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
Vvi17g416 . . . . . . . . . Cmo18g00110 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma18g00141 . . . . . . . . . . . . . . . . . . . . . .
Vvi17g417 . . Bda06g00506 Bda15g00637 Bpe12g00510 . . Bma12g00955 Cmo13g01097 . Cma10g00277 Cma11g00233 Car10g00259 Car11g00210 Sed08g0307 Cpe20g00094 Cpe04g01439 Bhi02g00050 Tan09g1999 Cmetu02g0900 . Hepe09g0297 . . Cla06g01518 Cam06g1675 Cec06g1736 Cco06g1732 Clacu06g1640 Cmu06g1588 Cre06g2399 . . Cone13ag0021 Cone19ag0030 Lsi02g00145 Csa01g00628 Chy12g01472 Cme12g01914 . Blo15g00347 . . Bpe07g00745 . . . Sed01g2275 Cmo10g00294 Cmo11g00236 Cma13g01054 . Car13g00889 . . Cpe18g00723 Bhi08g01049 Tan05g2320 Cmetu12g0108 . . . . Cla04g01132 Cam04g1185 Cec01g1697 Cco01g1743 Clacu04g1212 Cmu04g1191 Cre01g1490 Lsi06g01384 Csa01g00327 Chy02g02415 Cme02g01800
Vvi17g418 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g419 . . Bda06g00507 Bda15g00636 Bpe12g00511 . . Bma12g00956 Cmo13g01099 . Cma10g00278 Cma11g00232 Car10g00260 Car11g00208 . Cpe20g00093 Cpe04g01440 Bhi02g00051 . . . . . . Cla06g01519 Cam06g1676 Cec06g1737 Cco06g1733 Clacu06g1641 Cmu06g1589 Cre06g2400 . . Cone13ag0022 Cone19ag0031 Lsi02g00144 Csa01g00627 Chy12g01473 Cme12g01915 . Blo15g00346 . . . . . . . Cmo10g00295 Cmo11g00235 Cma13g01055 . Car13g00890 . . Cpe18g00722 Bhi08g01051 . . . . . . Cla04g01133 Cam04g1186 Cec01g1698 Cco01g1744 Clacu04g1213 Cmu04g1192 Cre01g1491 Lsi06g01385 Csa01g00328 Chy02g02414 Cme02g01801
Vvi17g420 . . . Bda15g00635 Bpe12g00513 . . . . . Cma10g00279 Cma11g00230 Car10g00262 Car11g00207 Sed08g0303 . Cpe04g01528 Bhi02g00053 Tan09g2002 Cmetu02g1950 . . . . Cla06g01625 Cam06g1806 Cec06g1857 Cco06g1863 Clacu06g1766 . Cre06g2528 . Cone16ag0242 . . . . . . . . . . . . . . . Cmo10g00296 Cmo11g00233 . . . . . Cpe18g00817 . . . . . . . . . . . . . . Lsi06g01506 Csa01g00330 Chy02g02413 Cme02g01923
Vvi17g421 . . Bda06g00568 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe07g00810 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g422 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g423 . Blo16g00241 . Bda15g00634 Bpe12g00514 . Bma06g00234 Bma12g01019 Cmo13g00918 . Cma10g00281 Cma11g00228 Car10g00264 Car11g00205 Sed08g0300 Cpe20g00241 Cpe04g01443 Bhi02g00056 Tan09g2004 Cmetu02g1182 . Hepe09g0293 . . Cla06g01522 Cam06g1679 Cec06g1740 Cco06g1737 Clacu06g1644 Cmu06g1592 Cre06g2403 Cone2ag0789 . Cone13ag0023 Cone19ag0032 Lsi02g00370 Csa01g00849 . Cme12g01696 Blo13g00035 . Bda11g01633 . . Bpe15g00563 Bma03g00870 Bma08g00252 . Cmo10g00299 Cmo11g00231 Cma13g00889 . Car13g00729 Car18g00159 . Cpe18g00719 . . . . . . . . . . . . . . Lsi06g01388 Csa01g00332 Chy02g02411 Cme02g01804
Vvi17g424 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g425 Blo04g00802 . . . . . . . Cmo13g01101 . . . . . . Cpe20g00092 . . . . . . . . . . . . . . . Cone2ag0790 Cone16ag0228 . . Lsi02g00142 Csa01g00626 Chy12g01475 Cme12g01916 . . . Bda14g00894 . Bpe15g00564 Bma03g00869 . Sed01g2279 . . Cma13g01057 . Car13g00892 . . . Bhi08g01054 Tan05g2323 Cmetu12g0469 Lac10g0188 Hepe07g2440 . . Cla04g01135 Cam04g1188 Cec01g1700 Cco01g1745 Clacu04g1214 Cmu04g1193 Cre01g1492 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 7174677 7178245 + Bda023757.1 Bda06g00506 506
6 7180787 7183552 - Bda023758.1 Bda06g00507 507
6 7954592 7966093 + Bda023830.1 Bda06g00568 568
11 50102785 50103909 - Bda008522.1 Bda11g01633 1633
14 6933888 6936480 - Bda027673.2 Bda14g00894 894
15 9475266 9476135 - Bda012478.1 Bda15g00634 634
15 9480454 9483690 + Bda012479.1 Bda15g00635 635
15 9496667 9499337 + Bda012481.1 Bda15g00636 636
15 9509280 9512105 - Bda012483.2 Bda15g00637 637
2 1039629 1046867 + XM_039024600.1 Bhi02g00050 50
2 1048352 1052256 - XM_039024601.1 Bhi02g00051 51
2 1071304 1078935 - XM_039023920.1 Bhi02g00053 53
2 1130090 1131299 + XM_039024041.1 Bhi02g00056 56
8 34444099 34449979 + XM_039038377.1 Bhi08g01049 1049
8 34451082 34454847 - XM_039038378.1 Bhi08g01051 1051
8 34523002 34525480 + XM_039037924.1 Bhi08g01054 1054
4 8236352 8241372 - BLOR13714 Blo04g00802 802
13 545508 550633 + BLOR05316 Blo13g00035 35
15 4376164 4378895 + BLOR06740 Blo15g00346 346
15 4381286 4385812 - BLOR06741 Blo15g00347 347
16 5559856 5560692 + BLOR07489 Blo16g00241 241
3 8450302 8452872 - Bma017187.1 Bma03g00869 869
3 8453637 8454554 - Bma017188.1 Bma03g00870 870
6 3023602 3024456 + Bma022860.1 Bma06g00234 234
8 3175003 3175878 + Bma027269.1 Bma08g00252 252
12 41484314 41487544 + Bma008297.1 Bma12g00955 955
12 41490317 41491996 - Bma008298.1 Bma12g00956 956
12 42242956 42255716 + Bma008367.1 Bma12g01019 1019
7 13981120 13984679 + Bpe021590.2 Bpe07g00745 745
7 14419899 14431143 + Bpe021655.1 Bpe07g00810 810
12 10951155 10958122 + Bpe005773.1 Bpe12g00510 510
12 10962352 10965062 - Bpe005774.1 Bpe12g00511 511
12 10977022 10979297 - Bpe005776.1 Bpe12g00513 513
12 10990661 10991530 + Bpe005777.1 Bpe12g00514 514
15 16651757 16652689 + Bpe001497.1 Bpe15g00563 563
15 16653390 16655995 + Bpe001498.1 Bpe15g00564 564
4 25958082 25963545 + CaPI482276_04g011850.1 Cam04g1185 1185
4 25964407 25966991 - CaPI482276_04g011860.1 Cam04g1186 1186
4 25978416 25980436 + CaPI482276_04g011880.1 Cam04g1188 1188
6 28116419 28122147 + CaPI482276_06g016750.1 Cam06g1675 1675
6 28123846 28127970 - CaPI482276_06g016760.1 Cam06g1676 1676
6 28176120 28177094 + CaPI482276_06g016790.1 Cam06g1679 1679
6 29139311 29153603 + CaPI482276_06g018060.1 Cam06g1806 1806
10 1233118 1238049 + Carg17884-RA Car10g00259 259
10 1238910 1240731 - Carg17883-RA Car10g00260 260
10 1246016 1250766 - Carg17881-RA Car10g00262 262
10 1260510 1261472 + Carg17879-RA Car10g00264 264
11 1181309 1182256 - Carg09184-RA Car11g00205 205
11 1190021 1196266 + Carg09182-RA Car11g00207 207
11 1200493 1203189 + Carg09181-RA Car11g00208 208
11 1204578 1209485 - Carg09179-RA Car11g00210 210
13 8422383 8423620 - Carg07679-RA Car13g00729 729
13 9310472 9315555 + Carg04782-RA Car13g00889 889
13 9315532 9319483 - Carg04781-RA Car13g00890 890
13 9322784 9325382 + Carg04779-RA Car13g00892 892
18 866683 867842 + Carg06725-RA Car18g00159 159
1 30198505 30203832 + CcPI632755_01g017430.1 Cco01g1743 1743
1 30204715 30207296 - CcPI632755_01g017440.1 Cco01g1744 1744
1 30221941 30226941 + CcPI632755_01g017450.1 Cco01g1745 1745
6 27810343 27816170 + CcPI632755_06g017320.1 Cco06g1732 1732
6 27818550 27821215 - CcPI632755_06g017330.1 Cco06g1733 1733
6 27874979 27875953 + CcPI632755_06g017370.1 Cco06g1737 1737
6 28853296 28867612 + CcPI632755_06g018630.1 Cco06g1863 1863
1 31630897 31635385 + CePI673135_01g016970.1 Cec01g1697 1697
1 31637057 31639642 - CePI673135_01g016980.1 Cec01g1698 1698
1 31649561 31651649 + CePI673135_01g017000.1 Cec01g1700 1700
6 30866819 30872645 + CePI673135_06g017360.1 Cec06g1736 1736
6 30875011 30877656 - CePI673135_06g017370.1 Cec06g1737 1737
6 30927475 30928449 + CePI673135_06g017400.1 Cec06g1740 1740
6 31918116 31932453 + CePI673135_06g018570.1 Cec06g1857 1857
2 27829988 27830995 - Chy2G046780.1 Chy02g02411 2411
2 27849442 27853835 + Chy2G046800.1 Chy02g02413 2413
2 27865781 27868629 + Chy2G046810.1 Chy02g02414 2414
2 27870793 27876331 - Chy2G046820.1 Chy02g02415 2415
12 18661897 18666494 + Chy12G220720.1 Chy12g01472 1472
12 18668282 18670710 - Chy12G220730.1 Chy12g01473 1473
12 18676122 18678165 + Chy12G220750.1 Chy12g01475 1475
4 26305895 26310399 + ClG42_04g0121200.10 Clacu04g1212 1212
4 26312057 26314642 - ClG42_04g0121300.10 Clacu04g1213 1213
4 26326168 26328268 + ClG42_04g0121400.10 Clacu04g1214 1214
6 27167166 27173966 + ClG42_06g0164000.10 Clacu06g1640 1640
6 27176335 27179000 - ClG42_06g0164100.10 Clacu06g1641 1641
6 27233471 27234445 + ClG42_06g0164400.10 Clacu06g1644 1644
6 28196277 28210511 + ClG42_06g0176600.10 Clacu06g1766 1766
4 26537762 26543821 + ClCG04G011530.1 Cla04g01132 1132
4 26544253 26547323 - ClCG04G011540.2 Cla04g01133 1133
4 26556214 26560831 + ClCG04G011555.1 Cla04g01135 1135
6 28700310 28708466 + ClCG06G015380.2 Cla06g01518 1518
6 28710267 28714250 - ClCG06G015390.2 Cla06g01519 1519
6 28771195 28775138 + ClCG06G015420.1 Cla06g01522 1522
6 29766306 29781200 + ClCG06G016580.2 Cla06g01625 1625
10 1225459 1230412 + CmaCh10G002770.1 Cma10g00277 277
10 1231012 1234275 - CmaCh10G002780.1 Cma10g00278 278
10 1238153 1242896 - CmaCh10G002790.1 Cma10g00279 279
10 1252523 1254420 + CmaCh10G002810.1 Cma10g00281 281
11 1151250 1152185 - CmaCh11G002280.1 Cma11g00228 228
11 1160847 1167354 + CmaCh11G002300.1 Cma11g00230 230
11 1172017 1174415 + CmaCh11G002320.1 Cma11g00232 232
11 1175536 1183582 - CmaCh11G002330.1 Cma11g00233 233
13 7183557 7185058 - CmaCh13G008890.1 Cma13g00889 889
13 8014569 8019187 + CmaCh13G010540.1 Cma13g01054 1054
13 8019556 8023584 - CmaCh13G010550.1 Cma13g01055 1055
13 8027109 8032472 + CmaCh13G010570.1 Cma13g01057 1057
18 708562 711284 - CmaCh18G001410.1 Cma18g00141 141
2 24783451 24790463 + MELO3C017257.2.1 Cme02g01800 1800
2 24792080 24795660 - MELO3C017256.2.1 Cme02g01801 1801
2 24832269 24833759 + MELO3C017253.2.1 Cme02g01804 1804
2 25614025 25627812 + MELO3C017136.2.1 Cme02g01923 1923
12 23849030 23850913 - MELO3C002264.2.1 Cme12g01696 1696
12 25208107 25213691 + MELO3C002057.2.1 Cme12g01914 1914
12 25214606 25218198 - MELO3C002056.2.1 Cme12g01915 1915
12 25222411 25225787 + MELO3C002054.2.1 Cme12g01916 1916
2 23125822 23133214 + PI0022179.1 Cmetu02g0900 900
2 23175545 23176815 + PI0027911.1 Cmetu02g1182 1182
2 23149361 23154335 - PI0001097.1 Cmetu02g1950 1950
12 938241 943777 - PI0005031.1 Cmetu12g0108 108
12 925911 928306 - PI0002202.1 Cmetu12g0469 469
10 1304106 1314071 + CmoCh10G002940.1 Cmo10g00294 294
10 1315005 1317878 - CmoCh10G002950.1 Cmo10g00295 295
10 1321980 1328036 - CmoCh10G002960.1 Cmo10g00296 296
10 1338892 1340795 + CmoCh10G002990.1 Cmo10g00299 299
11 1149128 1150063 - CmoCh11G002310.1 Cmo11g00231 231
11 1158379 1164611 + CmoCh11G002330.1 Cmo11g00233 233
11 1169356 1171605 + CmoCh11G002350.1 Cmo11g00235 235
11 1172874 1177724 - CmoCh11G002360.1 Cmo11g00236 236
13 8117156 8118644 - CmoCh13G009180.1 Cmo13g00918 918
13 9028150 9033668 + CmoCh13G010970.1 Cmo13g01097 1097
13 9034689 9037961 - CmoCh13G010990.1 Cmo13g01099 1099
13 9042063 9047588 + CmoCh13G011010.1 Cmo13g01101 1101
18 758497 761227 - CmoCh18G001100.1 Cmo18g00110 110
4 26487569 26492078 + CmPI595203_04g011910.1 Cmu04g1191 1191
4 26493737 26496322 - CmPI595203_04g011920.1 Cmu04g1192 1192
4 26504879 26509911 + CmPI595203_04g011930.1 Cmu04g1193 1193
6 27075803 27082603 + CmPI595203_06g015880.1 Cmu06g1588 1588
6 27084972 27087956 - CmPI595203_06g015890.1 Cmu06g1589 1589
6 27142230 27143204 + CmPI595203_06g015920.1 Cmu06g1592 1592
2 33879215 33880566 + Conep02aG0181600.1 Cone2ag0789 789
2 33883141 33886183 + Conep02aG0181700.1 Cone2ag0790 790
13 129915 136093 + Conep13aG0002300.1 Cone13ag0021 21
13 136417 140071 - Conep13aG0002400.1 Cone13ag0022 22
13 148128 149890 + Conep13aG0002500.1 Cone13ag0023 23
16 1688852 1691943 - Conep16aG0023200.1 Cone16ag0228 228
16 2642539 2650334 - Conep16aG0258900.1 Cone16ag0242 242
19 214741 220298 + Conep19aG0003300.1 Cone19ag0030 30
19 221203 224590 - Conep19aG0003400.1 Cone19ag0031 31
19 230583 234696 + Conep19aG0003500.1 Cone19ag0032 32
4 11502998 11511197 + Cp4.1LG04g14350.1 Cpe04g01439 1439
4 11509636 11512651 - Cp4.1LG04g14480.1 Cpe04g01440 1440
4 11530876 11531817 + Cp4.1LG04g14360.1 Cpe04g01443 1443
4 12010470 12023955 + Cp4.1LG04g15250.1 Cpe04g01528 1528
18 7070461 7071417 - Cp4.1LG18g07170.1 Cpe18g00719 719
18 7094380 7097618 + Cp4.1LG18g07120.1 Cpe18g00722 722
18 7098155 7103322 - Cp4.1LG18g07390.1 Cpe18g00723 723
18 7589752 7605818 + Cp4.1LG18g08200.1 Cpe18g00817 817
20 485850 489685 - Cp4.1LG20g00840.1 Cpe20g00092 92
20 492046 496024 + Cp4.1LG20g00970.1 Cpe20g00093 93
20 496764 501808 - Cp4.1LG20g01070.1 Cpe20g00094 94
20 1369484 1371377 + Cp4.1LG20g02280.1 Cpe20g00241 241
1 28152507 28157821 + CrPI670011_01g014900.1 Cre01g1490 1490
1 28158674 28161256 - CrPI670011_01g014910.1 Cre01g1491 1491
1 28170307 28175100 + CrPI670011_01g014920.1 Cre01g1492 1492
6 31877574 31884414 + CrPI670011_06g023990.1 Cre06g2399 2399
6 31886631 31890109 - CrPI670011_06g024000.1 Cre06g2400 2400
6 31939851 31940828 + CrPI670011_06g024030.1 Cre06g2403 2403
6 32916329 32930617 + CrPI670011_06g025280.1 Cre06g2528 2528
1 2026829 2032886 + CsaV3_1G003270.1 Csa01g00327 327
1 2034239 2038540 - CsaV3_1G003280.1 Csa01g00328 328
1 2048643 2053995 - CsaV3_1G003300.1 Csa01g00330 330
1 2070673 2071689 + CsaV3_1G003320.1 Csa01g00332 332
1 3991872 3995578 - CsaV3_1G006260.1 Csa01g00626 626
1 3998795 4002500 + CsaV3_1G006270.1 Csa01g00627 627
1 4002735 4008902 - CsaV3_1G006280.1 Csa01g00628 628
1 5317986 5319596 + CsaV3_1G008490.1 Csa01g00849 849
7 68759006 68761920 + Hsped.07g24400.1 Hepe07g2440 2440
9 2523595 2525108 - Hsped.09g02930.1 Hepe09g0293 293
9 2571322 2578267 - Hsped.09g02970.1 Hepe09g0297 297
10 1442727 1444969 - Lag0024233.1 Lac10g0188 188
2 1165612 1168592 - Lsi02G001420.1 Lsi02g00142 142
2 1180904 1184643 + Lsi02G001440.1 Lsi02g00144 144
2 1185492 1190922 - Lsi02G001450.1 Lsi02g00145 145
2 3192804 3194826 + Lsi02G003700.1 Lsi02g00370 370
6 24423829 24432006 + Lsi06G013840.1 Lsi06g01384 1384
6 24433157 24437297 - Lsi06G013850.1 Lsi06g01385 1385
6 24484328 24485314 + Lsi06G013880.1 Lsi06g01388 1388
6 25490687 25511259 + Lsi06G015060.1 Lsi06g01506 1506
1 17195041 17200386 + Sed0008386.8 Sed01g2275 2275
1 17213039 17215884 + Sed0023471.3 Sed01g2279 2279
8 1787968 1789465 - Sed0020179.1 Sed08g0300 300
8 1822414 1829020 + Sed0020266.2 Sed08g0303 303
8 1843988 1852767 - Sed0006842.3 Sed08g0307 307
5 74707673 74713509 + Tan0010529.4 Tan05g2320 2320
5 74753150 74755856 + Tan0018282.1 Tan05g2323 2323
9 70699606 70706545 + Tan0001888.2 Tan09g1999 1999
9 70722657 70728787 - Tan0005240.1 Tan09g2002 2002
9 70757357 70759529 + Tan0012205.1 Tan09g2004 2004
17 5160219 5164508 - Vvi17g416 Vvi17g416 416
17 5177471 5186799 + Vvi17g417 Vvi17g417 417
17 5186802 5186931 - Vvi17g418 Vvi17g418 418
17 5190269 5194632 - Vvi17g419 Vvi17g419 419
17 5199096 5205717 - Vvi17g420 Vvi17g420 420
17 5206884 5213522 + Vvi17g421 Vvi17g421 421
17 5221015 5227890 + Vvi17g422 Vvi17g422 422
17 5240729 5241938 + Vvi17g423 Vvi17g423 423
17 5244355 5248671 - Vvi17g424 Vvi17g424 424
17 5258945 5270412 + Vvi17g425 Vvi17g425 425
       

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