11g01702 . . . . . Sed08g2069 . . Cma13g01133 . Car13g00965 . . . Bhi08g01166 Tan05g2441 Cmetu12g0527 Lac10g0078 Hepe07g2508 . . Cla04g01198 Cam04g1257 Cec01g1768 Cco01g1815 Clacu04g1287 Cmu04g1263 Cre01g1556 . . . .
Vvi17g554 Blo04g00770 . . . . . . . Cmo13g01189 . . . . . . Cpe20g00017 . . . . . . . . . . . . . . . Cone2ag0845 Cone16ag0170 . . Lsi02g00075 Csa01g00552 Chy12g01538 Cme12g01990 . . . Bda14g00852 . Bpe15g00601 Bma03g00831 . . . . Cma13g01135 . Car13g00966 . . . Bhi08g01164 Tan05g2438 . Lac10g0079 Hepe07g2507 . . Cla04g01196 Cam04g1255 Cec01g1766 Cco01g1813 Clacu04g1285 Cmu04g1261 Cre01g1554 . . . .
Vvi17g555 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 7728529 7729762 - Bda023804.1 Bda06g00546 546
11 51257232 51259535 + Bda008600.1 Bda11g01702 1702
14 6537819 6538678 + Bda027622.1 Bda14g00849 849
14 6565351 6568994 - Bda027625.1 Bda14g00852 852
15 9231684 9232774 + Bda012445.1 Bda15g00601 601
2 6081757 6083105 - XM_039023688.1 Bhi02g00328 328
8 36567482 36571321 + XM_039039268.1 Bhi08g01164 1164
8 36573607 36576658 - XM_039037798.1 Bhi08g01166 1166
8 36764199 36765939 - XM_039037893.1 Bhi08g01169 1169
8 36781903 36786024 - XM_039038301.1 Bhi08g01170 1170
8 36786729 36788961 - XM_039038305.1 Bhi08g01172 1172
8 36822052 36823200 - XM_039040100.1 Bhi08g01175 1175
8 36824502 36825505 - XM_039040098.1 Bhi08g01176 1176
4 7555657 7559227 - BLOR13682 Blo04g00770 770
13 121008 122289 - BLOR05291 Blo13g00010 10
15 3482128 3483351 + BLOR06702 Blo15g00308 308
16 4198812 4201152 - BLOR07433 Blo16g00185 185
16 4216258 4216584 - BLOR07434 Blo16g00186 186
3 7654811 7655637 + Bma017138.1 Bma03g00824 824
3 7693083 7695011 + Bma017141.1 Bma03g00827 827
3 7699654 7700895 + Bma017142.1 Bma03g00828 828
3 7739139 7748958 - Bma017145.2 Bma03g00831 831
6 2177427 2179304 - Bma022786.2 Bma06g00171 171
6 2194806 2204765 - Bma022788.2 Bma06g00173 173
8 2714030 2715242 + Bma027229.1 Bma08g00218 218
12 42057358 42058555 - Bma008344.1 Bma12g00997 997
7 14275414 14276618 - Bpe021629.1 Bpe07g00784 784
12 11321866 11323081 - Bpe005813.1 Bpe12g00549 549
13 10773151 10775634 + Bpe006417.1 Bpe13g00291 291
13 10779927 10781175 + Bpe006418.1 Bpe13g00292 292
13 10805854 10808106 + Bpe006420.1 Bpe13g00294 294
15 16918974 16921996 + Bpe001535.1 Bpe15g00601 601
4 26520666 26523262 + CaPI482276_04g012550.1 Cam04g1255 1255
4 26525243 26528462 - CaPI482276_04g012570.1 Cam04g1257 1257
4 26583581 26584383 - CaPI482276_04g012640.1 Cam04g1264 1264
11 840619 844453 + Carg18186-RA Car11g00149 149
13 9692782 9694000 + Carg04707-RA Car13g00964 964
13 9696783 9699003 + Carg04706-RA Car13g00965 965
13 9701031 9704841 - Carg04705-RA Car13g00966 966
1 30782309 30786072 + CcPI632755_01g018130.1 Cco01g1813 1813
1 30788919 30795159 - CcPI632755_01g018150.1 Cco01g1815 1815
1 30847385 30848175 - CcPI632755_01g018220.1 Cco01g1822 1822
1 32201632 32204252 + CePI673135_01g017660.1 Cec01g1766 1766
1 32206229 32213218 - CePI673135_01g017680.1 Cec01g1768 1768
1 32264004 32264784 - CePI673135_01g017740.1 Cec01g1774 1774
2 28469844 28470928 - Chy2G047690.1 Chy02g02502 2502
12 19087572 19094928 + Chy12G221380.1 Chy12g01538 1538
12 19097729 19099923 - Chy12G221400.1 Chy12g01540 1540
12 19117049 19118080 - Chy12G221410.1 Chy12g01541 1541
12 19127074 19130690 - Chy12G221420.1 Chy12g01542 1542
12 19131760 19133688 - Chy12G221430.1 Chy12g01543 1543
12 19134693 19135503 - Chy12G221450.1 Chy12g01545 1545
12 19136634 19137441 - Chy12G221460.1 Chy12g01546 1546
4 26873638 26877409 + ClG42_04g0128500.10 Clacu04g1285 1285
4 26879996 26883071 - ClG42_04g0128700.10 Clacu04g1287 1287
4 26935821 26936601 - ClG42_04g0129300.10 Clacu04g1293 1293
4 27120786 27124334 + ClCG04G012230.2 Cla04g01196 1196
4 27126317 27129996 - ClCG04G012250.2 Cla04g01198 1198
4 27163375 27164877 - ClCG04G012270.2 Cla04g01200 1200
4 27179719 27188969 - ClCG04G012280.2 Cla04g01201 1201
4 27190439 27201118 - ClCG04G012300.1 Cla04g01202 1202
6 29478222 29481274 - ClCG06G016230.2 Cla06g01594 1594
11 777644 779039 - CmaCh11G001470.1 Cma11g00147 147
13 8380382 8381372 + CmaCh13G011290.1 Cma13g01129 1129
13 8381645 8382352 + CmaCh13G011300.1 Cma13g01130 1130
13 8382898 8384826 + CmaCh13G011310.1 Cma13g01131 1131
13 8389228 8390616 + CmaCh13G011320.1 Cma13g01132 1132
13 8393345 8396097 + CmaCh13G011330.1 Cma13g01133 1133
13 8398281 8401641 - CmaCh13G011350.1 Cma13g01135 1135
2 25403434 25404734 - MELO3C017170.2.1 Cme02g01888 1888
12 25629140 25633086 + MELO3C001985.2.1 Cme12g01990 1990
12 25635291 25638159 - MELO3C001983.2.1 Cme12g01992 1992
12 25660996 25662486 - MELO3C001981.2.1 Cme12g01994 1994
12 25671469 25675317 - MELO3C001980.2.1 Cme12g01995 1995
12 25676262 25678190 - MELO3C001979.2.1 Cme12g01996 1996
12 25679891 25680360 - MELO3C001978.2.1 Cme12g01997 1997
10 19368592 19369370 + PI0019229.1 Cmetu10g1222 1222
12 478067 481191 + PI0025506.1 Cmetu12g0527 527
12 445334 449421 + PI0021307.1 Cmetu12g1137 1137
11 808308 809565 + CmoCh11G001610.1 Cmo11g00161 161
13 9401517 9402294 + CmoCh13G011830.1 Cmo13g01183 1183
13 9402736 9406095 + CmoCh13G011850.1 Cmo13g01185 1185
13 9410118 9416297 + CmoCh13G011860.1 Cmo13g01186 1186
13 9418504 9422299 - CmoCh13G011890.1 Cmo13g01189 1189
4 27055253 27059024 + CmPI595203_04g012610.1 Cmu04g1261 1261
4 27061611 27064686 - CmPI595203_04g012630.1 Cmu04g1263 1263
4 27117508 27118288 - CmPI595203_04g012690.1 Cmu04g1269 1269
2 34436736 34440726 + Conep02aG0187500.1 Cone2ag0845 845
2 34463550 34465404 - Conep02aG0187700.1 Cone2ag0847 847
2 34480230 34482188 - Conep02aG0187800.1 Cone2ag0848 848
13 435542 437093 - Conep13aG0007500.1 Cone13ag0071 71
16 1016158 1018493 + Conep16aG0017000.1 Cone16ag0166 166
16 1035017 1036744 + Conep16aG0017100.1 Cone16ag0167 167
16 1070539 1073980 + Conep16aG0017300.1 Cone16ag0169 169
16 1074957 1079124 - Conep16aG0017400.1 Cone16ag0170 170
19 441414 443013 - Conep19aG0007700.1 Cone19ag0072 72
20 100348 105976 + Cp4.1LG20g00180.1 Cpe20g00017 17
20 106903 110544 - Cp4.1LG20g00250.1 Cpe20g00018 18
1 28726286 28728900 + CrPI670011_01g015540.1 Cre01g1554 1554
1 28730877 28734055 - CrPI670011_01g015560.1 Cre01g1556 1556
1 28793426 28795064 - CrPI670011_01g015620.1 Cre01g1562 1562
1 1476868 1478042 + CsaV3_1G002300.1 Csa01g00230 230
1 3547658 3548658 + CsaV3_1G005420.1 Csa01g00542 542
1 3551371 3552181 + CsaV3_1G005440.1 Csa01g00544 544
1 3553228 3555156 + CsaV3_1G005460.1 Csa01g00546 546
1 3555807 3560028 + CsaV3_1G005470.1 Csa01g00547 547
1 3568762 3570548 + CsaV3_1G005480.1 Csa01g00548 548
1 3585806 3589071 + CsaV3_1G005500.1 Csa01g00550 550
1 3591143 3595300 - CsaV3_1G005520.1 Csa01g00552 552
7 69404848 69408622 + Hsped.07g25070.1 Hepe07g2507 2507
7 69410969 69413928 - Hsped.07g25080.1 Hepe07g2508 2508
7 69450189 69454310 - Hsped.07g25110.1 Hepe07g2511 2511
7 69455011 69457129 - Hsped.07g25120.1 Hepe07g2512 2512
7 69459364 69460911 - Hsped.07g25130.1 Hepe07g2513 2513
10 574386 575177 + Lag0024117.1 Lac10g0072 72
10 576109 576888 + Lag0024118.1 Lac10g0073 73
10 578972 582944 + Lag0024119.1 Lac10g0074 74
10 620023 622391 + Lag0024123.1 Lac10g0078 78
10 625076 627716 - Lag0024124.1 Lac10g0079 79
2 589600 594257 + Lsi02G000690.1 Lsi02g00069 69
2 595161 601682 + Lsi02G000700.1 Lsi02g00070 70
2 615053 616798 + Lsi02G000710.1 Lsi02g00071 71
2 642125 645037 + Lsi02G000730.1 Lsi02g00073 73
2 647517 652249 - Lsi02G000750.1 Lsi02g00075 75
6 25205467 25206709 - Lsi06G014700.1 Lsi06g01470 1470
8 34873610 34878571 + Sed0000403.1 Sed08g2065 2065
8 34881424 34886596 + Sed0024719.1 Sed08g2066 2066
8 34921261 34924066 + Sed0023446.1 Sed08g2069 2069
5 75527835 75531961 + Tan0013481.1 Tan05g2438 2438
5 75533993 75537149 - Tan0020612.1 Tan05g2441 2441
5 75613694 75617898 - Tan0000707.1 Tan05g2445 2445
5 75636988 75638225 - Tan0017862.1 Tan05g2447 2447
17 6686592 6693719 + Vvi17g546 Vvi17g546 546
17 6701814 6702672 + Vvi17g547 Vvi17g547 547
17 6714950 6715998 - Vvi17g548 Vvi17g548 548
17 6737152 6740262 + Vvi17g549 Vvi17g549 549
17 6742443 6747234 + Vvi17g550 Vvi17g550 550
17 6754049 6756019 + Vvi17g551 Vvi17g551 551
17 6769395 6770752 + Vvi17g552 Vvi17g552 552
17 6778788 6782640 + Vvi17g553 Vvi17g553 553
17 6785895 6793004 - Vvi17g554 Vvi17g554 554
17 6793107 6793548 - Vvi17g555 Vvi17g555 555
       

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