Hierarchical alignments

  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 two 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.
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Select Download 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
Vvi8g1083 Blo01g01233 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi8g1084 . . . . Bpe04g01556 . Bma04g01609 . Cmo06g00421 . . . . . . . Cpe08g01062 . . . . . . . . . . . . . . . . . Cone19ag1214 . . . Cme04g02456 . Blo09g00526 Bda03g01695 Bda05g01199 . . . . Sed02g0587 . . Cma06g00426 . Car06g00366 . . . Bhi11g02013 Tan08g1804 Cmetu04g1992 . . . . Cla10g01862 Cam10g1919 Cec10g1974 Cco10g1946 Clacu10g1936 Cmu10g2680 Cre10g2068 Lsi03g01957 Csa03g03353 Chy04g01988 .
Vvi8g1085 . . . . Bpe04g01557 Bpe03g01262 Bma04g01610 Bma10g00064 . Cmo14g00244 . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag1215 . . . Cme04g02457 Blo07g01371 Blo09g00527 Bda03g01696 Bda05g01200 . . . . Sed04g1427 . . . Cma14g00253 . Car14g00231 . . Bhi11g02015 Tan08g1806 Cmetu04g0898 . . . . . . . . . . . Lsi03g01958 . . .
Vvi8g1086 . . Bda01g00372 . . Bpe03g01263 . Bma10g00063 Cmo06g00420 . . Cma07g00884 . Car07g00873 . . Cpe08g01063 Bhi03g01538 . . . Hepe04g0962 . . Cla04g00942 Cam04g0981 Cec04g1102 Cco04g1163 Clacu04g1008 Cmu04g0994 Cre04g1050 . . Cone13ag1230 . Lsi01g01276 Csa06g02633 Chy08g00891 Cme04g02458 Blo07g01372 . . Bda05g01201 . Bpe02g00737 Bma01g01975 . Sed04g1426 . Cmo07g00916 Cma06g00425 . Car06g00365 . Cpe03g00220 Cpe19g00441 Bhi11g02016 Tan08g1807 Cmetu04g0283 Lac10g2940 Hepe05g0316 . . Cla10g01863 Cam10g1920 Cec10g1975 Cco10g1947 Clacu10g1937 Cmu10g2681 Cre10g2069 Lsi03g01959 . . Cme08g01252
Vvi1g1001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi8g1087 . . . . . . . Bma10g00062 . Cmo14g00243 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed02g1646 . . . Cma14g00252 . Car14g00230 . . Bhi11g02018 Tan04g2363 Cmetu06g1316 . . . . . . . . . . . . . . .
Vvi8g1088 . . . . Bpe04g01558 . . . . Cmo14g00242 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda03g01697 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi8g1089 . . . . . Bpe03g01264 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme04g02459 Blo07g01373 . . Bda05g01202 . . . . Sed02g0588 . . . . . . Cpe03g00219 . Bhi11g02019 Tan08g1809 Cmetu09g1198 . . . . Cla10g01864 Cam10g1921 Cec10g1976 Cco10g1948 Clacu10g1938 Cmu10g2682 Cre10g2070 Lsi03g01960 . . .
Vvi8g1090 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi8g1091 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe03g00218 . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 29588154 29591127 + Bda002350.1 Bda01g00372 372
3 56380553 56393769 - Bda018256.1 Bda03g01695 1695
3 56394646 56398450 - Bda018257.1 Bda03g01696 1696
3 56401365 56402024 + Bda018258.1 Bda03g01697 1697
5 59991462 59997786 - Bda022369.1 Bda05g01199 1199
5 59998272 60001876 - Bda022370.1 Bda05g01200 1200
5 60003121 60006353 - Bda022371.1 Bda05g01201 1201
5 60007131 60010387 + Bda022372.1 Bda05g01202 1202
3 32976438 32990155 - XM_039026201.1 Bhi03g01538 1538
11 57264905 57274083 - XM_039049076.1 Bhi11g02013 2013
11 57382724 57387235 - XM_039049899.1 Bhi11g02015 2015
11 57424247 57428891 - XM_039047364.1 Bhi11g02016 2016
11 57436297 57439824 + XM_039050360.1 Bhi11g02018 2018
11 57436319 57439824 + XM_039050361.1 Bhi11g02019 2019
1 46585136 46592972 - BLOR01233 Blo01g01233 1233
7 33840541 33844024 - BLOR19303 Blo07g01371 1371
7 33846592 33849709 - BLOR19304 Blo07g01372 1372
7 33851653 33855062 + BLOR19305 Blo07g01373 1373
9 16468980 16474123 - BLOR21441 Blo09g00526 526
9 16476885 16480708 - BLOR21442 Blo09g00527 527
1 73575405 73578479 - Bma002757.1 Bma01g01975 1975
4 52024310 52036057 - Bma020537.1 Bma04g01609 1609
4 52037302 52041083 - Bma020538.1 Bma04g01610 1610
10 597551 600913 - Bma003681.1 Bma10g00062 62
10 601870 604827 + Bma003682.1 Bma10g00063 63
10 605967 609500 + Bma003683.1 Bma10g00064 64
2 5120631 5123708 + Bpe008574.3 Bpe02g00737 737
3 31206619 31210403 - Bpe013158.1 Bpe03g01262 1262
3 31211867 31215130 - Bpe013159.1 Bpe03g01263 1263
3 31216963 31224062 + Bpe013160.1 Bpe03g01264 1264
4 21894510 21906497 - Bpe016277.1 Bpe04g01556 1556
4 21907849 21911689 - Bpe016278.1 Bpe04g01557 1557
4 21913977 21914715 + Bpe016279.1 Bpe04g01558 1558
4 23945312 23950257 + CaPI482276_04g009810.1 Cam04g0981 981
10 33240298 33245519 - CaPI482276_10g019190.1 Cam10g1919 1919
10 33250459 33261827 - CaPI482276_10g019200.1 Cam10g1920 1920
10 33266696 33269461 + CaPI482276_10g019210.1 Cam10g1921 1921
6 2000531 2005239 + Carg00943-RA Car06g00365 365
6 2006098 2012092 + Carg00942-RA Car06g00366 366
7 4687123 4691427 - Carg25571-RA Car07g00873 873
14 1077851 1081189 - Carg03725-RA Car14g00230 230
14 1082388 1091769 + Carg03724-RA Car14g00231 231
4 27055488 27060404 + CcPI632755_04g011630.1 Cco04g1163 1163
10 33016569 33021815 - CcPI632755_10g019460.1 Cco10g1946 1946
10 33026718 33038034 - CcPI632755_10g019470.1 Cco10g1947 1947
10 33045048 33047817 + CcPI632755_10g019480.1 Cco10g1948 1948
4 30577808 30582768 + CePI673135_04g011020.1 Cec04g1102 1102
10 34514549 34519517 - CePI673135_10g019740.1 Cec10g1974 1974
10 34522892 34535834 - CePI673135_10g019750.1 Cec10g1975 1975
10 34541899 34545039 + CePI673135_10g019760.1 Cec10g1976 1976
4 25716007 25720378 - Chy4G087060.1 Chy04g01988 1988
8 16326256 16337249 + Chy8G154960.1 Chy08g00891 891
4 24313976 24318924 + ClG42_04g0100800.10 Clacu04g1008 1008
10 32953156 32958112 - ClG42_10g0193600.10 Clacu10g1936 1936
10 32962940 32974349 - ClG42_10g0193700.10 Clacu10g1937 1937
10 32978838 32981604 + ClG42_10g0193800.10 Clacu10g1938 1938
4 24478256 24483322 + ClCG04G009580.1 Cla04g00942 942
10 34527777 34533139 - ClCG10G019590.1 Cla10g01862 1862
10 34538337 34549774 - ClCG10G019600.2 Cla10g01863 1863
10 34554306 34557072 + ClCG10G019620.2 Cla10g01864 1864
6 1954931 1959683 + CmaCh06G004250.1 Cma06g00425 425
6 1960354 1965912 + CmaCh06G004260.1 Cma06g00426 426
7 4171047 4175925 - CmaCh07G008840.1 Cma07g00884 884
14 1097817 1101014 - CmaCh14G002520.1 Cma14g00252 252
14 1102157 1111915 + CmaCh14G002530.1 Cma14g00253 253
4 31123403 31128866 - MELO3C009413.2.1 Cme04g02456 2456
4 31131751 31135949 - MELO3C009412.2.1 Cme04g02457 2457
4 31136863 31142095 - MELO3C009411.2.1 Cme04g02458 2458
4 31142478 31145692 + MELO3C009410.2.1 Cme04g02459 2459
8 8967410 8973150 - MELO3C024496.2.1 Cme08g01252 1252
4 4662056 4666905 + PI0011130.4 Cmetu04g0283 283
4 4668024 4672576 + PI0017395.1 Cmetu04g0898 898
4 4674601 4680118 + PI0005409.1 Cmetu04g1992 1992
6 1319308 1326301 - PI0026648.1 Cmetu06g1316 1316
9 9794166 9799912 - PI0012551.1 Cmetu09g1198 1198
6 2018132 2022571 + CmoCh06G004200.1 Cmo06g00420 420
6 2023919 2030074 + CmoCh06G004210.1 Cmo06g00421 421
7 4389137 4394414 - CmoCh07G009160.1 Cmo07g00916 916
14 1113482 1114358 - CmoCh14G002420.1 Cmo14g00242 242
14 1115222 1118356 - CmoCh14G002430.1 Cmo14g00243 243
14 1119458 1128562 + CmoCh14G002440.1 Cmo14g00244 244
4 24490864 24495820 + CmPI595203_04g009940.1 Cmu04g0994 994
10 33572209 33577176 - CmPI595203_10g026800.1 Cmu10g2680 2680
10 33582008 33593415 - CmPI595203_10g026810.1 Cmu10g2681 2681
10 33597906 33600672 + CmPI595203_10g026820.1 Cmu10g2682 2682
13 9432965 9436303 - Conep13aG0126300.1 Cone13ag1230 1230
19 8455020 8458910 - Conep19aG0124900.1 Cone19ag1214 1214
19 8459986 8464478 - Conep19aG0125000.1 Cone19ag1215 1215
3 1090163 1091115 - Cp4.1LG03g01190.1 Cpe03g00218 218
3 1091527 1094735 - Cp4.1LG03g01210.1 Cpe03g00219 219
3 1095203 1104716 + Cp4.1LG03g01350.1 Cpe03g00220 220
8 8093533 8099610 - Cp4.1LG08g10630.1 Cpe08g01062 1062
8 8099955 8105047 - Cp4.1LG08g10640.1 Cpe08g01063 1063
19 3927821 3932779 + Cp4.1LG19g03750.1 Cpe19g00441 441
4 29149153 29156876 + CrPI670011_04g010500.1 Cre04g1050 1050
10 35363402 35368382 - CrPI670011_10g020680.1 Cre10g2068 2068
10 35373422 35384818 - CrPI670011_10g020690.1 Cre10g2069 2069
10 35391264 35394034 + CrPI670011_10g020700.1 Cre10g2070 2070
3 30357385 30362729 + CsaV3_3G036590.1 Csa03g03353 3353
6 23182726 23188308 + CsaV3_6G040190.1 Csa06g02633 2633
4 64023804 64032293 + Hsped.04g09620.1 Hepe04g0962 962
5 3910975 3915332 + Hsped.05g03160.1 Hepe05g0316 316
10 44007853 44012989 - Lag0026985.1 Lac10g2940 2940
1 11023916 11029394 - Lsi01G012760.1 Lsi01g01276 1276
3 30985417 30997834 - Lsi03G019570.1 Lsi03g01957 1957
3 30997958 31007051 - Lsi03G019580.1 Lsi03g01958 1958
3 31009007 31014004 - Lsi03G019590.1 Lsi03g01959 1959
3 31019511 31022792 + Lsi03G019600.1 Lsi03g01960 1960
2 43541060 43551570 - Sed0027110.1 Sed02g0587 587
2 43554557 43558091 + Sed0013470.1 Sed02g0588 588
2 51765807 51772741 + Sed0018792.2 Sed02g1646 1646
4 28830698 28834985 + Sed0020694.1 Sed04g1426 1426
4 28836323 28840690 + Sed0021738.1 Sed04g1427 1427
4 82160085 82165038 - Tan0002279.1 Tan04g2363 2363
8 69997893 70004202 - Tan0021438.2 Tan08g1804 1804
8 70006623 70011328 - Tan0013374.2 Tan08g1806 1806
8 70013148 70017668 - Tan0017329.1 Tan08g1807 1807
8 70025281 70028586 + Tan0003072.1 Tan08g1809 1809
1 15713489 15721119 + Vvi1g1001 Vvi1g1001 1001
8 18308665 18314201 + Vvi8g1083 Vvi8g1083 1083
8 18315485 18325154 - Vvi8g1084 Vvi8g1084 1084
8 18326469 18334223 - Vvi8g1085 Vvi8g1085 1085
8 18335898 18342508 - Vvi8g1086 Vvi8g1086 1086
8 18352789 18358484 + Vvi8g1087 Vvi8g1087 1087
8 18359685 18365996 + Vvi8g1088 Vvi8g1088 1088
8 18385617 18387861 + Vvi8g1089 Vvi8g1089 1089
8 18390357 18391452 - Vvi8g1090 Vvi8g1090 1090
8 18393887 18394471 + Vvi8g1091 Vvi8g1091 1091
       

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