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
Vvi16g804 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g805 . . . . . . . . Cmo16g00092 Cmo18g01314 . . . . Sed02g1696 . Cpe14g00072 Bhi01g01424 Tan01g0175 Cmetu06g0839 . Hepe07g0108 Mch10g0110 . Cla01g00212 Cam01g0217 Cec01g0211 Cco01g0215 Clacu01g0212 Cmu01g0206 Cre09g2301 Cone1ag1201 . . . Lsi05g01177 Csa05g00229 Chy09g01271 . . . . . . Bpe12g00371 . . . . . Cma16g00088 Cma18g01285 Car16g00078 Car18g01204 Cpe09g00055 . . . . . . . . Cla05g00931 Cam05g1018 Cec05g1022 Cco05g1018 Clacu05g1007 Cmu05g0960 Cre05g1041 . Csa03g02171 Chy06g01283 Cme09g01814
Vvi16g806 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g807 Blo06g01140 . . . . . . . . . . Cma15g01060 . . . . . . . . . . . . Cla01g00084 Cam01g0085 Cec01g0084 Cco01g0085 Clacu01g0083 Cmu01g0085 Cre09g2424 . . Cone14ag0045 Cone15ag0050 . Csa05g00097 Chy09g01397 . . . . Bda15g00708 . Bpe12g00445 . . . . Cmo15g01118 . . . . . Cpe13g00282 Bhi12g00767 . . Lac11g0083 . . Lcy12g0065 . . . . . . . Lsi09g00071 . . Cme09g01943
Vvi16g808 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g809 Blo06g01180 Blo15g00212 . . . . . . . . Cma02g01088 . Car02g00831 . . . . . . . . . . . . . . . . . . . Cone5ag0903 . . . . . . . . Bda06g00733 . . Bpe12g00487 . . . Cmo02g01109 . . . . . . . Bhi12g00765 . . . . . . . . . . . . . . . . .
Vvi16g810 . Blo15g00108 . . . . . . . . . Cma15g01059 . Car15g00982 . Cpe05g00632 . . . . . . . . Cla01g00082 Cam01g0082 Cec01g0083 Cco01g0083 Clacu01g0082 Cmu01g0084 Cre09g2425 . . . Cone15ag0049 . Csa05g00095 Chy09g01399 . . . . . . . . . . . Cmo15g01117 . . . . . Cpe13g00283 Bhi12g00764 . . . . . Lcy12g0068 . . . . . . . Lsi09g00068 . . Cme09g01945
Vvi16g811 . . . . . Bpe07g00999 . Bma14g02021 . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0044 . . . . . . . Bda06g00769 Bda15g00666 . . . Bma12g01184 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g812 Blo06g01066 Blo15g00106 . Bda07g01912 Bpe03g00163 Bpe07g01000 Bma10g01268 . . . Cma02g01091 Cma15g01057 Car02g00832 Car15g00981 . Cpe05g00631 . . . . . . . . Cla01g00081 Cam01g0081 Cec01g0082 Cco01g0082 Clacu01g0081 Cmu01g0083 Cre09g2426 Cone1ag1202 Cone5ag0904 . Cone15ag0048 . Csa05g00094 Chy09g01400 . Blo07g00357 Blo09g00050 . . . Bpe12g00360 . Bma12g01185 . Cmo02g01110 Cmo15g01116 . . . . . Cpe13g00284 Bhi12g00763 . . Lac11g0088 Hepe06g0736 . Lcy12g0069 . . . . . . . Lsi09g00066 . . Cme09g01946
Vvi16g813 Blo06g01067 Blo15g00104 Bda05g00105 . Bpe03g00249 Bpe07g01001 Bma10g01271 . Cmo16g00091 Cmo18g01316 Cma02g01092 Cma15g01055 Car02g00833 Car15g00980 Sed02g1698 Cpe05g00630 Cpe14g00071 Bhi01g01425 Tan01g0174 Cmetu06g0181 Lac11g0089 Hepe07g0107 Mch10g0109 . Cla01g00080 Cam01g0080 Cec01g0081 Cco01g0081 Clacu01g0080 Cmu01g0082 Cre09g2427 . . . . Lsi05g01176 Csa05g00093 Chy09g01401 Cme06g01055 . . Bda06g00770 Bda15g00768 . Bpe12g00361 . Bma12g01186 . Cmo02g01112 Cmo15g01114 Cma16g00087 Cma18g01287 Car16g00077 Car18g01205 Cpe09g00054 Cpe13g00289 Bhi12g00762 . . . . . Lcy12g0070 Cla05g00932 Cam05g1019 Cec05g1023 Cco05g1019 Clacu05g1008 Cmu05g0961 Cre05g1042 Lsi09g00065 Csa03g02172 Chy06g01282 Cme09g01947
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 5182318 5183034 - Bda020712.1 Bda05g00105 105
6 9973979 9985277 + Bda024036.1 Bda06g00733 733
6 10690578 10695734 - Bda024090.1 Bda06g00769 769
6 10701338 10702015 - Bda024091.1 Bda06g00770 770
7 36551513 36553320 + Bda028887.1 Bda07g01912 1912
15 10139245 10149266 - Bda012516.1 Bda15g00666 666
15 10506415 10508918 + Bda012563.1 Bda15g00708 708
15 11505746 11506336 - Bda012627.1 Bda15g00768 768
1 29032319 29039048 + XM_039022199.1 Bhi01g01424 1424
1 29043618 29045122 - XM_039044110.1 Bhi01g01425 1425
12 22808907 22810657 + XM_039050863.1 Bhi12g00762 762
12 22851890 22857167 - XM_039019296.1 Bhi12g00763 763
12 22964723 22972342 + XM_039018520.1 Bhi12g00764 764
12 22964723 22972342 + XM_039018519.1 Bhi12g00765 765
12 22978877 22991068 + XM_039018521.1 Bhi12g00767 767
6 34026759 34034343 + BLOR17649 Blo06g01066 1066
6 34036476 34037159 - BLOR17650 Blo06g01067 1067
6 34848175 34850741 - BLOR17723 Blo06g01140 1140
6 35261045 35271631 + BLOR17763 Blo06g01180 1180
7 5695551 5699689 - BLOR18289 Blo07g00357 357
9 775711 778412 - BLOR20965 Blo09g00050 50
15 876259 877161 + BLOR06498 Blo15g00104 104
15 881583 885012 - BLOR06500 Blo15g00106 106
15 901712 906585 + BLOR06502 Blo15g00108 108
15 2156495 2173447 + BLOR06606 Blo15g00212 212
10 45129734 45131896 + Bma005368.1 Bma10g01268 1268
10 45225394 45226131 - Bma005371.1 Bma10g01271 1271
12 44659318 44664304 - Bma008542.1 Bma12g01184 1184
12 44696030 44697823 + Bma008544.1 Bma12g01185 1185
12 44701175 44701852 - Bma008545.1 Bma12g01186 1186
14 43565363 43577894 - Bma012829.1 Bma14g02021 2021
3 2089063 2090907 + Bpe012009.1 Bpe03g00163 163
3 3334114 3334800 + Bpe012102.1 Bpe03g00249 249
7 15672117 15677335 - Bpe021843.2 Bpe07g00999 999
7 15694239 15696624 + Bpe021844.1 Bpe07g01000 1000
7 15698484 15699206 - Bpe021845.1 Bpe07g01001 1001
12 8855672 8857494 + Bpe005616.1 Bpe12g00360 360
12 8860214 8860924 - Bpe005617.2 Bpe12g00361 361
12 8986953 8990637 + Bpe005627.3 Bpe12g00371 371
12 10207745 10210293 - Bpe005704.1 Bpe12g00445 445
12 10672388 10682452 + Bpe005750.2 Bpe12g00487 487
1 1090491 1091922 + CaPI482276_01g000800.1 Cam01g0080 80
1 1101562 1104344 - CaPI482276_01g000810.1 Cam01g0081 81
1 1130530 1136910 + CaPI482276_01g000820.1 Cam01g0082 82
1 1142009 1145365 + CaPI482276_01g000850.1 Cam01g0085 85
1 2508658 2510320 - CaPI482276_01g002170.1 Cam01g0217 217
5 9188429 9191168 + CaPI482276_05g010180.1 Cam05g1018 1018
5 9199015 9199812 - CaPI482276_05g010190.1 Cam05g1019 1019
2 5984267 5990252 - Carg08390-RA Car02g00831 831
2 5996960 6001284 + Carg08389-RA Car02g00832 832
2 6014551 6015394 - Carg28192-RA Car02g00833 833
15 7497403 7498064 + Carg27013-RA Car15g00980 980
15 7529276 7534164 - Carg27014-RA Car15g00981 981
15 7544917 7556746 + Carg27015-RA Car15g00982 982
16 491184 492629 + Carg15096-RA Car16g00077 77
16 500014 501828 - Carg15097-RA Car16g00078 78
18 11630579 11632599 + Carg20366-RA Car18g01204 1204
18 11637382 11638080 - Carg20365-RA Car18g01205 1205
1 603612 605020 + CcPI632755_01g000810.1 Cco01g0081 81
1 614172 618028 - CcPI632755_01g000820.1 Cco01g0082 82
1 643840 650222 + CcPI632755_01g000830.1 Cco01g0083 83
1 655297 658681 + CcPI632755_01g000850.1 Cco01g0085 85
1 2113183 2114839 - CcPI632755_01g002150.1 Cco01g0215 215
5 8948389 8951117 + CcPI632755_05g010180.1 Cco05g1018 1018
5 8958980 8959780 - CcPI632755_05g010190.1 Cco05g1019 1019
1 646244 647677 + CePI673135_01g000810.1 Cec01g0081 81
1 656760 659641 - CePI673135_01g000820.1 Cec01g0082 82
1 693326 699713 + CePI673135_01g000830.1 Cec01g0083 83
1 704720 708097 + CePI673135_01g000840.1 Cec01g0084 84
1 2106908 2108567 - CePI673135_01g002110.1 Cec01g0211 211
5 8929542 8932211 + CePI673135_05g010220.1 Cec05g1022 1022
5 8939921 8940717 - CePI673135_05g010230.1 Cec05g1023 1023
6 11773859 11778456 + Chy6G118100.1 Chy06g01282 1282
6 11781424 11783870 - Chy6G118110.1 Chy06g01283 1283
9 14724250 14725884 + Chy9G169870.1 Chy09g01271 1271
9 15684837 15687067 - Chy9G171130.1 Chy09g01397 1397
9 15691286 15697670 - Chy9G171150.1 Chy09g01399 1399
9 15714676 15717427 + Chy9G171160.1 Chy09g01400 1400
9 15720530 15721994 - Chy9G171170.1 Chy09g01401 1401
1 700401 701869 + ClG42_01g0008000.10 Clacu01g0080 80
1 711672 714580 - ClG42_01g0008100.10 Clacu01g0081 81
1 741138 747512 + ClG42_01g0008200.10 Clacu01g0082 82
1 752721 756085 + ClG42_01g0008300.10 Clacu01g0083 83
1 2125688 2127337 - ClG42_01g0021200.10 Clacu01g0212 212
5 8905691 8908417 + ClG42_05g0100700.10 Clacu05g1007 1007
5 8916214 8917010 - ClG42_05g0100800.10 Clacu05g1008 1008
1 663409 664203 + ClCG01G000790.1 Cla01g00080 80
1 674970 677851 - ClCG01G000800.2 Cla01g00081 81
1 704442 711972 + ClCG01G000810.1 Cla01g00082 82
1 716550 720232 + ClCG01G000830.1 Cla01g00084 84
1 2149664 2151615 - ClCG01G002190.1 Cla01g00212 212
5 9212795 9215652 + ClCG05G008530.1 Cla05g00931 931
5 9224055 9226403 - ClCG05G008540.2 Cla05g00932 932
2 6468535 6477214 - CmaCh02G010880.1 Cma02g01088 1088
2 6484598 6488246 + CmaCh02G010910.1 Cma02g01091 1091
2 6489321 6494571 - CmaCh02G010920.1 Cma02g01092 1092
15 6668385 6669624 + CmaCh15G010550.1 Cma15g01055 1055
15 6692843 6697962 - CmaCh15G010570.1 Cma15g01057 1057
15 6706621 6713407 + CmaCh15G010590.1 Cma15g01059 1059
15 6723578 6727694 + CmaCh15G010600.1 Cma15g01060 1060
16 382713 385639 + CmaCh16G000870.1 Cma16g00087 87
16 386386 392192 - CmaCh16G000880.1 Cma16g00088 88
18 9921580 9923875 + CmaCh18G012850.1 Cma18g01285 1285
18 9929227 9931809 - CmaCh18G012870.1 Cma18g01287 1287
6 7678088 7679670 - MELO3C006960.2.1 Cme06g01055 1055
9 22462902 22465190 + MELO3C005725.2.1 Cme09g01814 1814
9 23435374 23439971 - MELO3C034012.2.1 Cme09g01943 1943
9 23442393 23449145 - MELO3C005849.2.1 Cme09g01945 1945
9 23463784 23467684 + MELO3C005850.2.1 Cme09g01946 1946
9 23470332 23472311 - MELO3C005851.2.1 Cme09g01947 1947
6 993760 994472 + PI0027814.1 Cmetu06g0181 181
6 7653132 7655429 + PI0014043.1 Cmetu06g0839 839
2 6698916 6705964 - CmoCh02G011090.1 Cmo02g01109 1109
2 6714946 6717615 + CmoCh02G011100.1 Cmo02g01110 1110
2 6721401 6722612 - CmoCh02G011120.1 Cmo02g01112 1112
15 7712853 7713605 + CmoCh15G011140.1 Cmo15g01114 1114
15 7753649 7757034 - CmoCh15G011160.1 Cmo15g01116 1116
15 7769078 7776490 + CmoCh15G011170.1 Cmo15g01117 1117
15 7777158 7781344 + CmoCh15G011180.1 Cmo15g01118 1118
16 422445 425529 + CmoCh16G000910.1 Cmo16g00091 91
16 430265 431980 - CmoCh16G000920.1 Cmo16g00092 92
18 12540430 12542698 + CmoCh18G013140.1 Cmo18g01314 1314
18 12547161 12547999 - CmoCh18G013160.1 Cmo18g01316 1316
1 644861 646320 + CmPI595203_01g000820.1 Cmu01g0082 82
1 656101 658982 - CmPI595203_01g000830.1 Cmu01g0083 83
1 685597 691972 + CmPI595203_01g000840.1 Cmu01g0084 84
1 697180 700543 + CmPI595203_01g000850.1 Cmu01g0085 85
1 2078839 2080488 - CmPI595203_01g002060.1 Cmu01g0206 206
5 8750828 8753554 + CmPI595203_05g009600.1 Cmu05g0960 960
5 8761350 8762146 - CmPI595203_05g009610.1 Cmu05g0961 961
1 55902357 55904119 + Conep01aG0125000.1 Cone1ag1201 1201
1 55906572 55908909 + Conep01aG0125100.1 Cone1ag1202 1202
5 3871261 3875323 - Conep05aG0092900.1 Cone5ag0903 903
5 3877535 3879857 + Conep05aG0093000.1 Cone5ag0904 904
14 290164 295120 + Conep14aG0004600.1 Cone14ag0044 44
14 296576 298453 + Conep14aG0004700.1 Cone14ag0045 45
15 297431 299638 - Conep15aG0005000.1 Cone15ag0048 48
15 307190 311876 + Conep15aG0005100.1 Cone15ag0049 49
15 312899 313917 + Conep15aG0005200.1 Cone15ag0050 50
5 3845536 3855121 + Cp4.1LG05g06310.1 Cpe05g00630 630
5 3852371 3856664 - Cp4.1LG05g06340.1 Cpe05g00631 631
5 3863595 3871930 + Cp4.1LG05g06300.1 Cpe05g00632 632
9 329773 330682 + Cp4.1LG09g00540.1 Cpe09g00054 54
9 335019 337266 - Cp4.1LG09g00590.1 Cpe09g00055 55
13 2223161 2227859 - Cp4.1LG13g02870.1 Cpe13g00282 282
13 2228672 2235896 - Cp4.1LG13g02860.1 Cpe13g00283 283
13 2244245 2249613 + Cp4.1LG13g02770.1 Cpe13g00284 284
13 2285454 2287039 - Cp4.1LG13g02920.1 Cpe13g00289 289
14 393066 395934 + Cp4.1LG14g06460.1 Cpe14g00071 71
14 400297 402366 - Cp4.1LG14g06360.1 Cpe14g00072 72
5 9631846 9634612 + CrPI670011_05g010410.1 Cre05g1041 1041
5 9642338 9643135 - CrPI670011_05g010420.1 Cre05g1042 1042
9 42207983 42209638 + CrPI670011_09g023010.1 Cre09g2301 2301
9 43617069 43621058 - CrPI670011_09g024240.1 Cre09g2424 2424
9 43626183 43632602 - CrPI670011_09g024250.1 Cre09g2425 2425
9 43658480 43662328 + CrPI670011_09g024260.1 Cre09g2426 2426
9 43671488 43672924 - CrPI670011_09g024270.1 Cre09g2427 2427
3 18852264 18855412 + CsaV3_3G021710.1 Csa03g02171 2171
3 18861323 18863139 - CsaV3_3G021720.1 Csa03g02172 2172
5 448289 450175 + CsaV3_5G000930.1 Csa05g00093 93
5 452375 457331 - CsaV3_5G000940.1 Csa05g00094 94
5 471727 478752 + CsaV3_5G000950.1 Csa05g00095 95
5 481929 485458 + CsaV3_5G000970.1 Csa05g00097 97
5 1400483 1403241 - CsaV3_5G002290.1 Csa05g00229 229
6 53482605 53485801 + Hsped.06g07360.1 Hepe06g0736 736
7 1011406 1016901 + Hsped.07g01070.1 Hepe07g0107 107
7 1019861 1023526 - Hsped.07g01080.1 Hepe07g0108 108
11 736686 740030 - Lag0030721.1 Lac11g0083 83
11 795354 798477 + Lag0030726.1 Lac11g0088 88
11 808942 809726 - Lag0030727.1 Lac11g0089 89
12 958822 962750 - Maker00038411 Lcy12g0065 65
12 971639 979346 - Maker00038731 Lcy12g0068 68
12 1005219 1008568 + Maker00038979 Lcy12g0069 69
12 1016876 1018836 - Maker00038865 Lcy12g0070 70
5 19685598 19686451 + Lsi05G011760.1 Lsi05g01176 1176
5 19689445 19696744 - Lsi05G011770.1 Lsi05g01177 1177
9 541922 542690 + Lsi09G000650.1 Lsi09g00065 65
9 551435 557626 - Lsi09G000660.1 Lsi09g00066 66
9 586185 588976 + Lsi09G000680.1 Lsi09g00068 68
9 593810 598313 + Lsi09G000710.1 Lsi09g00071 71
10 644820 645494 + MC10g_new0016 Mch10g0109 109
10 652085 654880 - MC10g0094 Mch10g0110 110
2 52054628 52057620 + Sed0012568.1 Sed02g1696 1696
2 52070636 52071481 - Sed0004021.1 Sed02g1698 1698
1 1602780 1604004 + Tan0017252.1 Tan01g0174 174
1 1613668 1616139 - Tan0010999.1 Tan01g0175 175
16 18732034 18733702 - Vvi16g804 Vvi16g804 804
16 18741351 18742994 + Vvi16g805 Vvi16g805 805
16 18743091 18743343 - Vvi16g806 Vvi16g806 806
16 18744124 18747793 - Vvi16g807 Vvi16g807 807
16 18748450 18748819 - Vvi16g808 Vvi16g808 808
16 18748877 18753944 - Vvi16g809 Vvi16g809 809
16 18755872 18768116 - Vvi16g810 Vvi16g810 810
16 18768336 18777529 - Vvi16g811 Vvi16g811 811
16 18791602 18798648 + Vvi16g812 Vvi16g812 812
16 18812894 18822232 - Vvi16g813 Vvi16g813 813
       

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