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
Vvi19g214 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g215 . . . . Bpe09g00235 . Bma10g00497 Bma13g00953 . . Cma01g01209 Cma09g00862 Car01g01034 Car09g00775 Sed01g2386 Cpe06g00686 Cpe02g00701 Bhi09g03432 Tan01g4391 Cmetu07g0639 . Hepe01g1388 Mch11g1067 . Cla11g01760 Cam11g1827 Cec11g1847 Cco11g1854 Clacu11g1987 Cmu11g1796 Cre11g2204 Cone6ag0148 Cone9ag0173 . . Lsi04g02071 Csa04g02341 Chy07g00073 . . Blo10g00763 Bda05g00772 Bda12g00839 . Bpe03g00839 . . . Cmo01g01263 Cmo09g00852 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g216 Blo03g00653 . . . . . . . Cmo16g00431 Cmo04g00584 . Cma09g00864 . Car09g00776 . Cpe06g00687 . Bhi09g03431 Tan01g0809 . . Hepe01g1387 Mch11g1068 . Cla11g01761 Cam11g1828 Cec11g1848 Cco11g1855 Clacu11g1988 Cmu11g1797 Cre11g2205 Cone6ag0147 Cone9ag0172 Cone14ag1061 Cone15ag1053 Lsi04g02072 Csa04g02342 Chy07g00074 . . Blo10g00764 . Bda12g00840 Bpe11g00482 . . Bma14g00240 . . Cmo09g00853 Cma04g00550 Cma16g00397 Car04g00520 Car16g00362 Cpe14g00335 Cpe01g00493 Bhi11g00778 . . . Hepe07g1034 Mch10g1089 . Cla05g01007 Cam05g1096 Cec05g1106 Cco05g1099 Clacu05g1092 Cmu05g1043 Cre05g1116 Lsi05g00748 . Chy06g01158 .
Vvi19g217 . . Bda07g00298 . . Bpe08g01023 . . . . . . . Car09g00777 . . . Bhi09g02022 . . . . . . . . . . . . . . . . . Lsi04g02073 . . . . Blo10g00765 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g218 . . . Bda09g00507 . . . Bma13g00954 . . . Cma09g00865 . . . Cpe06g00688 Cpe02g00702 Bhi09g03428 Tan01g4394 . . . Mch11g1069 . Cla11g01762 Cam11g1829 Cec11g1849 Cco11g1856 Clacu11g1989 Cmu11g1798 Cre11g2206 . . . . . Csa04g02344 Chy07g00076 . . . . . Bpe11g00483 . . Bma14g00239 . . Cmo09g00854 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g219 . . . . . . . . . . Cma01g01208 . Car01g01033 Car09g00778 Sed04g2397 . . Bhi09g03427 Tan01g4395 Cmetu07g0812 . Hepe01g1386 . . . . . . . . . . . Cone14ag1062 Cone15ag1054 . . . . . . . . . . . . . Cmo01g01262 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g220 Blo03g00652 . Bda07g00297 Bda09g00506 . Bpe08g01024 . . Cmo16g00430 Cmo04g00583 . . . . . . . . . . . . . . . . . . . . . Cone6ag0146 Cone9ag0171 Cone14ag1063 . . . . . . . . . Bpe11g00484 . . Bma14g00238 . . . Cma04g00549 Cma16g00396 Car04g00518 Car16g00361 Cpe14g00334 Cpe01g00492 . . . . . . . Cla05g01008 Cam05g1097 Cec05g1107 Cco05g1100 Clacu05g1093 Cmu05g1044 Cre05g1117 . . Chy06g01157 .
Vvi19g221 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g222 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g223 . . . . . . Bma10g00499 Bma13g00955 . . . Cma09g00866 . Car09g00779 . Cpe06g00689 . Bhi09g03417 . . . . . . Cla11g01763 . Cec11g1850 Cco11g1857 Clacu11g1990 Cmu11g1799 . Cone6ag0145 Cone9ag0170 Cone14ag1064 . Lsi04g01334 Csa04g02345 Chy07g00077 . . . Bda05g00771 . . Bpe03g00837 . . . . Cmo09g00855 . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 56172633 56177127 - Bda021921.1 Bda05g00771 771
5 56190026 56192804 + Bda021922.1 Bda05g00772 772
7 4073929 4079241 + Bda025379.1 Bda07g00297 297
7 4081493 4087121 + Bda025380.2 Bda07g00298 298
9 6707338 6711759 + Bda031105.1 Bda09g00506 506
9 6716292 6722666 + Bda031106.1 Bda09g00507 507
12 38039680 38042368 - Bda009357.1 Bda12g00839 839
12 38049279 38050116 + Bda009358.1 Bda12g00840 840
9 56788297 56798703 + XM_039042581.1 Bhi09g02022 2022
9 86639042 86658532 - XM_039041708.1 Bhi09g03417 3417
9 86666892 86671814 + XM_039041795.1 Bhi09g03427 3427
9 86666896 86674573 + XM_039041794.1 Bhi09g03428 3428
9 86719178 86722094 - XM_039043342.1 Bhi09g03431 3431
9 86733634 86738471 + XM_039042100.1 Bhi09g03432 3432
11 21016281 21021876 - XM_039047518.1 Bhi11g00778 778
3 27727342 27742671 + BLOR11833 Blo03g00652 652
3 27743086 27744604 - BLOR11834 Blo03g00653 653
10 23884513 23891117 - BLOR02553 Blo10g00763 763
10 23907148 23909059 + BLOR02554 Blo10g00764 764
10 23909586 23913338 - BLOR02555 Blo10g00765 765
10 5868705 5871491 - Bma004188.1 Bma10g00497 497
10 5881066 5885138 + Bma004190.3 Bma10g00499 499
13 40673244 40675928 - Bma010052.1 Bma13g00953 953
13 40684466 40688567 - Bma010053.3 Bma13g00954 954
13 40725174 40728818 + Bma010054.1 Bma13g00955 955
14 2878166 2883565 + Bma010649.1 Bma14g00238 238
14 2885522 2891136 + Bma010650.1 Bma14g00239 239
14 2891466 2892977 - Bma010651.1 Bma14g00240 240
3 28246575 28250004 - Bpe012746.2 Bpe03g00837 837
3 28257569 28260403 + Bpe012748.1 Bpe03g00839 839
8 12483240 12488510 - Bpe023147.1 Bpe08g01023 1023
8 12492491 12496907 - Bpe023148.1 Bpe08g01024 1024
9 1696357 1699051 + Bpe023905.1 Bpe09g00235 235
11 3717041 3718557 + Bpe003852.1 Bpe11g00482 482
11 3718950 3723636 - Bpe003853.1 Bpe11g00483 483
11 3726087 3731417 - Bpe003854.1 Bpe11g00484 484
5 10039539 10041380 + CaPI482276_05g010960.1 Cam05g1096 1096
5 10044173 10049679 - CaPI482276_05g010970.1 Cam05g1097 1097
11 30801769 30805008 - CaPI482276_11g018270.1 Cam11g1827 1827
11 30815602 30817446 + CaPI482276_11g018280.1 Cam11g1828 1828
11 30819583 30828055 - CaPI482276_11g018290.1 Cam11g1829 1829
1 9792886 9799147 + Carg14697-RA Car01g01033 1033
1 9801427 9810815 + Carg14698-RA Car01g01034 1034
4 2917917 2923185 + Carg13190-RA Car04g00518 518
4 2924217 2925780 - Carg13187-RA Car04g00520 520
9 4569314 4573264 - Carg17097-RA Car09g00775 775
9 4577580 4580459 + Carg17098-RA Car09g00776 776
9 4579651 4582132 - Carg17099-RA Car09g00777 777
9 4583874 4586852 - Carg17100-RA Car09g00778 778
9 4591360 4600055 + Carg17101-RA Car09g00779 779
16 2244419 2249441 + Carg11328-RA Car16g00361 361
16 2249988 2252269 - Carg11329-RA Car16g00362 362
5 9807587 9809355 + CcPI632755_05g010990.1 Cco05g1099 1099
5 9812202 9817734 - CcPI632755_05g011000.1 Cco05g1100 1100
11 31227036 31230285 - CcPI632755_11g018540.1 Cco11g1854 1854
11 31239738 31241598 + CcPI632755_11g018550.1 Cco11g1855 1855
11 31243764 31252011 - CcPI632755_11g018560.1 Cco11g1856 1856
11 31259310 31268958 + CcPI632755_11g018570.1 Cco11g1857 1857
5 9796335 9798190 + CePI673135_05g011060.1 Cec05g1106 1106
5 9800993 9806509 - CePI673135_05g011070.1 Cec05g1107 1107
11 32667538 32670735 - CePI673135_11g018470.1 Cec11g1847 1847
11 32681202 32682956 + CePI673135_11g018480.1 Cec11g1848 1848
11 32685092 32693197 - CePI673135_11g018490.1 Cec11g1849 1849
11 32700450 32710024 + CePI673135_11g018500.1 Cec11g1850 1850
6 10239150 10244677 + Chy6G116850.1 Chy06g01157 1157
6 10247149 10248949 - Chy6G116860.1 Chy06g01158 1158
7 683619 686725 - Chy7G129030.1 Chy07g00073 73
7 695155 696882 + Chy7G129040.1 Chy07g00074 74
7 701204 707058 - Chy7G129060.1 Chy07g00076 76
7 716837 721856 + Chy7G129070.1 Chy07g00077 77
5 9781633 9783447 + ClG42_05g0109200.10 Clacu05g1092 1092
5 9786229 9791738 - ClG42_05g0109300.10 Clacu05g1093 1093
11 30840200 30843437 - ClG42_11g0198700.10 Clacu11g1987 1987
11 30853818 30855571 + ClG42_11g0198800.10 Clacu11g1988 1988
11 30857550 30865143 - ClG42_11g0198900.10 Clacu11g1989 1989
11 30872868 30882518 + ClG42_11g0199000.10 Clacu11g1990 1990
5 10152930 10156476 + ClCG05G009330.1 Cla05g01007 1007
5 10158398 10166591 - ClCG05G009340.1 Cla05g01008 1008
11 31214947 31218968 - ClCG11G018050.2 Cla11g01760 1760
11 31227611 31230503 + ClCG11G018060.2 Cla11g01761 1761
11 31231858 31240848 - ClCG11G018070.2 Cla11g01762 1762
11 31247700 31257720 + ClCG11G018080.2 Cla11g01763 1763
1 8752931 8760038 + CmaCh01G012080.1 Cma01g01208 1208
1 8761620 8765348 + CmaCh01G012090.1 Cma01g01209 1209
4 2787202 2792174 + CmaCh04G005490.1 Cma04g00549 549
4 2793326 2795143 - CmaCh04G005500.1 Cma04g00550 550
9 4227156 4230941 - CmaCh09G008620.1 Cma09g00862 862
9 4234694 4237613 + CmaCh09G008640.1 Cma09g00864 864
9 4237452 4244060 - CmaCh09G008650.1 Cma09g00865 865
9 4249162 4257508 + CmaCh09G008660.1 Cma09g00866 866
16 1972196 1977500 + CmaCh16G003960.1 Cma16g00396 396
16 1977879 1980428 - CmaCh16G003970.1 Cma16g00397 397
7 22015053 22018596 - PI0027820.1 Cmetu07g0639 639
7 22035025 22040926 - PI0007039.1 Cmetu07g0812 812
1 10107433 10113020 + CmoCh01G012620.1 Cmo01g01262 1262
1 10115879 10118869 + CmoCh01G012630.1 Cmo01g01263 1263
4 2911153 2916800 + CmoCh04G005830.1 Cmo04g00583 583
4 2918354 2919918 - CmoCh04G005840.1 Cmo04g00584 584
9 4388728 4392733 - CmoCh09G008520.1 Cmo09g00852 852
9 4396849 4399270 + CmoCh09G008530.1 Cmo09g00853 853
9 4399282 4406097 - CmoCh09G008540.1 Cmo09g00854 854
9 4410409 4419999 + CmoCh09G008550.1 Cmo09g00855 855
16 2044031 2048013 + CmoCh16G004300.1 Cmo16g00430 430
16 2048959 2051520 - CmoCh16G004310.1 Cmo16g00431 431
5 9622103 9623853 + CmPI595203_05g010430.1 Cmu05g1043 1043
5 9626629 9632141 - CmPI595203_05g010440.1 Cmu05g1044 1044
11 30089566 30099055 - CmPI595203_11g017960.1 Cmu11g1796 1796
11 30109433 30111185 + CmPI595203_11g017970.1 Cmu11g1797 1797
11 30113162 30121292 - CmPI595203_11g017980.1 Cmu11g1798 1798
11 30128467 30137625 + CmPI595203_11g017990.1 Cmu11g1799 1799
6 735467 739038 - Conep06aG0014600.1 Cone6ag0145 145
6 740829 744179 + Conep06aG0014700.1 Cone6ag0146 146
6 744832 747698 - Conep06aG0014800.1 Cone6ag0147 147
6 750120 753633 + Conep06aG0014900.1 Cone6ag0148 148
9 754961 758386 - Conep09aG0017200.1 Cone9ag0170 170
9 760275 764332 + Conep09aG0017300.1 Cone9ag0171 171
9 764777 767756 - Conep09aG0017400.1 Cone9ag0172 172
9 770423 772616 + Conep09aG0017500.1 Cone9ag0173 173
14 8947452 8950245 + Conep14aG0108200.1 Cone14ag1061 1061
14 8950375 8955445 - Conep14aG0108300.1 Cone14ag1062 1062
14 8962512 8967215 - Conep14aG0108400.1 Cone14ag1063 1063
14 8968171 8972417 + Conep14aG0108500.1 Cone14ag1064 1064
15 8719911 8721405 + Conep15aG0107500.1 Cone15ag1053 1053
15 8721448 8726865 - Conep15aG0107600.1 Cone15ag1054 1054
1 2843378 2849790 + Cp4.1LG01g01780.1 Cpe01g00492 492
1 2850989 2853948 - Cp4.1LG01g01670.1 Cpe01g00493 493
2 4427960 4432235 - Cp4.1LG02g01730.1 Cpe02g00701 701
2 4434128 4440665 - Cp4.1LG02g01590.1 Cpe02g00702 702
6 4270826 4275131 - Cp4.1LG06g06860.1 Cpe06g00686 686
6 4278303 4282630 + Cp4.1LG06g06760.1 Cpe06g00687 687
6 4281224 4287806 - Cp4.1LG06g06870.1 Cpe06g00688 688
6 4292741 4301517 + Cp4.1LG06g06960.1 Cpe06g00689 689
14 2027755 2032540 + Cp4.1LG14g03880.1 Cpe14g00334 334
14 2033479 2036941 - Cp4.1LG14g03850.1 Cpe14g00335 335
5 10510783 10512618 + CrPI670011_05g011160.1 Cre05g1116 1116
5 10515345 10521062 - CrPI670011_05g011170.1 Cre05g1117 1117
11 33763604 33766870 - CrPI670011_11g022040.1 Cre11g2204 2204
11 33777398 33779152 + CrPI670011_11g022050.1 Cre11g2205 2205
11 33781215 33789425 - CrPI670011_11g022060.1 Cre11g2206 2206
4 23866189 23869734 - CsaV3_4G033670.1 Csa04g02341 2341
4 23875312 23881239 + CsaV3_4G033690.1 Csa04g02342 2342
4 23882327 23889214 - CsaV3_4G033700.1 Csa04g02344 2344
4 23896902 23907136 + CsaV3_4G033710.1 Csa04g02345 2345
1 79068710 79075488 + Hsped.01g13860.1 Hepe01g1386 1386
1 79076915 79079804 - Hsped.01g13870.1 Hepe01g1387 1387
1 79088023 79092990 + Hsped.01g13880.1 Hepe01g1388 1388
7 14909036 14912417 + Hsped.07g10340.1 Hepe07g1034 1034
4 21111087 21135969 - Lsi04G013340.1 Lsi04g01334 1334
4 27855433 27859783 - Lsi04G020710.1 Lsi04g02071 2071
4 27868821 27871910 + Lsi04G020720.1 Lsi04g02072 2072
4 27874013 27883383 - Lsi04G020730.1 Lsi04g02073 2073
5 10347575 10351208 + Lsi05G007480.1 Lsi05g00748 748
10 8036370 8040383 + MC10g0929 Mch10g1089 1089
11 7426182 7430628 - MC11g0874 Mch11g1067 1067
11 7438029 7440971 + MC11g0875 Mch11g1068 1068
11 7444657 7452486 - MC11g0876 Mch11g1069 1069
1 17918208 17928182 - Sed0027880.1 Sed01g2386 2386
4 37272132 37279169 + Sed0021610.3 Sed04g2397 2397
1 7865722 7869373 - Tan0018291.1 Tan01g0809 809
1 109018304 109022007 - Tan0004734.1 Tan01g4391 4391
1 109042610 109063711 - Tan0000462.1 Tan01g4394 4394
1 109042610 109063711 - Tan0000462.2 Tan01g4395 4395
19 2702487 2703384 + Vvi19g214 Vvi19g214 214
19 2703384 2708789 - Vvi19g215 Vvi19g215 215
19 2716632 2720479 + Vvi19g216 Vvi19g216 216
19 2720596 2723239 - Vvi19g217 Vvi19g217 217
19 2723239 2724364 - Vvi19g218 Vvi19g218 218
19 2724363 2732381 - Vvi19g219 Vvi19g219 219
19 2734506 2744265 - Vvi19g220 Vvi19g220 220
19 2754664 2757270 + Vvi19g221 Vvi19g221 221
19 2760836 2762169 - Vvi19g222 Vvi19g222 222
19 2770458 2777826 + Vvi19g223 Vvi19g223 223
       

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