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
Vvi19g594 . . Bda07g00386 . . . . . . . Cma01g01101 . Car01g00973 . Sed09g1199 . Cpe02g00800 Bhi09g01719 Tan01g3145 Cmetu01g2066 . Hepe01g1235 Mch11g1230 . . . . . . . . Cone6ag0037 Cone9ag0040 . . Lsi02g01866 Csa07g00987 . . . . . . Bpe11g00564 . . Bma14g00316 . Cmo01g01147 . . . . . . . . . . . . . . Cla09g02040 Cam09g2129 Cec09g2194 . . . . . . Chy01g01074 Cme01g00977
Vvi19g595 Blo03g00534 Blo03g01464 Bda07g00389 Bda09g00415 . Bpe08g01107 . Bma13g01101 . . Cma01g01100 Cma09g00980 Car01g00972 Car09g00891 Sed07g2717 Cpe06g00790 Cpe02g00801 Bhi09g01720 Tan01g3146 Cmetu01g1383 . Hepe01g1234 Mch11g1232 . . . . . . . . Cone6ag0036 Cone9ag0039 Cone14ag1192 Cone15ag1212 Lsi02g01864 Csa07g00986 . . . Blo10g00857 . Bda12g00943 Bpe11g00565 . Bma07g01273 Bma14g00315 . Cmo01g01146 Cmo09g00981 . . . . . . . . . . . . . Cla09g02041 Cam09g2130 Cec09g2195 . . . . . . Chy01g01075 Cme01g00976
Vvi19g596 . Blo03g01465 . . . Bpe08g01106 . . Cmo16g00975 . Cma01g01099 Cma09g00981 . Car09g00892 Sed07g2719 Cpe06g00791 Cpe02g00802 Bhi09g01721 Tan01g3148 Cmetu07g0242 . Hepe01g1233 Mch11g1233 . Cla10g00439 Cam10g0438 Cec10g0460 Cco10g0449 Clacu10g0446 Cmu10g1278 Cre10g0693 Cone6ag0035 Cone9ag0037 . . Lsi02g01863 Csa07g00984 . Cme06g02805 . . . . . . Bma07g01272 . Sed02g1057 Cmo01g01145 Cmo09g00982 . Cma16g00937 . Car16g00901 Cpe14g00761 . Bhi11g00512 Tan01g1796 Cmetu06g2474 . . . . Cla09g02042 Cam09g2131 Cec09g2196 . . . . Lsi05g00531 . Chy06g01869 Cme01g00973
Vvi19g597 . Blo03g01466 Bda07g00391 . . . . . . . . Cma09g00982 . Car09g00893 Sed07g2720 Cpe06g00793 . Bhi09g01723 Tan01g3149 Cmetu01g1530 . Hepe01g1232 Mch11g1234 . . . . . . . . . . Cone14ag1193 Cone15ag1213 Lsi02g01862 Csa07g00981 . . . . . . Bpe11g00569 . . Bma14g00310 . . Cmo09g00984 . . . . . . . . . . . . . Cla09g02043 Cam09g2132 Cec09g2197 . . . . . . Chy01g01077 Cme01g00970
Vvi19g598 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g599 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone15ag1214 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g600 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g601 . . . . Bpe09g00140 . Bma10g00584 Bma13g01103 . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0034 Cone9ag0036 Cone14ag1194 Cone15ag1216 . . . . Blo07g00876 Blo10g00858 Bda05g00690 Bda12g00946 . Bpe03g00764 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g602 Blo03g00529 . Bda07g00392 . . . . . . . . Cma09g00983 . Car09g00894 Sed04g3681 Cpe06g00794 . Bhi09g01725 Tan01g3151 Cmetu01g1653 . . Mch11g1237 . . . . . . . . . Cone9ag0035 . . Lsi02g01861 Csa07g00980 . . . . . . Bpe11g00570 . . Bma14g00309 . . Cmo09g00985 . . . . . . . . . . . . . Cla09g02045 Cam09g2133 Cec09g2198 . . . . . . Chy01g01078 Cme01g00966
Vvi19g603 . . . . Bpe09g00139 . Bma10g00585 Bma13g01104 Cmo16g00976 . . . . . . . . . . . . . . . Cla10g00438 Cam10g0437 Cec10g0459 Cco10g0448 Clacu10g0445 Cmu10g1276 Cre10g0692 Cone6ag0032 Cone9ag0034 . . . Csa03g00447 . Cme06g02804 . Blo10g00859 Bda05g00689 Bda12g00947 . Bpe03g00763 . . Sed13g1501 . . . Cma16g00938 . Car16g00902 Cpe14g00762 . Bhi11g00511 Tan01g1798 Cmetu12g0455 . . . . . . . . . . . Lsi05g00530 . Chy06g01870 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 55200409 55202128 + Bda021824.1 Bda05g00689 689
5 55203168 55204961 + Bda021825.1 Bda05g00690 690
7 4847301 4850768 - Bda025470.1 Bda07g00386 386
7 4876368 4880331 + Bda025474.1 Bda07g00389 389
7 4894427 4896901 + Bda025476.1 Bda07g00391 391
7 4898407 4900419 + Bda025477.1 Bda07g00392 392
9 5133560 5138664 + Bda030992.1 Bda09g00415 415
12 40508837 40514052 + Bda009488.1 Bda12g00943 943
12 40538757 40540616 - Bda009492.1 Bda12g00946 946
12 40541791 40544417 - Bda009493.1 Bda12g00947 947
9 46676370 46686073 - XM_039041347.1 Bhi09g01719 1719
9 46794158 46802507 + XM_039042692.1 Bhi09g01720 1720
9 46845472 46849094 + XM_039041293.1 Bhi09g01721 1721
9 46867232 46870624 + XM_039043501.1 Bhi09g01723 1723
9 46901839 46904462 + XM_039040259.1 Bhi09g01725 1725
11 12022965 12028721 + XM_039048916.1 Bhi11g00511 511
11 12069585 12072414 - XM_039049275.1 Bhi11g00512 512
3 20034612 20036659 + BLOR11710 Blo03g00529 529
3 20369706 20374779 - BLOR11715 Blo03g00534 534
3 41264535 41270113 + BLOR12645 Blo03g01464 1464
3 41293616 41295392 + BLOR12646 Blo03g01465 1465
3 41296582 41298922 + BLOR12647 Blo03g01466 1466
7 27470620 27477778 + BLOR18808 Blo07g00876 876
10 27100804 27109624 + BLOR02647 Blo10g00857 857
10 27116099 27118212 - BLOR02648 Blo10g00858 858
10 27127056 27129235 - BLOR02649 Blo10g00859 859
7 48268993 48271084 - Bma026539.2 Bma07g01272 1272
7 48272961 48275843 - Bma026540.1 Bma07g01273 1273
10 7171284 7179860 - Bma004289.1 Bma10g00584 584
10 7180696 7182423 - Bma004290.1 Bma10g00585 585
13 43974270 43979640 + Bma010228.1 Bma13g01101 1101
13 43984538 43985568 - Bma010230.1 Bma13g01103 1103
13 43987373 43989645 - Bma030624 Bma13g01104 1104
14 3860998 3863033 - Bma010732.1 Bma14g00309 309
14 3864322 3866741 - Bma010733.1 Bma14g00310 310
14 3909676 3939663 - Bma010738.1 Bma14g00315 315
14 3944965 3948704 + Bma010739.1 Bma14g00316 316
3 27667553 27669418 + Bpe012673.1 Bpe03g00763 763
3 27670442 27672271 + Bpe012674.1 Bpe03g00764 764
8 13107665 13109592 - Bpe023233.1 Bpe08g01106 1106
8 13111403 13116054 - Bpe023234.1 Bpe08g01107 1107
9 941525 943966 + Bpe023813.1 Bpe09g00139 139
9 945949 947788 + Bpe023814.1 Bpe09g00140 140
11 4330297 4334034 - Bpe003930.1 Bpe11g00564 564
11 4341057 4345948 + Bpe003931.1 Bpe11g00565 565
11 4371960 4374364 + Bpe003935.1 Bpe11g00569 569
11 4375596 4377470 + Bpe003936.1 Bpe11g00570 570
9 35841769 35849303 - CaPI482276_09g021290.1 Cam09g2129 2129
9 35858212 35868000 + CaPI482276_09g021300.1 Cam09g2130 2130
9 35876908 35880318 + CaPI482276_09g021310.1 Cam09g2131 2131
9 35885855 35888411 + CaPI482276_09g021320.1 Cam09g2132 2132
9 35892253 35894713 + CaPI482276_09g021330.1 Cam09g2133 2133
10 6733879 6740423 + CaPI482276_10g004370.1 Cam10g0437 437
10 6754886 6757490 - CaPI482276_10g004380.1 Cam10g0438 438
1 9265160 9271949 - Carg22390-RA Car01g00972 972
1 9275838 9282983 + Carg22389-RA Car01g00973 973
9 5495693 5503266 + Carg12845-RA Car09g00891 891
9 5505751 5512260 + Carg12846-RA Car09g00892 892
9 5516066 5519290 + Carg12847-RA Car09g00893 893
9 5521606 5525547 + Carg12848-RA Car09g00894 894
16 7360881 7362290 + Carg22353-RA Car16g00901 901
16 7365001 7368918 - Carg22352-RA Car16g00902 902
10 5284967 5291477 + CcPI632755_10g004480.1 Cco10g0448 448
10 5301700 5304236 - CcPI632755_10g004490.1 Cco10g0449 449
9 38864805 38872369 - CePI673135_09g021940.1 Cec09g2194 2194
9 38884111 38891258 + CePI673135_09g021950.1 Cec09g2195 2195
9 38898611 38902060 + CePI673135_09g021960.1 Cec09g2196 2196
9 38907651 38910204 + CePI673135_09g021970.1 Cec09g2197 2197
9 38913403 38915863 + CePI673135_09g021980.1 Cec09g2198 2198
10 5477655 5484251 + CePI673135_10g004590.1 Cec10g0459 459
10 5505570 5508171 - CePI673135_10g004600.1 Cec10g0460 460
1 12076630 12082928 - Chy1G010740.1 Chy01g01074 1074
1 12104380 12111200 + Chy1G010750.1 Chy01g01075 1075
1 12174425 12177057 + Chy1G010770.1 Chy01g01077 1077
1 12194321 12196858 + Chy1G010780.1 Chy01g01078 1078
6 22566950 22574064 + Chy6G123970.1 Chy06g01869 1869
6 22575662 22579842 - Chy6G123980.1 Chy06g01870 1870
10 5530568 5537072 + ClG42_10g0044500.10 Clacu10g0445 445
10 5551941 5554505 - ClG42_10g0044600.10 Clacu10g0446 446
9 37969153 37977126 - ClCG09G020950.2 Cla09g02040 2040
9 37989207 37999290 + ClCG09G020970.2 Cla09g02041 2041
9 38008530 38012224 + ClCG09G020980.2 Cla09g02042 2042
9 38017430 38020517 + ClCG09G020990.1 Cla09g02043 2043
9 38023763 38026669 + ClCG09G021010.1 Cla09g02045 2045
10 5887438 5896946 + ClCG10G004660.2 Cla10g00438 438
10 5909581 5912318 - ClCG10G004670.2 Cla10g00439 439
1 8058082 8062387 - CmaCh01G010990.1 Cma01g01099 1099
1 8063260 8070561 - CmaCh01G011000.1 Cma01g01100 1100
1 8073976 8083094 + CmaCh01G011010.1 Cma01g01101 1101
9 4982997 4990532 + CmaCh09G009800.1 Cma09g00980 980
9 4993888 5000316 + CmaCh09G009810.1 Cma09g00981 981
9 5003892 5008912 + CmaCh09G009820.1 Cma09g00982 982
9 5010595 5014892 + CmaCh09G009830.1 Cma09g00983 983
16 7193013 7196701 + CmaCh16G009370.1 Cma16g00937 937
16 7199480 7203431 - CmaCh16G009380.1 Cma16g00938 938
1 11289874 11292504 - MELO3C024895.2.1 Cme01g00966 966
1 11324038 11329264 - MELO3C024890.2.1 Cme01g00970 970
1 11384306 11388057 - MELO3C013100.2.1 Cme01g00973 973
1 11457959 11465636 - MELO3C013101.2.1 Cme01g00976 976
1 11494596 11500364 + MELO3C013102.2.1 Cme01g00977 977
6 35249459 35253667 + MELO3C014143.2.1 Cme06g02804 2804
6 35254658 35256624 - MELO3C014144.2.1 Cme06g02805 2805
1 11823796 11831691 - PI0019991.2 Cmetu01g1383 1383
1 12656100 12659602 + PI0014457.1 Cmetu01g1530 1530
1 12696679 12699778 + PI0016903.1 Cmetu01g1653 1653
1 24454336 24462381 - PI0028285.1 Cmetu01g2066 2066
6 26850030 26851978 + PI0007115.1 Cmetu06g2474 2474
7 3046601 3049074 + PI0008602.1 Cmetu07g0242 242
12 24553437 24558518 - PI0019714.1 Cmetu12g0455 455
1 9388579 9393398 - CmoCh01G011450.1 Cmo01g01145 1145
1 9395372 9402800 - CmoCh01G011460.1 Cmo01g01146 1146
1 9406608 9416026 + CmoCh01G011470.1 Cmo01g01147 1147
9 5199176 5206892 + CmoCh09G009810.1 Cmo09g00981 981
9 5209836 5216211 + CmoCh09G009820.1 Cmo09g00982 982
9 5220949 5224907 + CmoCh09G009840.1 Cmo09g00984 984
9 5227339 5231371 + CmoCh09G009850.1 Cmo09g00985 985
16 6636999 6638446 + CmoCh16G009750.1 Cmo16g00975 975
16 6641397 6645388 - CmoCh16G009760.1 Cmo16g00976 976
10 5667383 5673891 + CmPI595203_10g012760.1 Cmu10g1276 1276
10 5688773 5691429 - CmPI595203_10g012780.1 Cmu10g1278 1278
6 196173 200074 + Conep06aG0003200.1 Cone6ag0032 32
6 207780 208616 + Conep06aG0003400.1 Cone6ag0034 34
6 209648 211008 - Conep06aG0003500.1 Cone6ag0035 35
6 216015 220827 - Conep06aG0003600.1 Cone6ag0036 36
6 225996 228842 + Conep06aG0003700.1 Cone6ag0037 37
9 149885 151714 + Conep09aG0003400.1 Cone9ag0034 34
9 153860 155444 - Conep09aG0003500.1 Cone9ag0035 35
9 155629 159086 + Conep09aG0003600.1 Cone9ag0036 36
9 158582 160073 - Conep09aG0003700.1 Cone9ag0037 37
9 167576 172214 - Conep09aG0003900.1 Cone9ag0039 39
9 173759 176599 + Conep09aG0004000.1 Cone9ag0040 40
14 9726814 9732010 + Conep14aG0121600.1 Cone14ag1192 1192
14 9732893 9736220 + Conep14aG0121700.1 Cone14ag1193 1193
14 9737571 9739545 - Conep14aG0121800.1 Cone14ag1194 1194
15 9632991 9663695 + Conep15aG0124100.1 Cone15ag1212 1212
15 9668927 9672185 + Conep15aG0124200.1 Cone15ag1213 1213
15 9673319 9675263 + Conep15aG0124300.1 Cone15ag1214 1214
15 9676918 9678875 - Conep15aG0124500.1 Cone15ag1216 1216
2 5117043 5124508 - Cp4.1LG02g00760.1 Cpe02g00800 800
2 5128672 5135765 + Cp4.1LG02g00830.1 Cpe02g00801 801
2 5136619 5141398 + Cp4.1LG02g00660.1 Cpe02g00802 802
6 5040377 5048029 + Cp4.1LG06g08650.1 Cpe06g00790 790
6 5063967 5069342 + Cp4.1LG06g08620.1 Cpe06g00791 791
6 5075379 5080539 + Cp4.1LG06g08660.1 Cpe06g00793 793
6 5082336 5086553 + Cp4.1LG06g08630.1 Cpe06g00794 794
14 5978983 5979682 + Cp4.1LG14g07620.1 Cpe14g00761 761
14 5982340 5986924 - Cp4.1LG14g07600.1 Cpe14g00762 762
10 6588228 6594778 + CrPI670011_10g006920.1 Cre10g0692 692
10 6607628 6610244 - CrPI670011_10g006930.1 Cre10g0693 693
3 3777136 3782031 + CsaV3_3G004470.1 Csa03g00447 447
7 8644483 8646997 - CsaV3_7G018710.1 Csa07g00980 980
7 8662406 8665083 - CsaV3_7G018720.1 Csa07g00981 981
7 8713044 8716345 - CsaV3_7G018750.1 Csa07g00984 984
7 8736540 8743389 - CsaV3_7G018770.1 Csa07g00986 986
7 8761829 8769840 + CsaV3_7G018780.1 Csa07g00987 987
1 77549723 77553248 - Hsped.01g12320.1 Hepe01g1232 1232
1 77561440 77564852 - Hsped.01g12330.1 Hepe01g1233 1233
1 77569017 77576568 - Hsped.01g12340.1 Hepe01g1234 1234
1 77591897 77601170 + Hsped.01g12350.1 Hepe01g1235 1235
2 24366170 24369737 - Lsi02G018610.1 Lsi02g01861 1861
2 24374295 24377726 - Lsi02G018620.1 Lsi02g01862 1862
2 24382275 24386083 - Lsi02G018630.1 Lsi02g01863 1863
2 24391716 24399489 - Lsi02G018640.1 Lsi02g01864 1864
2 24431593 24434033 + Lsi02G018660.1 Lsi02g01866 1866
5 6636179 6641050 + Lsi05G005300.1 Lsi05g00530 530
5 6642421 6645394 - Lsi05G005310.1 Lsi05g00531 531
11 8702967 8710886 - MC11g1018 Mch11g1230 1230
11 8732080 8739808 + MC11g1020 Mch11g1232 1232
11 8743503 8747086 + MC11g1021 Mch11g1233 1233
11 8753575 8755778 + MC11g1022 Mch11g1234 1234
11 8763748 8767036 + MC11g1023 Mch11g1237 1237
2 47931084 47933458 + Sed0010853.1 Sed02g1057 1057
4 45780540 45788857 - Sed0012266.1 Sed04g3681 3681
7 42373583 42382130 + Sed0001590.1 Sed07g2717 2717
7 42384795 42389205 + Sed0019587.2 Sed07g2719 2719
7 42391248 42394887 + Sed0018719.1 Sed07g2720 2720
9 36182154 36192351 - Sed0006128.1 Sed09g1199 1199
13 20210570 20216386 - Sed0012478.1 Sed13g1501 1501
1 19208511 19211256 + Tan0005741.2 Tan01g1796 1796
1 19213615 19218547 - Tan0016270.1 Tan01g1798 1798
1 84949977 84961392 - Tan0018811.1 Tan01g3145 3145
1 84994266 85004525 + Tan0007690.1 Tan01g3146 3146
1 85019506 85023197 + Tan0006231.2 Tan01g3148 3148
1 85037835 85041615 + Tan0008934.1 Tan01g3149 3149
1 85046114 85049869 + Tan0022271.2 Tan01g3151 3151
19 7518930 7525059 - Vvi19g594 Vvi19g594 594
19 7546610 7555444 + Vvi19g595 Vvi19g595 595
19 7622502 7624507 + Vvi19g596 Vvi19g596 596
19 7636005 7640409 + Vvi19g597 Vvi19g597 597
19 7640415 7641515 - Vvi19g598 Vvi19g598 598
19 7643695 7652234 + Vvi19g599 Vvi19g599 599
19 7653782 7658169 + Vvi19g600 Vvi19g600 600
19 7659803 7663373 - Vvi19g601 Vvi19g601 601
19 7666718 7669351 + Vvi19g602 Vvi19g602 602
19 7671331 7674058 - Vvi19g603 Vvi19g603 603
       

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