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
Vvi3g126 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g127 . . . . . . . . . . . . . . Sed05g2229 . . Bhi05g01735 Tan02g0703 Cmetu01g2553 . . . . Cla02g00440 Cam02g0449 Cec02g0448 Cco02g0467 Clacu02g0451 Cmu02g0445 Cre02g0779 Cone12ag1220 . . . . . Chy11g00283 Cme01g01278 . Blo13g00522 Bda15g01043 . Bpe15g00824 . . Bma08g00763 . . . . . . . . . Bhi10g01879 Tan05g1171 . . Hepe08g0271 . . . . . . . . . . Csa02g01366 Chy01g00692 Cme11g00405
Vvi3g128 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma19g00726 . . . . . . . . . . . . . . . . . . . . . .
Vvi3g129 . . . . . Bpe12g00112 . . Cmo19g00737 . . . . . Sed08g0469 . Cpe15g00583 Bhi05g01734 Tan02g0702 Cmetu06g1183 . Hepe02g0438 . . Cla02g00439 Cam02g0448 Cec02g0446 Cco02g0466 Clacu02g0450 Cmu02g0444 Cre02g0778 Cone2ag0203 Cone16ag0840 . . . Csa07g00087 . Cme01g01277 Blo04g00558 Blo13g00521 . Bda14g00607 Bpe15g00822 . Bma03g00599 Bma08g00616 . . . Cma11g01385 Cma19g00728 . Car19g00558 . . . . . . . . . . . . . . . . Lsi11g01187 . Chy01g00691 .
Vvi3g130 . . . . . Bpe12g00113 . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag1222 Cone8ag1274 . . . . . . . Blo13g00520 Bda15g01042 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g131 . Blo15g00370 . . Bpe07g00724 . . Bma12g00931 . . Cma02g00322 . Car02g00203 Car20g00668 . . . . . . . . . . . . . . . . . . . . . Lsi10g00474 . Chy11g00280 . Blo04g00559 . . Bda14g00608 Bpe15g00821 . Bma03g00600 . Sed01g0210 Cmo02g00316 . . . . . Cpe16g00303 Cpe05g01319 Bhi10g01876 Tan05g1167 Cmetu11g0584 . Hepe08g0274 . . Cla02g01147 Cam02g1224 Cec02g1231 Cco02g1273 Clacu02g1202 Cmu02g1172 Cre02g1482 . Csa02g01368 . Cme11g00400
Vvi3g132 . . . . . Bpe12g00114 . . Cmo19g00738 . . . . . . . Cpe15g00584 Bhi05g01732 . . . . . . Cla02g00438 Cam02g0447 Cec02g0445 Cco02g0464 Clacu02g0449 Cmu02g0443 Cre02g0777 . . . . . Csa07g00088 . Cme01g01276 . Blo13g00519 Bda15g01041 . . . . Bma08g00761 . . . . Cma19g00729 . Car19g00559 . . . . . . . . . . . . . . . . Lsi11g01188 . Chy01g00690 .
Vvi3g133 . . . . . Bpe12g00115 . . . . . . . Car20g00667 . . . . . . . . . . . . . . . . . Cone8ag0852 . . Cone9ag1605 . . Chy11g00279 . Blo04g00560 Blo13g00517 Bda15g01040 Bda14g00609 Bpe15g00820 . Bma03g00601 Bma08g00760 . . . . . . . Cpe16g00304 . . . . . . . . Cla02g01148 Cam02g1225 Cec02g1232 Cco02g1274 Clacu02g1205 Cmu02g1174 Cre02g1483 . Csa02g01369 . Cme11g00399
Vvi3g134 . . . . . . . . . . Cma02g00321 . Car02g00202 Car20g00666 . . . . . . . . . . . . . . . . . . . . . Lsi10g00476 . Chy11g00278 . . . . . . . . . Sed01g0209 Cmo02g00315 . . . . . Cpe16g00305 Cpe05g01320 Bhi10g01872 Tan05g1164 Cmetu11g2261 . Hepe08g0276 . . Cla02g01149 Cam02g1226 Cec02g1233 Cco02g1275 Clacu02g1206 Cmu02g1175 Cre02g1484 . Csa02g01370 . Cme11g00398
Vvi3g135 . . . . . Bpe12g00116 . . Cmo19g00739 . . . . . Sed01g3135 . Cpe15g00585 Bhi05g01731 Tan02g0700 Cmetu01g0199 . Hepe02g0435 . . Cla02g00437 Cam02g0446 Cec02g0444 Cco02g0462 Clacu02g0448 Cmu02g0442 Cre02g0776 Cone12ag1224 Cone8ag1275 . . . . . Cme01g01275 Blo04g00561 Blo13g00516 Bda15g01039 Bda14g00610 Bpe15g00819 . Bma03g00602 . . . . . Cma19g00731 . Car19g00560 . . . . . . . . . . . . . . . . Lsi11g01191 . Chy01g00689 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
14 4580977 4584675 - Bda027361.1 Bda14g00607 607
14 4586965 4587921 + Bda027362.1 Bda14g00608 608
14 4588985 4589491 + Bda027363.1 Bda14g00609 609
14 4590760 4591362 + Bda027364.2 Bda14g00610 610
15 19432940 19433539 - Bda013027.1 Bda15g01039 1039
15 19435646 19435981 - Bda013028.1 Bda15g01040 1040
15 19454149 19457456 + Bda013029.1 Bda15g01041 1041
15 19458662 19460182 - Bda013030.1 Bda15g01042 1042
15 19468093 19469988 - Bda013031.1 Bda15g01043 1043
5 55884506 55885752 - XM_039032892.1 Bhi05g01731 1731
5 55893446 55897298 + XM_039030923.1 Bhi05g01732 1732
5 55907369 55912007 + XM_039032784.1 Bhi05g01734 1734
5 55945186 55947944 - XM_039031496.1 Bhi05g01735 1735
10 46709921 46712234 - XM_039045005.1 Bhi10g01872 1872
10 46824672 46825945 - XM_039046861.1 Bhi10g01876 1876
10 46915787 46920013 - XM_039044984.1 Bhi10g01879 1879
4 4819538 4823371 - BLOR13470 Blo04g00558 558
4 4825994 4826947 + BLOR13471 Blo04g00559 559
4 4835515 4836153 + BLOR13472 Blo04g00560 560
4 4837151 4837774 + BLOR13473 Blo04g00561 561
13 26688647 26689198 - BLOR05797 Blo13g00516 516
13 26692031 26692537 - BLOR05798 Blo13g00517 517
13 26706060 26712536 + BLOR05800 Blo13g00519 519
13 26746045 26747880 - BLOR05801 Blo13g00520 520
13 26749672 26753277 + BLOR05802 Blo13g00521 521
13 26770517 26772619 - BLOR05803 Blo13g00522 522
15 5091731 5092687 + BLOR06764 Blo15g00370 370
3 4942267 4945965 - Bma016890.1 Bma03g00599 599
3 4950448 4951404 + Bma016891.1 Bma03g00600 600
3 4952437 4952778 + Bma016892.1 Bma03g00601 601
3 4953951 4954565 + Bma016893.1 Bma03g00602 602
8 38648055 38651066 + Bma027922.1 Bma08g00616 616
8 44594133 44594738 - Bma028137.1 Bma08g00760 760
8 44605421 44608144 + Bma028138.3 Bma08g00761 761
8 44621086 44656917 - Bma028140.1 Bma08g00763 763
12 40980794 40981750 - Bma008270.1 Bma12g00931 931
7 13793000 13793956 - Bpe021568.1 Bpe07g00724 724
12 805137 808760 - Bpe005352.1 Bpe12g00112 112
12 811053 812888 + Bpe005353.1 Bpe12g00113 113
12 814765 824040 - Bpe005354.2 Bpe12g00114 114
12 826960 827466 + Bpe005355.1 Bpe12g00115 115
12 829545 830425 + Bpe005356.1 Bpe12g00116 116
15 18319189 18319791 - Bpe001745.1 Bpe15g00819 819
15 18320877 18321212 - Bpe001746.1 Bpe15g00820 820
15 18322243 18323199 - Bpe001747.1 Bpe15g00821 821
15 18328173 18331904 + Bpe001748.1 Bpe15g00822 822
15 18334320 18336249 - Bpe024582 Bpe15g00824 824
2 5181037 5181660 - CaPI482276_02g004460.1 Cam02g0446 446
2 5195947 5203653 + CaPI482276_02g004470.1 Cam02g0447 447
2 5203675 5208281 + CaPI482276_02g004480.1 Cam02g0448 448
2 5212029 5214212 - CaPI482276_02g004490.1 Cam02g0449 449
2 24222775 24223731 + CaPI482276_02g012240.1 Cam02g1224 1224
2 24295216 24295665 + CaPI482276_02g012250.1 Cam02g1225 1225
2 24319439 24321379 + CaPI482276_02g012260.1 Cam02g1226 1226
2 1221099 1222731 - Carg19792-RA Car02g00202 202
2 1224388 1225344 - Carg19793-RA Car02g00203 203
19 7104072 7107734 - Carg19361-RA Car19g00558 558
19 7107750 7115127 - Carg19360-RA Car19g00559 559
19 7116188 7118484 + Carg19359-RA Car19g00560 560
20 3754462 3756378 - Carg16186-RA Car20g00666 666
20 3758146 3758586 - Carg16187-RA Car20g00667 667
20 3759898 3760854 - Carg16188-RA Car20g00668 668
2 4182867 4183889 - CcPI632755_02g004620.1 Cco02g0462 462
2 4200619 4204433 + CcPI632755_02g004640.1 Cco02g0464 464
2 4212170 4212842 + CcPI632755_02g004660.1 Cco02g0466 466
2 4216638 4218822 - CcPI632755_02g004670.1 Cco02g0467 467
2 24190738 24191763 + CcPI632755_02g012730.1 Cco02g1273 1273
2 24257300 24257743 + CcPI632755_02g012740.1 Cco02g1274 1274
2 24290491 24292431 + CcPI632755_02g012750.1 Cco02g1275 1275
2 4203714 4204738 - CePI673135_02g004440.1 Cec02g0444 444
2 4217993 4222212 + CePI673135_02g004450.1 Cec02g0445 445
2 4225704 4229399 + CePI673135_02g004460.1 Cec02g0446 446
2 4233986 4236151 - CePI673135_02g004480.1 Cec02g0448 448
2 28671908 28672864 + CePI673135_02g012310.1 Cec02g1231 1231
2 28752831 28753274 + CePI673135_02g012320.1 Cec02g1232 1232
2 28786548 28788488 + CePI673135_02g012330.1 Cec02g1233 1233
1 5037180 5037822 - Chy1G006890.1 Chy01g00689 689
1 5045258 5049714 + Chy1G006900.1 Chy01g00690 690
1 5053160 5056930 + Chy1G006910.1 Chy01g00691 691
1 5059981 5061932 - Chy1G006920.1 Chy01g00692 692
11 2570827 2572764 - Chy11G188580.1 Chy11g00278 278
11 2576365 2576718 - Chy11G188590.1 Chy11g00279 279
11 2579033 2579989 - Chy11G188600.1 Chy11g00280 280
11 2603104 2605239 - Chy11G188630.1 Chy11g00283 283
2 4056524 4057546 - ClG42_02g0044800.10 Clacu02g0448 448
2 4071975 4079725 + ClG42_02g0044900.10 Clacu02g0449 449
2 4079747 4084317 + ClG42_02g0045000.10 Clacu02g0450 450
2 4087998 4090180 - ClG42_02g0045100.10 Clacu02g0451 451
2 24376517 24377473 + ClG42_02g0120200.10 Clacu02g1202 1202
2 24453736 24454185 + ClG42_02g0120500.10 Clacu02g1205 1205
2 24478180 24480120 + ClG42_02g0120600.10 Clacu02g1206 1206
2 4305437 4306459 - ClCG02G004220.2 Cla02g00437 437
2 4322190 4329765 + ClCG02G004230.2 Cla02g00438 438
2 4329946 4335083 + ClCG02G004240.1 Cla02g00439 439
2 4338495 4340677 - ClCG02G004250.2 Cla02g00440 440
2 24652614 24653570 + ClCG02G011700.1 Cla02g01147 1147
2 24732202 24732651 + ClCG02G011710.1 Cla02g01148 1148
2 24758461 24760401 + ClCG02G011720.1 Cla02g01149 1149
2 1549047 1550999 - CmaCh02G003210.1 Cma02g00321 321
2 1552393 1553349 - CmaCh02G003220.1 Cma02g00322 322
11 9127841 9131449 - CmaCh11G013850.1 Cma11g01385 1385
19 7325682 7333957 + CmaCh19G007260.1 Cma19g00726 726
19 7336324 7339983 - CmaCh19G007280.1 Cma19g00728 728
19 7340005 7346906 - CmaCh19G007290.1 Cma19g00729 729
19 7348385 7350955 + CmaCh19G007310.1 Cma19g00731 731
1 16131685 16132748 - MELO3C013368.2.1 Cme01g01275 1275
1 16136845 16139198 + MELO3C013369.2.1 Cme01g01276 1276
1 16143740 16148462 + MELO3C013370.2.1 Cme01g01277 1277
1 16151567 16154031 - MELO3C013371.2.1 Cme01g01278 1278
11 4042327 4044264 - MELO3C020800.2.1 Cme11g00398 398
11 4046444 4047259 - MELO3C020799.2.1 Cme11g00399 399
11 4051623 4052871 - MELO3C020798.2.1 Cme11g00400 400
11 4074577 4077257 - MELO3C020794.2.1 Cme11g00405 405
1 5345965 5347117 - PI0019228.1 Cmetu01g0199 199
1 5369174 5371125 - PI0021801.1 Cmetu01g2553 2553
6 30376635 30380329 - PI0028379.2 Cmetu06g1183 1183
11 28400239 28401848 + PI0018694.1 Cmetu11g0584 584
11 28412065 28414237 + PI0004525.1 Cmetu11g2261 2261
2 1615228 1617180 - CmoCh02G003150.1 Cmo02g00315 315
2 1618836 1619792 - CmoCh02G003160.1 Cmo02g00316 316
19 7592431 7596093 - CmoCh19G007370.1 Cmo19g00737 737
19 7598424 7603491 - CmoCh19G007380.1 Cmo19g00738 738
19 7604933 7607125 + CmoCh19G007390.1 Cmo19g00739 739
2 4052565 4053590 - CmPI595203_02g004420.1 Cmu02g0442 442
2 4068012 4072423 + CmPI595203_02g004430.1 Cmu02g0443 443
2 4075806 4079513 + CmPI595203_02g004440.1 Cmu02g0444 444
2 4084055 4086237 - CmPI595203_02g004450.1 Cmu02g0445 445
2 24244353 24245309 + CmPI595203_02g011720.1 Cmu02g1172 1172
2 24321476 24321925 + CmPI595203_02g011740.1 Cmu02g1174 1174
2 24345867 24347807 + CmPI595203_02g011750.1 Cmu02g1175 1175
2 1068730 1072550 + Conep02aG0020800.1 Cone2ag0203 203
8 8468277 8469063 + Conep08aG0087800.1 Cone8ag0852 852
8 10520468 10522596 + Conep08aG0131200.1 Cone8ag1274 1274
8 10525508 10527010 + Conep08aG0131300.1 Cone8ag1275 1275
9 11489957 11490578 + Conep09aG0165500.1 Cone9ag1605 1605
12 9489621 9492021 + Conep12aG0126000.1 Cone12ag1220 1220
12 9503891 9506148 + Conep12aG0126200.1 Cone12ag1222 1222
12 9510955 9512655 + Conep12aG0126400.1 Cone12ag1224 1224
16 9022307 9025942 - Conep16aG0320700.1 Cone16ag0840 840
5 9261183 9262139 + Cp4.1LG05g13190.1 Cpe05g01319 1319
5 9264437 9266389 + Cp4.1LG05g13200.1 Cpe05g01320 1320
15 6633573 6637232 - Cp4.1LG15g05830.1 Cpe15g00583 583
15 6639493 6644598 - Cp4.1LG15g05810.1 Cpe15g00584 584
15 6646077 6646643 + Cp4.1LG15g05730.1 Cpe15g00585 585
16 4955817 4956773 + Cp4.1LG16g03060.1 Cpe16g00303 303
16 4958063 4958503 + Cp4.1LG16g02970.1 Cpe16g00304 304
16 4960519 4962435 + Cp4.1LG16g02960.1 Cpe16g00305 305
2 4621019 4622036 - CrPI670011_02g007760.1 Cre02g0776 776
2 4638035 4642012 + CrPI670011_02g007770.1 Cre02g0777 777
2 4645884 4650388 + CrPI670011_02g007780.1 Cre02g0778 778
2 4654069 4656251 - CrPI670011_02g007790.1 Cre02g0779 779
2 26770240 26771196 + CrPI670011_02g014820.1 Cre02g1482 1482
2 26856287 26856730 + CrPI670011_02g014830.1 Cre02g1483 1483
2 26882677 26884617 + CrPI670011_02g014840.1 Cre02g1484 1484
2 13124263 13128085 + CsaV3_2G015820.1 Csa02g01366 1366
2 13144660 13146584 + CsaV3_2G015840.1 Csa02g01368 1368
2 13149526 13150014 + CsaV3_2G015850.1 Csa02g01369 1369
2 13152737 13155074 + CsaV3_2G015860.1 Csa02g01370 1370
7 807914 813459 - CsaV3_7G000870.1 Csa07g00087 87
7 817402 821430 - CsaV3_7G000880.1 Csa07g00088 88
2 4199571 4200904 - Hsped.02g04350.1 Hepe02g0435 435
2 4214610 4220251 + Hsped.02g04380.1 Hepe02g0438 438
8 2469922 2472016 + Hsped.08g02710.1 Hepe08g0271 271
8 2484404 2485742 + Hsped.08g02740.1 Hepe08g0274 274
8 2496954 2498897 + Hsped.08g02760.1 Hepe08g0276 276
10 6867863 6869391 + Lsi10G004740.1 Lsi10g00474 474
10 6882761 6884701 + Lsi10G004760.1 Lsi10g00476 476
11 20341825 20345532 - Lsi11G011870.1 Lsi11g01187 1187
11 20352628 20356964 - Lsi11G011880.1 Lsi11g01188 1188
11 20362963 20363589 + Lsi11G011910.1 Lsi11g01191 1191
1 1678412 1680597 - Sed0004005.1 Sed01g0209 209
1 1682899 1684342 - Sed0011058.1 Sed01g0210 210
1 54530914 54531990 - Sed0025854.1 Sed01g3135 3135
5 35040420 35042921 - Sed0027530.1 Sed05g2229 2229
8 2936419 2940376 - Sed0028230.1 Sed08g0469 469
2 6564220 6565295 - Tan0002232.1 Tan02g0700 700
2 6581603 6587341 + Tan0017687.2 Tan02g0702 702
2 6589098 6591103 - Tan0012310.1 Tan02g0703 703
5 10917445 10919655 - Tan0012668.1 Tan05g1164 1164
5 11004493 11006103 - Tan0008851.1 Tan05g1167 1167
5 11187814 11189751 - Tan0020546.1 Tan05g1171 1171
3 1397563 1400843 + Vvi3g126 Vvi3g126 126
3 1402022 1405517 + Vvi3g127 Vvi3g127 127
3 1405935 1408542 + Vvi3g128 Vvi3g128 128
3 1424546 1429397 - Vvi3g129 Vvi3g129 129
3 1436851 1438669 + Vvi3g130 Vvi3g130 130
3 1441275 1442006 + Vvi3g131 Vvi3g131 131
3 1443095 1447485 - Vvi3g132 Vvi3g132 132
3 1449295 1450092 + Vvi3g133 Vvi3g133 133
3 1459599 1461579 + Vvi3g134 Vvi3g134 134
3 1468179 1469527 + Vvi3g135 Vvi3g135 135
       

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