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
Vvi16g874 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g875 . . . . . . . . . . . . Car02g00917 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi12g00624 . . Lac11g0143 Hepe06g0780 . Lcy12g0122 . . . . . . . . . . Cme09g01971
Vvi16g876 . . . . Bpe03g00178 . . . Cmo16g00071 . . . . . . . Cpe14g00053 Bhi01g01461 . . . . Mch10g0084 . . . . . . . . . . . . . . . Cme06g01082 . . . . . . . . . . . Cma16g00067 . Car16g00059 . . . . . . . . . . Cla05g00952 Cam05g1042 Cec05g1047 Cco05g1041 Clacu05g1033 Cmu05g0983 Cre05g1062 . . . .
Vvi16g877 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g878 . . . . . . . . . . Cma02g01106 Cma15g01033 Car02g00916 Car15g00965 . . . . . . . . . . Cla01g00054 Cam01g0052 Cec01g0052 Cco01g0054 Clacu01g0054 Cmu01g0052 Cre09g2455 Cone1ag0961 Cone5ag0647 . . . . Chy09g01427 Cme06g01103 . . . . . . . . . Cmo02g01134 Cmo15g01095 . . . . . Cpe13g00309 . . . . . . . . . . . . . . Lsi09g00033 Csa03g02200 . .
Vvi16g879 . . Bda05g00153 . Bpe03g00241 Bpe07g01008 Bma10g01289 . . . . . Car02g00915 . . Cpe05g00610 . . . . . . . . . . . . . . . . . . . . Csa05g00064 . . . . Bda06g00777 . . . . Bma12g01192 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g880 . . . . . . . . . . . . Car02g00913 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g881 . . . . . . . . . . Cma02g01161 . . . . Cpe05g00567 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g882 . Blo15g00090 . . . Bpe07g01011 . . . Cmo18g01338 Cma02g01110 . . . Sed05g0421 Cpe05g00606 . Bhi01g01471 Tan01g0127 Cmetu09g1394 Lac11g0146 Hepe07g0078 Mch10g0078 . Cla01g00051 Cam01g0048 Cec01g0048 Cco01g0050 Clacu01g0051 Cmu01g0048 Cre09g2459 Cone1ag0965 . Cone14ag0022 Cone15ag0025 . Csa05g00058 Chy09g01431 Cme06g01114 . . Bda06g00781 . . . . Bma12g01194 . Cmo02g01138 . . Cma18g01308 . Car18g01222 Cpe09g00034 . Bhi12g00627 . . . . . Lcy12g0124 Cla05g00957 Cam05g1048 Cec05g1053 Cco05g1047 Clacu05g1041 Cmu05g0991 Cre05g1068 Lsi09g00028 . Chy06g01236 Cme09g01974
Vvi16g883 . . . . Bpe03g00182 . . . Cmo16g00068 . . . . . Sed07g0841 . Cpe14g00050 Bhi01g01472 Tan01g0125 Cmetu06g1353 . Hepe07g0077 Mch10g0077 . . . . . . . . Cone1ag0966 Cone5ag0672 . . . . . Cme06g01115 . Blo09g00035 . . . . . . . . . Cma16g00062 . Car16g00056 . . Cpe13g00356 . . . . . . . Cla05g00958 Cam05g1049 Cec05g1054 Cco05g1048 Clacu05g1042 Cmu05g0992 Cre05g1069 . Csa03g02203 Chy06g01234 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 6383583 6389037 - Bda020780.1 Bda05g00153 153
6 10778566 10786038 + Bda024098.2 Bda06g00777 777
6 10866933 10869503 - Bda033776 Bda06g00781 781
1 29694591 29697743 - XM_039050755.1 Bhi01g01461 1461
1 30195354 30199683 - XM_039022791.1 Bhi01g01471 1471
1 30292843 30295767 - XM_039047678.1 Bhi01g01472 1472
12 19082071 19089108 - XM_039018554.1 Bhi12g00624 624
12 19125998 19131362 - XM_039050538.1 Bhi12g00627 627
9 465676 469371 + BLOR20950 Blo09g00035 35
15 751268 758414 + BLOR06484 Blo15g00090 90
10 45724872 45730384 + Bma005394.1 Bma10g01289 1289
12 44742821 44750275 + Bma008551.1 Bma12g01192 1192
12 44803947 44806408 - Bma030544 Bma12g01194 1194
3 2203508 2205583 - Bpe012024.1 Bpe03g00178 178
3 2223585 2224916 - Bpe012028.1 Bpe03g00182 182
3 3190017 3195140 - Bpe012094.1 Bpe03g00241 241
7 15730878 15738413 + Bpe021852.1 Bpe07g01008 1008
7 15749947 15752577 - Bpe026087 Bpe07g01011 1011
1 862856 866870 + CaPI482276_01g000480.1 Cam01g0048 48
1 898168 899925 + CaPI482276_01g000520.1 Cam01g0052 52
5 9425766 9428492 - CaPI482276_05g010420.1 Cam05g1042 1042
5 9496389 9498622 - CaPI482276_05g010480.1 Cam05g1048 1048
5 9518755 9521039 - CaPI482276_05g010490.1 Cam05g1049 1049
2 6477148 6480354 + Carg14028-RA Car02g00913 913
2 6488113 6492666 + Carg14026-RA Car02g00915 915
2 6493932 6496168 - Carg14025-RA Car02g00916 916
2 6500138 6503975 - Carg14024-RA Car02g00917 917
15 7118175 7120481 + Carg26214-RA Car15g00965 965
16 379458 381993 + Carg15075-RA Car16g00056 56
16 392611 396366 + Carg15078-RA Car16g00059 59
18 11756476 11760158 - Carg20348-RA Car18g01222 1222
1 376142 381360 + CcPI632755_01g000500.1 Cco01g0050 50
1 413105 414864 + CcPI632755_01g000540.1 Cco01g0054 54
5 9184140 9186824 - CcPI632755_05g010410.1 Cco05g1041 1041
5 9248472 9250691 - CcPI632755_05g010470.1 Cco05g1047 1047
5 9269419 9273520 - CcPI632755_05g010480.1 Cco05g1048 1048
1 404828 410441 + CePI673135_01g000480.1 Cec01g0048 48
1 441321 443080 + CePI673135_01g000520.1 Cec01g0052 52
5 9161678 9164438 - CePI673135_05g010470.1 Cec05g1047 1047
5 9229322 9231570 - CePI673135_05g010530.1 Cec05g1053 1053
5 9250624 9252696 - CePI673135_05g010540.1 Cec05g1054 1054
6 11214979 11217161 + Chy6G117620.1 Chy06g01234 1234
6 11254563 11256691 + Chy6G117640.1 Chy06g01236 1236
9 15860205 15862545 - Chy9G171430.1 Chy09g01427 1427
9 15891305 15894569 - Chy9G171470.1 Chy09g01431 1431
1 471484 475499 + ClG42_01g0005100.10 Clacu01g0051 51
1 506446 508199 + ClG42_01g0005400.10 Clacu01g0054 54
5 9151011 9153733 - ClG42_05g0103300.10 Clacu05g1033 1033
5 9227254 9229495 - ClG42_05g0104100.10 Clacu05g1041 1041
5 9251315 9253585 - ClG42_05g0104200.10 Clacu05g1042 1042
1 410613 415411 + ClCG01G000500.2 Cla01g00051 51
1 446397 448957 + ClCG01G000530.1 Cla01g00054 54
5 9483674 9486778 - ClCG05G008760.2 Cla05g00952 952
5 9562166 9565698 - ClCG05G008810.1 Cla05g00957 957
5 9583656 9588707 - ClCG05G008820.2 Cla05g00958 958
2 6572435 6574708 - CmaCh02G011060.1 Cma02g01106 1106
2 6595343 6599859 - CmaCh02G011100.1 Cma02g01110 1110
2 6842627 6846241 - CmaCh02G011610.1 Cma02g01161 1161
15 6460868 6463472 + CmaCh15G010330.1 Cma15g01033 1033
16 273810 276290 + CmaCh16G000620.1 Cma16g00062 62
16 287937 289940 + CmaCh16G000670.1 Cma16g00067 67
18 10046705 10049263 - CmaCh18G013080.1 Cma18g01308 1308
6 8016445 8022812 + MELO3C006984.2.1 Cme06g01082 1082
6 8318397 8321700 + MELO3C026930.2.1 Cme06g01103 1103
6 8439241 8443524 - MELO3C008477.2.1 Cme06g01114 1114
6 8480427 8483004 - MELO3C008478.2.1 Cme06g01115 1115
9 23609620 23616549 - MELO3C005875.2.1 Cme09g01971 1971
9 23631657 23635433 - MELO3C005877.2.1 Cme09g01974 1974
6 7986416 7989398 - PI0011172.1 Cmetu06g1353 1353
9 323895 328522 + PI0017517.2 Cmetu09g1394 1394
2 6871587 6874443 - CmoCh02G011340.1 Cmo02g01134 1134
2 6895248 6900444 - CmoCh02G011380.1 Cmo02g01138 1138
15 7330579 7333751 + CmoCh15G010950.1 Cmo15g01095 1095
16 309222 311521 + CmoCh16G000680.1 Cmo16g00068 68
16 320941 330775 + CmoCh16G000710.1 Cmo16g00071 71
18 12673980 12676421 - CmoCh18G013380.1 Cmo18g01338 1338
1 416315 420328 + CmPI595203_01g000480.1 Cmu01g0048 48
1 451301 453054 + CmPI595203_01g000520.1 Cmu01g0052 52
5 8996458 8999180 - CmPI595203_05g009830.1 Cmu05g0983 983
5 9072670 9074911 - CmPI595203_05g009910.1 Cmu05g0991 991
5 9096777 9099047 - CmPI595203_05g009920.1 Cmu05g0992 992
1 54838435 54840035 - Conep01aG0100600.1 Cone1ag0961 961
1 54859250 54862782 - Conep01aG0101000.1 Cone1ag0965 965
1 54864311 54866387 - Conep01aG0101100.1 Cone1ag0966 966
5 2762679 2764382 + Conep05aG0066900.1 Cone5ag0647 647
5 2877495 2879397 - Conep05aG0069600.1 Cone5ag0672 672
14 190174 193350 + Conep14aG0002300.1 Cone14ag0022 22
15 183233 185303 + Conep15aG0002600.1 Cone15ag0025 25
5 3427347 3431420 + Cp4.1LG05g05680.1 Cpe05g00567 567
5 3689453 3695802 + Cp4.1LG05g06010.1 Cpe05g00606 606
5 3719145 3724167 - Cp4.1LG05g06200.1 Cpe05g00610 610
9 211486 215769 + Cp4.1LG09g00380.1 Cpe09g00034 34
13 2603592 2608836 - Cp4.1LG13g03120.1 Cpe13g00309 309
13 3616021 3618188 - Cp4.1LG13g03550.1 Cpe13g00356 356
14 282020 284452 + Cp4.1LG14g06690.1 Cpe14g00050 50
14 296573 298432 + Cp4.1LG14g06680.1 Cpe14g00053 53
5 9869735 9872496 - CrPI670011_05g010620.1 Cre05g1062 1062
5 9939456 9941702 - CrPI670011_05g010680.1 Cre05g1068 1068
5 9954650 9959902 - CrPI670011_05g010690.1 Cre05g1069 1069
9 43872975 43875146 - CrPI670011_09g024550.1 Cre09g2455 2455
9 43906522 43910558 - CrPI670011_09g024590.1 Cre09g2459 2459
3 19093676 19095745 - CsaV3_3G022000.1 Csa03g02200 2200
3 19119262 19125138 - CsaV3_3G022030.1 Csa03g02203 2203
5 286728 292487 + CsaV3_5G000580.1 Csa05g00058 58
5 324043 332954 - CsaV3_5G000640.1 Csa05g00064 64
6 54430932 54435676 - Hsped.06g07800.1 Hepe06g0780 780
7 740930 743762 + Hsped.07g00770.1 Hepe07g0077 77
7 753350 757074 + Hsped.07g00780.1 Hepe07g0078 78
11 1307616 1309877 - Lag0030781.1 Lac11g0143 143
11 1336248 1347069 - Lag0030784.1 Lac11g0146 146
12 1529931 1536544 - Maker00038764 Lcy12g0122 122
12 1559978 1564864 - Maker00039044 Lcy12g0124 124
9 272284 278593 + Lsi09G000280.1 Lsi09g00028 28
9 314057 316783 + Lsi09G000330.1 Lsi09g00033 33
10 433518 440058 + MC10g0070 Mch10g0077 77
10 441820 444843 + MC10g0071 Mch10g0078 78
10 478060 480377 + MC10g0075 Mch10g0084 84
5 2827020 2834468 + Sed0009588.1 Sed05g0421 421
7 6130534 6132952 - Sed0015278.2 Sed07g0841 841
1 1219063 1221708 + Tan0014819.2 Tan01g0125 125
1 1244431 1248796 + Tan0002862.2 Tan01g0127 127
16 19553501 19561941 - Vvi16g874 Vvi16g874 874
16 19568864 19573229 + Vvi16g875 Vvi16g875 875
16 19584304 19587018 + Vvi16g876 Vvi16g876 876
16 19588380 19600987 - Vvi16g877 Vvi16g877 877
16 19636836 19641201 + Vvi16g878 Vvi16g878 878
16 19642628 19664832 - Vvi16g879 Vvi16g879 879
16 19665907 19669286 - Vvi16g880 Vvi16g880 880
16 19670038 19676461 - Vvi16g881 Vvi16g881 881
16 19678031 19685549 - Vvi16g882 Vvi16g882 882
16 19697453 19699843 - Vvi16g883 Vvi16g883 883
       

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