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
Vvi2g562 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g563 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g564 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g565 . . . . . . . . . . . . . . . . Cpe05g00213 . . . . . . . . . . . . . . Cone8ag0435 Cone12ag0420 . . . . . . Blo03g00461 . . . . . . . Sed01g4058 . . . . . . . . Bhi05g00572 Tan07g1905 Cmetu04g0109 Lac11g2346 Hepe06g1720 . Lcy12g1881 Cla09g01204 Cam09g1271 Cec09g1285 Cco09g1319 . . Cre09g1231 . . . .
Vvi2g566 . . . . . . Bma07g00989 . . Cmo16g01148 . . . . . . . Bhi11g00091 . . . . Mch10g1605 . Cla10g00204 Cam10g0210 Cec10g0215 Cco10g0216 Clacu10g0213 Cmu10g1056 Cre10g0464 . . . Cone9ag0633 Lsi07g01245 . . Cme06g02516 . . . Bda09g00675 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g567 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g568 . . . . . . . . . . Cma02g01577 . Car02g01341 . . . . . . . . . . . . . . . . . . . . . . . . Chy04g00031 . . . . . . . . . . Cmo02g01619 . . . . . . . . . . . . . . . . . . . . . . Csa03g04670 . Cme04g00041
Vvi2g569 . . . . . . Bma07g00988 . Cmo06g00847 . . . . . Sed07g1307 . . Bhi11g00092 Tan01g2115 Cmetu06g0637 . . . . . . . . . . . . . . . . . . . . Blo19g00157 . Bda09g00687 Bpe08g00873 . . . . . . Cma06g00825 . . . . . . . . . . . . . . . . . . . . Csa03g00219 Chy06g02101 .
Vvi2g570 . . . . . . . . . . Cma02g01578 . Car02g01342 . . . Cpe05g00212 . . . . . . . . . . . . . . Cone8ag0436 Cone12ag0421 Cone6ag0629 Cone9ag0632 . . Chy04g00032 . . Blo19g00259 . . . . . . Sed01g4060 . Cmo19g00397 . . . . . . Bhi05g00570 Tan07g1906 Cmetu04g2898 . Hepe06g1721 . Lcy12g1882 Cla09g01203 Cam09g1270 Cec09g1284 Cco09g1318 . . Cre09g1230 . Csa03g04669 . Cme04g00042
Vvi2g571 . Blo03g00134 Bda06g01305 . . Bpe07g00201 . . Cmo06g00849 Cmo16g01146 . . . . Sed05g2359 Cpe14g00907 . Bhi11g00093 Tan01g2116 Cmetu06g0894 . Hepe06g1074 Mch10g1606 . Cla10g00203 Cam10g0209 Cec10g0214 Cco10g0215 Clacu10g0212 Cmu10g1055 Cre10g0463 . . Cone6ag0628 Cone9ag0631 Lsi07g01244 . . Cme06g02515 . . . . . . . Bma12g00195 . . Cmo19g00513 Cma06g00826 Cma16g01097 . Car16g01039 . . . . . . . . . . . . . . . . . Csa03g00218 Chy06g02102 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 43725635 43728993 - Bda023159.1 Bda06g01305 1305
9 10316351 10317611 + Bda034121 Bda09g00675 675
9 10771007 10773311 + Bda031347.1 Bda09g00687 687
5 14090909 14095778 - XM_039032164.1 Bhi05g00570 570
5 14114938 14122196 - XM_039032129.1 Bhi05g00572 572
11 2190735 2194534 + XM_039050076.1 Bhi11g00091 91
11 2190736 2194534 + XM_039050075.1 Bhi11g00092 92
11 2231360 2235612 + XM_039048614.1 Bhi11g00093 93
3 3840454 3852875 - BLOR11315 Blo03g00134 134
3 15057957 15075241 - BLOR11642 Blo03g00461 461
19 6227189 6229459 + BLOR09500 Blo19g00157 157
19 14985929 14988952 - BLOR09602 Blo19g00259 259
7 38482932 38484304 - Bma026148.1 Bma07g00988 988
7 38498769 38499649 - Bma031390 Bma07g00989 989
12 2621134 2624232 + Bma007081.1 Bma12g00195 195
7 1375638 1379545 + Bpe021011.1 Bpe07g00201 201
8 11123061 11124071 - Bpe026155 Bpe08g00873 873
9 14941870 14946317 - CaPI482276_09g012700.1 Cam09g1270 1270
9 14957809 14964768 - CaPI482276_09g012710.1 Cam09g1271 1271
10 3791496 3794971 - CaPI482276_10g002090.1 Cam10g0209 209
10 3804933 3807429 - CaPI482276_10g002100.1 Cam10g0210 210
2 8867121 8873063 + Carg08808-RA Car02g01341 1341
2 8874727 8878407 + Carg08809-RA Car02g01342 1342
16 8910234 8914006 - Carg23243-RA Car16g01039 1039
9 14971529 14975898 - CcPI632755_09g013180.1 Cco09g1318 1318
9 14990473 14997191 - CcPI632755_09g013190.1 Cco09g1319 1319
10 2238438 2241615 - CcPI632755_10g002150.1 Cco10g0215 215
10 2250791 2254187 - CcPI632755_10g002160.1 Cco10g0216 216
9 15129760 15134129 - CePI673135_09g012840.1 Cec09g1284 1284
9 15156116 15163104 - CePI673135_09g012850.1 Cec09g1285 1285
10 2340894 2344076 - CePI673135_10g002140.1 Cec10g0214 214
10 2353270 2356671 - CePI673135_10g002150.1 Cec10g0215 215
4 311884 317990 + Chy4G067490.1 Chy04g00031 31
4 320505 325316 + Chy4G067500.1 Chy04g00032 32
6 25190938 25193171 + Chy6G126290.1 Chy06g02101 2101
6 25199610 25202525 + Chy6G126300.1 Chy06g02102 2102
10 2537304 2540466 - ClG42_10g0021200.10 Clacu10g0212 212
10 2549678 2553065 - ClG42_10g0021300.10 Clacu10g0213 213
9 14987684 14992427 - ClCG09G012620.1 Cla09g01203 1203
9 15004475 15011435 - ClCG09G012630.2 Cla09g01204 1204
10 2352105 2355975 - ClCG10G002090.2 Cla10g00203 203
10 2372138 2376152 - ClCG10G002100.2 Cla10g00204 204
2 8955716 8961764 + CmaCh02G015770.1 Cma02g01577 1577
2 8961840 8966659 + CmaCh02G015780.1 Cma02g01578 1578
6 4472904 4476443 + CmaCh06G008250.1 Cma06g00825 825
6 4480486 4483649 + CmaCh06G008260.1 Cma06g00826 826
16 8449840 8454322 - CmaCh16G010970.1 Cma16g01097 1097
4 267364 274135 + MELO3C003340.2.1 Cme04g00041 41
4 276124 281416 + MELO3C003341.2.1 Cme04g00042 42
6 32195241 32198794 - MELO3C013890.2.1 Cme06g02515 2515
6 32204663 32208186 - MELO3C013891.2.1 Cme06g02516 2516
4 33181197 33188861 - PI0003623.2 Cmetu04g0109 109
4 33173312 33179072 - PI0018045.1 Cmetu04g2898 2898
6 29199320 29203064 + PI0009676.1 Cmetu06g0637 637
6 29208150 29211958 + PI0017087.1 Cmetu06g0894 894
2 9328397 9338328 + CmoCh02G016190.1 Cmo02g01619 1619
6 4748818 4751223 + CmoCh06G008470.1 Cmo06g00847 847
6 4754717 4758407 + CmoCh06G008490.1 Cmo06g00849 849
16 8183021 8187464 - CmoCh16G011460.1 Cmo16g01146 1146
16 8193903 8196087 - CmoCh16G011480.1 Cmo16g01148 1148
19 4605624 4610666 - CmoCh19G003970.1 Cmo19g00397 397
19 6058440 6059891 - CmoCh19G005130.1 Cmo19g00513 513
10 2688273 2691432 - CmPI595203_10g010550.1 Cmu10g1055 1055
10 2700670 2704057 - CmPI595203_10g010560.1 Cmu10g1056 1056
6 3174802 3177022 - Conep06aG0064700.1 Cone6ag0628 628
6 3178446 3181597 - Conep06aG0064800.1 Cone6ag0629 629
8 2724456 2734831 + Conep08aG0045200.1 Cone8ag0435 435
8 2735860 2738654 + Conep08aG0045300.1 Cone8ag0436 436
9 2996991 2998364 - Conep09aG0064600.1 Cone9ag0631 631
9 3000540 3003695 - Conep09aG0064700.1 Cone9ag0632 632
9 3003897 3006159 - Conep09aG0064800.1 Cone9ag0633 633
12 2500472 2506193 + Conep12aG0043500.1 Cone12ag0420 420
12 2506852 2509669 + Conep12aG0043600.1 Cone12ag0421 421
5 1176750 1181406 - Cp4.1LG05g01870.1 Cpe05g00212 212
5 1181920 1188785 - Cp4.1LG05g01900.1 Cpe05g00213 213
14 7633708 7638086 - Cp4.1LG14g09040.1 Cpe14g00907 907
9 15104302 15108620 - CrPI670011_09g012300.1 Cre09g1230 1230
9 15121548 15128555 - CrPI670011_09g012310.1 Cre09g1231 1231
10 3653892 3657050 - CrPI670011_10g004630.1 Cre10g0463 463
10 3665633 3669055 - CrPI670011_10g004640.1 Cre10g0464 464
3 1762398 1766605 - CsaV3_3G002180.1 Csa03g00218 218
3 1770624 1774309 - CsaV3_3G002190.1 Csa03g00219 219
3 40616967 40623093 - CsaV3_3G049750.1 Csa03g04669 4669
3 40624993 40631062 - CsaV3_3G049760.1 Csa03g04670 4670
6 59107826 59111693 - Hsped.06g10740.1 Hepe06g1074 1074
6 68199840 68206270 + Hsped.06g17200.1 Hepe06g1720 1720
6 68207726 68212040 + Hsped.06g17210.1 Hepe06g1721 1721
11 39519810 39524251 + Lag0032984.1 Lac11g2346 2346
12 39997657 40004529 + Maker00038013 Lcy12g1881 1881
12 40006974 40011421 + Maker00038229 Lcy12g1882 1882
7 18177447 18181332 - Lsi07G012440.1 Lsi07g01244 1244
7 18188723 18192123 - Lsi07G012450.1 Lsi07g01245 1245
10 16142508 16144951 + MC10g1272 Mch10g1605 1605
10 16150858 16154305 + MC10g1273 Mch10g1606 1606
1 69551085 69558504 + Sed0020438.1 Sed01g4058 4058
1 69559720 69565005 + Sed0005760.2 Sed01g4060 4060
5 36099403 36102045 - Sed0001675.2 Sed05g2359 2359
7 9829471 9833547 + Sed0003222.1 Sed07g1307 1307
1 24347737 24351586 + Tan0005780.1 Tan01g2115 2115
1 24369321 24373241 + Tan0022381.1 Tan01g2116 2116
7 70600513 70609172 + Tan0003188.1 Tan07g1905 1905
7 70610289 70615045 + Tan0013337.1 Tan07g1906 1906
2 5599005 5602022 + Vvi2g562 Vvi2g562 562
2 5602091 5602465 - Vvi2g563 Vvi2g563 563
2 5625022 5625771 - Vvi2g564 Vvi2g564 564
2 5652306 5660093 + Vvi2g565 Vvi2g565 565
2 5660754 5666970 + Vvi2g566 Vvi2g566 566
2 5669659 5669797 - Vvi2g567 Vvi2g567 567
2 5674911 5683893 + Vvi2g568 Vvi2g568 568
2 5684000 5689314 + Vvi2g569 Vvi2g569 569
2 5692457 5701159 + Vvi2g570 Vvi2g570 570
2 5701865 5714378 + Vvi2g571 Vvi2g571 571
       

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