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
Vvi2g342 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00297 Chy09g01209 . . . . . . . . . . . . . . . . . . Bhi12g00232 . . Lac11g2111 Hepe06g1560 . Lcy12g1668 Cla01g00278 Cam01g0288 Cec01g0281 Cco01g0294 Clacu01g0287 Cmu01g0274 Cre09g2233 Lsi09g00276 . . .
Vvi2g343 . Blo03g00204 . . . . . Bma14g00616 . . Cma02g01467 Cma15g01217 . Car15g01097 . . Cpe05g00320 . . . . . . . . . . . . . . . . . . . . Chy09g01208 . . . Bda07g00476 . . Bpe11g00653 . . . Cmo02g01504 Cmo15g01282 . . . . . . Bhi12g00231 . . . . . . Cla01g00279 Cam01g0289 Cec01g0282 Cco01g0295 Clacu01g0288 Cmu01g0275 Cre09g2232 Lsi09g00277 . . Cme09g01745
Vvi2g344 . . . . . . . Bma14g00614 . . Cma02g01468 Cma15g01216 Car02g01231 . . . . . . . . . . . . . . . . . . Cone8ag0316 Cone12ag0315 . . . Csa05g00298 Chy09g01207 . . . Bda07g00475 . . Bpe11g00654 . Bma12g00089 . Cmo02g01505 Cmo15g01280 . . . . . Cpe13g00163 Bhi12g00230 . . Lac11g2112 Hepe06g1561 . Lcy12g1669 Cla01g00280 Cam01g0290 Cec01g0283 Cco01g0296 Clacu01g0289 Cmu01g0276 Cre09g2231 Lsi09g00279 . . Cme09g01744
Vvi2g345 Blo02g01105 Blo03g00203 Bda06g00083 . Bpe05g00637 Bpe07g00115 . Bma14g00613 . Cmo16g00637 Cma02g01064 Cma15g01215 Car02g00807 Car15g01096 . Cpe14g00498 Cpe05g00319 . . . . . . . Cla07g00764 Cam07g0819 Cec07g0878 Cco07g0854 Clacu07g0797 Cmu07g0804 Cre07g1159 Cone8ag0317 Cone12ag0316 . Cone9ag0766 . Csa05g00299 Chy09g01206 . . . . . . . Bma05g00813 Bma12g00090 . Cmo02g01506 Cmo15g01279 Cma06g00414 Cma16g00588 . . . Cpe13g00164 Bhi12g00228 . . . . . . Cla01g00281 Cam01g0291 Cec01g0284 Cco01g0297 Clacu01g0290 Cmu01g0277 Cre09g2230 Lsi09g00280 . . Cme09g01743
Vvi2g346 Blo02g01104 . . Bda08g00526 Bpe05g00636 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme07g01623 . . . . . . Bma05g00812 . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00602 Chy07g01210 .
Vvi2g347 . . . . . . . . Cmo06g01081 . Cma02g01472 . Car02g01233 . . . Cpe05g00657 . . . . . . . . . . . . . . . Cone12ag0317 . Cone9ag0765 . . Chy09g01204 . . . . . . Bpe11g00655 . . . Cmo02g01507 . Cma06g01060 . Car06g00892 . Cpe08g00557 . Bhi12g00226 . . . . . . Cla01g00283 Cam01g0293 Cec01g0286 Cco01g0299 Clacu01g0292 Cmu01g0278 Cre09g2229 Lsi09g00282 . . Cme09g01741
Vvi2g348 . . . . . . . . Cmo06g01115 . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00080 Chy09g01411 . . . . . . . . . . . . Cma06g01089 . Car06g00924 . Cpe08g00529 . . . . . . . . Cla01g00071 Cam01g0070 Cec01g0071 Cco01g0071 Clacu01g0071 Cmu01g0072 Cre09g2437 Lsi09g00051 . . Cme09g01955
Vvi2g349 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g350 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g351 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 824772 829318 + Bda023256.1 Bda06g00083 83
7 6028809 6029704 + Bda025577.1 Bda07g00475 475
7 6031618 6032528 + Bda025578.1 Bda07g00476 476
8 5273937 5274296 + Bda024981.1 Bda08g00526 526
12 7277180 7281541 - XM_039020209.1 Bhi12g00226 226
12 7385587 7390973 + XM_039018424.1 Bhi12g00228 228
12 7401104 7402231 - XM_039019293.1 Bhi12g00230 230
12 7401107 7402212 - XM_039019294.1 Bhi12g00231 231
12 7465291 7471412 + XM_039019109.1 Bhi12g00232 232
2 42020477 42020836 - BLOR10834 Blo02g01104 1104
2 42030697 42034441 + BLOR10835 Blo02g01105 1105
3 4756519 4761097 + BLOR11384 Blo03g00203 203
3 4765144 4778813 - BLOR11385 Blo03g00204 204
5 45432641 45433000 - Bma021915.1 Bma05g00812 812
5 45453539 45457743 + Bma021917.2 Bma05g00813 813
12 1587534 1588314 + Bma006960.1 Bma12g00089 89
12 1590176 1594763 - Bma006961.1 Bma12g00090 90
14 6645919 6648106 + Bma011053.1 Bma14g00613 613
14 6649010 6649926 - Bma011054.1 Bma14g00614 614
14 6667165 6668092 - Bma011056.1 Bma14g00616 616
5 20211021 20211380 - Bpe018052.1 Bpe05g00636 636
5 20217228 20220233 + Bpe018053.1 Bpe05g00637 637
7 830752 835266 - Bpe020928.1 Bpe07g00115 115
11 5026896 5027788 + Bpe004009.1 Bpe11g00653 653
11 5032898 5033796 + Bpe004010.1 Bpe11g00654 654
11 5045114 5045742 + Bpe004012.1 Bpe11g00655 655
1 1011505 1018024 + CaPI482276_01g000700.1 Cam01g0070 70
1 3225680 3230307 - CaPI482276_01g002880.1 Cam01g0288 288
1 3258105 3258934 + CaPI482276_01g002890.1 Cam01g0289 289
1 3268182 3269565 + CaPI482276_01g002900.1 Cam01g0290 290
1 3269962 3274750 - CaPI482276_01g002910.1 Cam01g0291 291
1 3303394 3306157 + CaPI482276_01g002930.1 Cam01g0293 293
7 20559376 20566667 + CaPI482276_07g008190.1 Cam07g0819 819
2 5870596 5871802 + Carg08414-RA Car02g00807 807
2 8336001 8340878 + Carg02517-RA Car02g01231 1231
2 8352666 8355017 + Carg02515-RA Car02g01233 1233
6 6928607 6931903 - Carg24637-RA Car06g00892 892
6 7169298 7175153 - Carg24940-RA Car06g00924 924
15 8633344 8638311 + Carg16646-RA Car15g01096 1096
15 8638885 8644871 - Carg16645-RA Car15g01097 1097
1 528077 534608 + CcPI632755_01g000710.1 Cco01g0071 71
1 2869875 2874536 - CcPI632755_01g002940.1 Cco01g0294 294
1 2886743 2887572 + CcPI632755_01g002950.1 Cco01g0295 295
1 2897129 2898509 + CcPI632755_01g002960.1 Cco01g0296 296
1 2898898 2903693 - CcPI632755_01g002970.1 Cco01g0297 297
1 2938907 2941757 + CcPI632755_01g002990.1 Cco01g0299 299
7 19825236 19832638 + CcPI632755_07g008540.1 Cco07g0854 854
1 554795 561317 + CePI673135_01g000710.1 Cec01g0071 71
1 2837876 2842423 - CePI673135_01g002810.1 Cec01g0281 281
1 2854225 2855060 + CePI673135_01g002820.1 Cec01g0282 282
1 2867296 2868552 + CePI673135_01g002830.1 Cec01g0283 283
1 2868941 2873729 - CePI673135_01g002840.1 Cec01g0284 284
1 2905547 2908427 + CePI673135_01g002860.1 Cec01g0286 286
7 21724505 21731839 + CePI673135_07g008780.1 Cec07g0878 878
7 16922735 16927813 + Chy7G140400.1 Chy07g01210 1210
9 14186818 14189395 - Chy9G169200.1 Chy09g01204 1204
9 14203475 14208193 + Chy9G169220.1 Chy09g01206 1206
9 14208937 14209938 - Chy9G169230.1 Chy09g01207 1207
9 14216262 14216996 - Chy9G169240.1 Chy09g01208 1208
9 14226366 14230134 + Chy9G169250.1 Chy09g01209 1209
9 15776838 15782170 - Chy9G171270.1 Chy09g01411 1411
1 620108 626636 + ClG42_01g0007100.10 Clacu01g0071 71
1 2852767 2857396 - ClG42_01g0028700.10 Clacu01g0287 287
1 2868924 2869753 + ClG42_01g0028800.10 Clacu01g0288 288
1 2881630 2883013 + ClG42_01g0028900.10 Clacu01g0289 289
1 2883407 2888195 - ClG42_01g0029000.10 Clacu01g0290 290
1 2919502 2922414 + ClG42_01g0029200.10 Clacu01g0292 292
7 20274108 20281393 + ClG42_07g0079700.10 Clacu07g0797 797
1 581548 588966 + ClCG01G000700.1 Cla01g00071 71
1 2922190 2926819 - ClCG01G002880.2 Cla01g00278 278
1 2940675 2941735 + ClCG01G002890.1 Cla01g00279 279
1 2953647 2954672 + ClCG01G002900.2 Cla01g00280 280
1 2955157 2960375 - ClCG01G002910.2 Cla01g00281 281
1 2991388 2994618 + ClCG01G002930.2 Cla01g00283 283
7 21385508 21393134 + ClCG07G008010.2 Cla07g00764 764
2 6351079 6357060 + CmaCh02G010640.1 Cma02g01064 1064
2 8418997 8420012 + CmaCh02G014670.1 Cma02g01467 1467
2 8422805 8424212 + CmaCh02G014680.1 Cma02g01468 1468
2 8437165 8438228 + CmaCh02G014720.1 Cma02g01472 1472
6 1917891 1923829 - CmaCh06G004140.1 Cma06g00414 414
6 7127300 7130700 - CmaCh06G010600.1 Cma06g01060 1060
6 7351210 7357215 - CmaCh06G010890.1 Cma06g01089 1089
15 7688029 7695341 + CmaCh15G012150.1 Cma15g01215 1215
15 7693210 7694546 - CmaCh15G012160.1 Cma15g01216 1216
15 7699112 7700137 - CmaCh15G012170.1 Cma15g01217 1217
16 3040853 3047304 + CmaCh16G005880.1 Cma16g00588 588
7 22011662 22012015 + MELO3C016347.2.1 Cme07g01623 1623
9 21939369 21942505 - MELO3C005653.2.1 Cme09g01741 1741
9 21956332 21961507 + MELO3C005655.2.1 Cme09g01743 1743
9 21961595 21963418 - MELO3C005656.2.1 Cme09g01744 1744
9 21970190 21971326 - MELO3C005657.2.1 Cme09g01745 1745
9 23520889 23526957 - MELO3C005860.2.1 Cme09g01955 1955
2 8781791 8782742 + CmoCh02G015040.1 Cmo02g01504 1504
2 8785835 8787363 + CmoCh02G015050.1 Cmo02g01505 1505
2 8787388 8792668 - CmoCh02G015060.1 Cmo02g01506 1506
2 8799542 8801797 + CmoCh02G015070.1 Cmo02g01507 1507
6 8349756 8353146 - CmoCh06G010810.1 Cmo06g01081 1081
6 8585371 8591474 - CmoCh06G011150.1 Cmo06g01115 1115
15 8767724 8772403 + CmoCh15G012790.1 Cmo15g01279 1279
15 8772957 8773835 - CmoCh15G012800.1 Cmo15g01280 1280
15 8777997 8779020 - CmoCh15G012820.1 Cmo15g01282 1282
16 3143248 3150006 + CmoCh16G006370.1 Cmo16g00637 637
1 564932 571473 + CmPI595203_01g000720.1 Cmu01g0072 72
1 2808919 2813553 - CmPI595203_01g002740.1 Cmu01g0274 274
1 2825129 2825958 + CmPI595203_01g002750.1 Cmu01g0275 275
1 2837690 2839073 + CmPI595203_01g002760.1 Cmu01g0276 276
1 2839466 2844254 - CmPI595203_01g002770.1 Cmu01g0277 277
1 2875567 2878471 + CmPI595203_01g002780.1 Cmu01g0278 278
7 20488104 20495389 + CmPI595203_07g008040.1 Cmu07g0804 804
8 1833240 1834102 + Conep08aG0033100.1 Cone8ag0316 316
8 1835185 1839753 - Conep08aG0033200.1 Cone8ag0317 317
9 3668515 3669666 + Conep09aG0078200.1 Cone9ag0765 765
9 3673158 3678458 + Conep09aG0078300.1 Cone9ag0766 766
12 1729783 1730601 + Conep12aG0033000.1 Cone12ag0315 315
12 1730697 1735122 - Conep12aG0033100.1 Cone12ag0316 316
12 1738322 1739840 + Conep12aG0033200.1 Cone12ag0317 317
5 1778901 1788618 + Cp4.1LG05g03520.1 Cpe05g00319 319
5 1784993 1787823 - Cp4.1LG05g03410.1 Cpe05g00320 320
5 4001147 4002479 + Cp4.1LG05g06440.1 Cpe05g00657 657
8 3428920 3435158 + Cp4.1LG08g01510.1 Cpe08g00529 529
8 3662266 3665902 + Cp4.1LG08g01210.1 Cpe08g00557 557
13 1229292 1230419 + Cp4.1LG13g01640.1 Cpe13g00163 163
13 1233807 1241400 - Cp4.1LG13g01670.1 Cpe13g00164 164
14 3163908 3169473 + Cp4.1LG14g02180.1 Cpe14g00498 498
7 23808406 23815803 + CrPI670011_07g011590.1 Cre07g1159 1159
9 41436735 41439599 - CrPI670011_09g022290.1 Cre09g2229 2229
9 41469270 41474078 + CrPI670011_09g022300.1 Cre09g2230 2230
9 41474953 41475844 - CrPI670011_09g022310.1 Cre09g2231 2231
9 41485386 41486209 - CrPI670011_09g022320.1 Cre09g2232 2232
9 41500291 41504981 + CrPI670011_09g022330.1 Cre09g2233 2233
9 43748222 43754691 - CrPI670011_09g024370.1 Cre09g2437 2437
4 3971972 3973216 - CsaV3_4G006020.1 Csa04g00602 602
5 395605 402070 + CsaV3_5G000800.1 Csa05g00080 80
5 1869686 1873208 - CsaV3_5G002970.1 Csa05g00297 297
5 1881719 1882912 + CsaV3_5G002980.1 Csa05g00298 298
5 1888919 1896154 - CsaV3_5G002990.1 Csa05g00299 299
6 66320650 66325613 - Hsped.06g15600.1 Hepe06g1560 1560
6 66343018 66343946 + Hsped.06g15610.1 Hepe06g1561 1561
11 37074560 37079505 - Lag0032749.1 Lac11g2111 2111
11 37096313 37097121 + Lag0032750.1 Lac11g2112 2112
12 37096288 37102267 - Maker00029339 Lcy12g1668 1668
12 37132644 37133914 + Maker00029351 Lcy12g1669 1669
9 428363 436432 + Lsi09G000510.1 Lsi09g00051 51
9 2891718 2896780 - Lsi09G002760.1 Lsi09g00276 276
9 2909797 2910773 + Lsi09G002770.1 Lsi09g00277 277
9 2924742 2927081 + Lsi09G002790.1 Lsi09g00279 279
9 2924748 2931687 - Lsi09G002800.1 Lsi09g00280 280
9 2961531 2966816 + Lsi09G002820.1 Lsi09g00282 282
2 3227218 3231782 - Vvi2g342 Vvi2g342 342
2 3236090 3242957 + Vvi2g343 Vvi2g343 343
2 3248583 3249811 + Vvi2g344 Vvi2g344 344
2 3250300 3255775 - Vvi2g345 Vvi2g345 345
2 3263714 3264065 + Vvi2g346 Vvi2g346 346
2 3274707 3276088 + Vvi2g347 Vvi2g347 347
2 3284194 3293203 - Vvi2g348 Vvi2g348 348
2 3301516 3302335 + Vvi2g349 Vvi2g349 349
2 3335863 3346096 + Vvi2g350 Vvi2g350 350
2 3352540 3353184 + Vvi2g351 Vvi2g351 351
       

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