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
Vvi5g939 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g940 . Blo12g00105 Bda03g01137 . Bpe04g01080 . . . . . . . Car06g01056 Car14g01706 Sed02g1524 Cpe08g00410 Cpe03g01606 Bhi01g00201 Tan10g0500 Cmetu06g1928 Lac12g1917 Hepe05g1774 . Lcy11g1789 Cla06g00779 Cam06g0833 Cec06g0848 Cco06g0858 Clacu06g0836 Cmu06g0807 Cre06g1588 . . . . Lsi05g01856 Csa02g00902 . Cme06g00369 . . Bda11g00339 . . . . . . Cmo06g01241 Cmo14g01960 . . . . . . Bhi12g01473 Tan06g2276 . . . . . Cla05g00333 Cam05g0365 Cec05g0369 Cco05g0370 Clacu05g0360 Cmu05g0345 Cre05g0409 Lsi09g01120 Csa03g01081 Chy06g00350 .
Vvi5g941 . Blo12g00106 Bda03g01136 . Bpe04g01079 . Bma04g01165 . . Cmo17g00090 . . . . . . . . . . . . . . Cla06g00780 Cam06g0834 Cec06g0849 Cco06g0859 Clacu06g0837 Cmu06g0808 Cre06g1589 Cone14ag0243 Cone15ag0261 . . . Csa02g00901 . . . . . . . . . . . . . . Cma17g00083 . Car17g00078 Cpe12g00077 . . . . . . . . . . . . . . . Lsi09g01119 . . .
Vvi5g942 . . . . . . . . . . . . Car06g01057 Car14g01705 Sed02g1523 Cpe08g00409 Cpe03g01605 Bhi01g00203 Tan10g0501 Cmetu06g1022 . . . . . . . . . . . . . Cone7ag0406 . Lsi05g01855 . . Cme06g00370 . . Bda11g00340 . . Bpe13g00866 . . . . Cmo14g01959 . . . . . . . . . . . . . Cla05g00334 Cam05g0366 Cec05g0370 Cco05g0371 Clacu05g0361 Cmu05g0346 Cre05g0410 . Csa03g01082 Chy06g00351 .
Vvi5g943 . . . . . . . . . . . Cma14g01904 Car06g01058 . Sed02g1522 Cpe08g00408 Cpe03g01604 Bhi01g00204 Tan10g0502 Cmetu06g0591 . Hepe05g1772 . Lcy11g1787 . . . . . . . . . . . . . . Cme06g00371 . . . . . . . . . Cmo06g01242 Cmo14g01958 . . . . . . . . . . . . . Cla05g00335 Cam05g0367 Cec05g0371 Cco05g0372 Clacu05g0362 Cmu05g0347 Cre05g0411 . . . .
Vvi5g944 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g945 . . . . . . . . . . . . Car06g01059 . Sed05g1470 Cpe08g00407 . Bhi01g00206 Tan04g2631 Cmetu04g2155 . . . . . . . . . . . . . Cone7ag0405 . Lsi05g01854 . . Cme06g00372 . . Bda11g00341 . . Bpe13g00865 . Bma06g01275 . Cmo06g01243 . . . . . . . . . . . . . . Cla05g00336 . Cec05g0372 . . . . . Csa03g01083 Chy06g00352 .
Vvi5g946 . . . . . . . . . . . . . Car14g01704 Sed02g1520 . Cpe03g01603 Bhi01g00211 Tan10g0505 Cmetu06g1239 . . . . . . . . . . . . . Cone7ag0404 . Lsi05g01853 . . Cme06g00373 . . Bda11g00342 . . Bpe13g00864 . Bma06g01276 . . Cmo14g01956 . . . . . . . . . . . . . Cla05g00337 Cam05g0370 Cec05g0374 Cco05g0375 Clacu05g0364 Cmu05g0349 Cre05g0413 . Csa03g01084 . .
Vvi5g947 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla05g00339 Cam05g0371 Cec05g0375 Cco05g0376 Clacu05g0365 Cmu05g0350 Cre05g0414 . Csa03g01086 . .
Vvi5g948 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 11978042 11979361 - Bda017184.1 Bda03g01136 1136
3 11981051 11983418 - Bda017185.1 Bda03g01137 1137
11 3802095 3805789 + Bda033024 Bda11g00339 339
11 3806720 3810145 - Bda005072.2 Bda11g00340 340
11 3811785 3835062 + Bda005073.1 Bda11g00341 341
11 3836111 3837431 - Bda005074.1 Bda11g00342 342
1 3986665 3994625 + XM_039041650.1 Bhi01g00201 201
1 3995455 4002902 - XM_039041631.1 Bhi01g00203 203
1 4022855 4026941 - XM_039018367.1 Bhi01g00204 204
1 4029154 4068703 + XM_039018321.1 Bhi01g00206 206
1 4070588 4075472 - XM_039020003.1 Bhi01g00211 211
12 47591992 47597142 - XM_039051076.1 Bhi12g01473 1473
12 7673944 7676057 + BLOR04124 Blo12g00105 105
12 7677051 7678376 + BLOR04125 Blo12g00106 106
4 30107550 30108869 + Bma019901.1 Bma04g01165 1165
6 49840065 49859307 + Bma024384.1 Bma06g01275 1275
6 49860419 49861428 - Bma024385.1 Bma06g01276 1276
4 8303103 8304422 - Bpe015751.1 Bpe04g01079 1079
4 8306106 8308462 - Bpe015752.2 Bpe04g01080 1080
13 14804240 14805669 + Bpe010551.1 Bpe13g00864 864
13 14806612 14831395 - Bpe010552.1 Bpe13g00865 865
13 14838113 14841594 + Bpe010553.1 Bpe13g00866 866
5 3367058 3373580 + CaPI482276_05g003650.1 Cam05g0365 365
5 3374847 3379505 - CaPI482276_05g003660.1 Cam05g0366 366
5 3379558 3384076 - CaPI482276_05g003670.1 Cam05g0367 367
5 3405487 3405883 - CaPI482276_05g003700.1 Cam05g0370 370
5 3411824 3423073 - CaPI482276_05g003710.1 Cam05g0371 371
6 11740870 11746370 + CaPI482276_06g008330.1 Cam06g0833 833
6 11754135 11755451 + CaPI482276_06g008340.1 Cam06g0834 834
6 7923726 7929788 + Carg06303-RA Car06g01056 1056
6 7930428 7936177 - Carg06302-RA Car06g01057 1057
6 7938715 7942971 - Carg06301-RA Car06g01058 1058
6 7944283 7960208 + Carg06300-RA Car06g01059 1059
14 13536093 13538691 + Carg24771-RA Car14g01704 1704
14 13540030 13548969 + Carg24772-RA Car14g01705 1705
14 13549527 13555233 - Carg24773-RA Car14g01706 1706
17 450672 451991 - Carg10154-RA Car17g00078 78
5 2998628 3005577 + CcPI632755_05g003700.1 Cco05g0370 370
5 3006386 3011014 - CcPI632755_05g003710.1 Cco05g0371 371
5 3011067 3015656 - CcPI632755_05g003720.1 Cco05g0372 372
5 3037141 3037519 - CcPI632755_05g003750.1 Cco05g0375 375
5 3043377 3053225 - CcPI632755_05g003760.1 Cco05g0376 376
6 10554340 10559849 + CcPI632755_06g008580.1 Cco06g0858 858
6 10567204 10568520 + CcPI632755_06g008590.1 Cco06g0859 859
5 3010736 3017003 + CePI673135_05g003690.1 Cec05g0369 369
5 3018352 3023009 - CePI673135_05g003700.1 Cec05g0370 370
5 3024946 3027692 - CePI673135_05g003710.1 Cec05g0371 371
5 3032281 3043930 + CePI673135_05g003720.1 Cec05g0372 372
5 3049162 3049540 - CePI673135_05g003740.1 Cec05g0374 374
5 3055606 3065411 - CePI673135_05g003750.1 Cec05g0375 375
6 10630217 10635707 + CePI673135_06g008480.1 Cec06g0848 848
6 10642980 10644296 + CePI673135_06g008490.1 Cec06g0849 849
6 2325871 2329541 + Chy6G108780.1 Chy06g00350 350
6 2330981 2339676 - Chy6G108790.1 Chy06g00351 351
6 2343765 2355631 + Chy6G108800.1 Chy06g00352 352
5 3081196 3087647 + ClG42_05g0036000.10 Clacu05g0360 360
5 3088932 3093574 - ClG42_05g0036100.10 Clacu05g0361 361
5 3093627 3098041 - ClG42_05g0036200.10 Clacu05g0362 362
5 3115944 3119807 - ClG42_05g0036400.10 Clacu05g0364 364
5 3125571 3136902 - ClG42_05g0036500.10 Clacu05g0365 365
6 10373891 10379384 + ClG42_06g0083600.10 Clacu06g0836 836
6 10386975 10388291 + ClG42_06g0083700.10 Clacu06g0837 837
5 3023698 3030283 + ClCG05G003170.1 Cla05g00333 333
5 3031434 3036076 - ClCG05G003180.2 Cla05g00334 334
5 3038165 3041993 - ClCG05G003190.1 Cla05g00335 335
5 3045131 3056688 + ClCG05G003200.2 Cla05g00336 336
5 3057965 3062542 - ClCG05G003210.2 Cla05g00337 337
5 3068037 3077941 - ClCG05G003230.1 Cla05g00339 339
6 10687662 10693754 + ClCG06G008000.1 Cla06g00779 779
6 10702048 10703364 + ClCG06G008005.1 Cla06g00780 780
14 13454898 13465763 + CmaCh14G019040.1 Cma14g01904 1904
17 419246 420565 - CmaCh17G000830.1 Cma17g00083 83
6 2286112 2291264 + MELO3C006298.2.1 Cme06g00369 369
6 2292610 2297575 - MELO3C006299.2.1 Cme06g00370 370
6 2298811 2302906 - MELO3C006300.2.1 Cme06g00371 371
6 2304737 2317061 + MELO3C006301.2.1 Cme06g00372 372
6 2318069 2321823 - MELO3C006302.2.1 Cme06g00373 373
4 9527786 9530263 - PI0018686.1 Cmetu04g2155 2155
6 2509705 2513492 - PI0004150.1 Cmetu06g0591 591
6 2502961 2508137 - PI0022222.2 Cmetu06g1022 1022
6 2529506 2533149 - PI0015872.3 Cmetu06g1239 1239
6 2497012 2502428 + PI0021399.1 Cmetu06g1928 1928
6 9365283 9372083 + CmoCh06G012410.1 Cmo06g01241 1241
6 9380898 9384004 - CmoCh06G012420.1 Cmo06g01242 1242
6 9385875 9402568 + CmoCh06G012430.1 Cmo06g01243 1243
14 14447256 14453730 + CmoCh14G019560.1 Cmo14g01956 1956
14 14456369 14458733 + CmoCh14G019580.1 Cmo14g01958 1958
14 14459677 14464448 + CmoCh14G019590.1 Cmo14g01959 1959
14 14465219 14471250 - CmoCh14G019600.1 Cmo14g01960 1960
17 484935 486254 - CmoCh17G000900.1 Cmo17g00090 90
5 2919692 2926143 + CmPI595203_05g003450.1 Cmu05g0345 345
5 2927428 2932070 - CmPI595203_05g003460.1 Cmu05g0346 346
5 2932123 2936540 - CmPI595203_05g003470.1 Cmu05g0347 347
5 2954355 2957787 - CmPI595203_05g003490.1 Cmu05g0349 349
5 2964075 2975397 - CmPI595203_05g003500.1 Cmu05g0350 350
6 10190419 10196242 + CmPI595203_06g008070.1 Cmu06g0807 807
6 10203547 10204863 + CmPI595203_06g008080.1 Cmu06g0808 808
7 1790911 1793068 + Conep07aG0041400.1 Cone7ag0404 404
7 1792810 1796911 - Conep07aG0041500.1 Cone7ag0405 405
7 1798983 1801594 + Conep07aG0041600.1 Cone7ag0406 406
14 1113521 1115384 - Conep14aG0024800.1 Cone14ag0243 243
15 1222656 1224661 - Conep15aG0026700.1 Cone15ag0261 261
3 12350695 12354558 + Cp4.1LG03g18010.1 Cpe03g01603 1603
3 12355791 12359431 + Cp4.1LG03g18030.1 Cpe03g01604 1604
3 12360127 12365238 + Cp4.1LG03g18000.1 Cpe03g01605 1605
3 12366362 12371069 - Cp4.1LG03g17960.1 Cpe03g01606 1606
8 2601837 2617995 - Cp4.1LG08g02620.1 Cpe08g00407 407
8 2619244 2623702 + Cp4.1LG08g02700.1 Cpe08g00408 408
8 2626207 2633905 + Cp4.1LG08g02690.1 Cpe08g00409 409
8 2628433 2638469 - Cp4.1LG08g02640.1 Cpe08g00410 410
12 459849 461168 - Cp4.1LG12g00770.1 Cpe12g00077 77
5 3698534 3704988 + CrPI670011_05g004090.1 Cre05g0409 409
5 3706346 3711013 - CrPI670011_05g004100.1 Cre05g0410 410
5 3711066 3715634 - CrPI670011_05g004110.1 Cre05g0411 411
5 3733682 3737127 - CrPI670011_05g004130.1 Cre05g0413 413
5 3743606 3752089 - CrPI670011_05g004140.1 Cre05g0414 414
6 11280775 11286377 + CrPI670011_06g015880.1 Cre06g1588 1588
6 11294078 11295394 + CrPI670011_06g015890.1 Cre06g1589 1589
2 8407875 8411089 - CsaV3_2G011170.1 Csa02g00901 901
2 8412120 8419210 - CsaV3_2G011180.1 Csa02g00902 902
3 8571569 8577539 + CsaV3_3G010810.1 Csa03g01081 1081
3 8577215 8585508 - CsaV3_3G010820.1 Csa03g01082 1082
3 8589261 8601632 + CsaV3_3G010830.1 Csa03g01083 1083
3 8603001 8606566 - CsaV3_3G010840.1 Csa03g01084 1084
3 8610775 8617106 - CsaV3_3G010860.1 Csa03g01086 1086
5 68031739 68036414 + Hsped.05g17720.1 Hepe05g1772 1772
5 68044461 68051229 - Hsped.05g17740.1 Hepe05g1774 1774
12 35803441 35812944 - Lag0016289.1 Lac12g1917 1917
11 41671231 41675112 + Maker00031762 Lcy11g1787 1787
11 41683647 41691798 - Maker00031831 Lcy11g1789 1789
5 25763855 25768567 + Lsi05G018530.1 Lsi05g01853 1853
5 25769647 25782191 - Lsi05G018540.1 Lsi05g01854 1854
5 25784852 25797237 + Lsi05G018550.1 Lsi05g01855 1855
5 25796427 25803880 - Lsi05G018560.1 Lsi05g01856 1856
9 17906146 17907462 - Lsi09G011190.1 Lsi09g01119 1119
9 17914588 17920148 - Lsi09G011200.1 Lsi09g01120 1120
2 50957876 50963501 + Sed0014975.4 Sed02g1520 1520
2 50980671 50984247 + Sed0024686.1 Sed02g1522 1522
2 50987458 50992778 + Sed0019269.1 Sed02g1523 1523
2 50993502 51001758 - Sed0025821.1 Sed02g1524 1524
5 28441210 28441776 + Sed0009771.1 Sed05g1470 1470
4 85709122 85711606 - Tan0013908.1 Tan04g2631 2631
6 73700679 73707569 - Tan0014456.5 Tan06g2276 2276
10 4012074 4020785 + Tan0000127.1 Tan10g0500 500
10 4021590 4031971 - Tan0002966.1 Tan10g0501 501
10 4034405 4038815 - Tan0013046.1 Tan10g0502 502
10 4064102 4067351 - Tan0016520.1 Tan10g0505 505
5 15553006 15557507 + Vvi5g939 Vvi5g939 939
5 15578598 15596564 + Vvi5g940 Vvi5g940 940
5 15607719 15609012 + Vvi5g941 Vvi5g941 941
5 15612759 15655133 - Vvi5g942 Vvi5g942 942
5 15668461 15682244 - Vvi5g943 Vvi5g943 943
5 15682245 15683832 - Vvi5g944 Vvi5g944 944
5 15690673 15841680 + Vvi5g945 Vvi5g945 945
5 15844801 15849126 - Vvi5g946 Vvi5g946 946
5 15855334 15863727 - Vvi5g947 Vvi5g947 947
5 15873532 15875532 - Vvi5g948 Vvi5g948 948
       

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