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
Vvi19g664 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g665 . . . . Bpe09g00127 . . Bma13g01115 . Cmo06g00686 . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1218 Cone15ag1239 . . . . . Blo10g00865 . Bda12g00964 . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi05g00496 . . .
Vvi19g666 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g667 . Blo03g01483 . Bda09g00438 . Bpe08g01091 . . Cmo16g01004 . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1219 Cone15ag1240 . . . . . . . . . . Bma07g01246 . . . . . Cma16g00963 . Car16g00928 Cpe14g00789 . . . . . . . . . . . . . . . Lsi05g00497 . . .
Vvi19g668 . Blo03g01484 Bda07g00412 Bda09g00439 Bpe09g00126 Bpe08g01090 . Bma13g01116 . Cmo06g00685 Cma01g01075 Cma09g01013 Car01g00951 . Sed07g2749 Cpe06g00821 Cpe02g00823 Bhi09g01777 Tan01g3193 Cmetu01g1443 . . Mch11g1277 . Cla10g00408 Cam10g0405 Cec10g0427 Cco10g0417 Clacu10g0412 Cmu10g1244 Cre10g0661 Cone6ag0009 . Cone14ag1220 Cone15ag1241 Lsi02g01825 . . Cme06g02759 . . . Bda12g00965 Bpe11g00589 . Bma07g01245 Bma14g00680 . Cmo01g01120 Cmo09g01015 . . . . . . . . . . . . . Cla09g02079 Cam09g2166 Cec09g2231 . . . . Lsi05g00498 . Chy01g01144 Cme01g00903
Vvi19g669 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0008 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g670 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g671 . . . . . . . . . . . Cma09g01014 . . Sed04g3651 Cpe06g00822 . Bhi09g01778 Tan01g3196 Cmetu01g1518 . . Mch11g1279 . . . . . . . . . . Cone14ag1221 Cone15ag1242 Lsi02g01823 . . . . . . . . . . . . . Cmo09g01017 . . . . . . . . . . . . . Cla09g02081 Cam09g2169 Cec09g2234 . . . . . . Chy01g01142 .
Vvi19g672 . . . . . . . . Cmo16g01006 Cmo06g00683 . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g00426 . . . . . . . . . . . . . . Cma16g00965 . . Cpe14g00788 . . . . . . . . . . . . . . . . . . .
Vvi19g673 . . . . . . . . . Cmo06g00682 . . . . . . . . . . . . . . Cla10g00404 Cam10g0401 Cec10g0423 Cco10g0413 Clacu10g0408 Cmu10g1240 Cre10g0657 . . Cone14ag1222 Cone15ag1295 . Csa03g00425 . Cme06g02755 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi05g00494 . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 5291133 5292464 + Bda025504.1 Bda07g00412 412
9 5814205 5814825 + Bda034096 Bda09g00438 438
9 5816106 5817332 + Bda031028.1 Bda09g00439 439
12 40830617 40834864 + Bda009512.1 Bda12g00964 964
12 40836886 40838106 + Bda009513.1 Bda12g00965 965
9 48206948 48208667 + XM_039044095.1 Bhi09g01777 1777
9 48249895 48276883 - XM_039044107.1 Bhi09g01778 1778
3 41606224 41606850 + BLOR12664 Blo03g01483 1483
3 41609459 41611653 + BLOR12665 Blo03g01484 1484
10 27349892 27355560 + BLOR02655 Blo10g00865 865
7 47445880 47446416 - Bma026499.2 Bma07g01245 1245
7 47448329 47448859 - Bma026500.1 Bma07g01246 1246
13 44273526 44277715 + Bma010245.1 Bma13g01115 1115
13 44279852 44281072 + Bma010246.1 Bma13g01116 1116
14 7350550 7351653 - Bma011131.1 Bma14g00680 680
8 12993345 12994568 - Bpe023215.1 Bpe08g01090 1090
8 12995926 12996558 - Bpe023216.1 Bpe08g01091 1091
9 857455 858669 - Bpe023801.1 Bpe09g00126 126
9 866682 868880 - Bpe023802.1 Bpe09g00127 127
11 4479768 4480991 + Bpe003954.1 Bpe11g00589 589
9 36162624 36163880 + CaPI482276_09g021660.1 Cam09g2166 2166
9 36180117 36194947 - CaPI482276_09g021690.1 Cam09g2169 2169
10 6374111 6374638 + CaPI482276_10g004010.1 Cam10g0401 401
10 6401241 6402002 + CaPI482276_10g004050.1 Cam10g0405 405
1 9130798 9132045 - Carg22412-RA Car01g00951 951
16 7601111 7601773 - Carg22326-RA Car16g00928 928
10 4919341 4919868 + CcPI632755_10g004130.1 Cco10g0413 413
10 4949389 4950150 + CcPI632755_10g004170.1 Cco10g0417 417
9 39187830 39190540 + CePI673135_09g022310.1 Cec09g2231 2231
9 39217397 39223598 - CePI673135_09g022340.1 Cec09g2234 2234
10 5109684 5110211 + CePI673135_10g004230.1 Cec10g0423 423
10 5138202 5138966 + CePI673135_10g004270.1 Cec10g0427 427
1 13259451 13308359 + Chy1G011420.1 Chy01g01142 1142
1 13360272 13361519 - Chy1G011440.1 Chy01g01144 1144
10 5163115 5163642 + ClG42_10g0040800.10 Clacu10g0408 408
10 5190708 5191469 + ClG42_10g0041200.10 Clacu10g0412 412
9 38320692 38321945 + ClCG09G021350.1 Cla09g02079 2079
9 38330925 38352049 - ClCG09G021370.1 Cla09g02081 2081
10 5486885 5487412 + ClCG10G004280.1 Cla10g00404 404
10 5515940 5516701 + ClCG10G004330.1 Cla10g00408 408
1 7935571 7936818 - CmaCh01G010750.1 Cma01g01075 1075
9 5165830 5167077 + CmaCh09G010130.1 Cma09g01013 1013
9 5169648 5186556 - CmaCh09G010140.1 Cma09g01014 1014
16 7449484 7450143 - CmaCh16G009630.1 Cma16g00963 963
16 7456100 7456648 - CmaCh16G009650.1 Cma16g00965 965
1 10454479 10456183 - MELO3C024938.2.1 Cme01g00903 903
6 34811100 34811558 + MELO3C014103.2.1 Cme06g02755 2755
6 34825517 34826364 + MELO3C014107.2.1 Cme06g02759 2759
1 13758920 13760539 + PI0018203.1 Cmetu01g1443 1443
1 13837541 13875063 - PI0017716.1 Cmetu01g1518 1518
1 9254560 9255807 - CmoCh01G011200.1 Cmo01g01120 1120
6 3468038 3468691 + CmoCh06G006820.1 Cmo06g00682 682
6 3472988 3474614 + CmoCh06G006830.1 Cmo06g00683 683
6 3480599 3481360 - CmoCh06G006850.1 Cmo06g00685 685
6 3482481 3485960 - CmoCh06G006860.1 Cmo06g00686 686
9 5395104 5396351 + CmoCh09G010150.1 Cmo09g01015 1015
9 5411127 5413585 - CmoCh09G010170.1 Cmo09g01017 1017
16 6907505 6908167 - CmoCh16G010040.1 Cmo16g01004 1004
16 6914249 6914791 - CmoCh16G010060.1 Cmo16g01006 1006
10 5304306 5304833 + CmPI595203_10g012400.1 Cmu10g1240 1240
10 5331912 5332673 + CmPI595203_10g012440.1 Cmu10g1244 1244
6 83567 86542 + Conep06aG0000800.1 Cone6ag0008 8
6 86745 87944 - Conep06aG0000900.1 Cone6ag0009 9
14 9911613 9914854 + Conep14aG0125000.1 Cone14ag1218 1218
14 9915491 9916334 + Conep14aG0125100.1 Cone14ag1219 1219
14 9917855 9919339 + Conep14aG0125200.1 Cone14ag1220 1220
14 9920796 9924961 + Conep14aG0125300.1 Cone14ag1221 1221
14 9927622 9928116 + Conep14aG0125400.1 Cone14ag1222 1222
15 9795465 9798788 + Conep15aG0126800.1 Cone15ag1239 1239
15 9799370 9800415 + Conep15aG0126900.1 Cone15ag1240 1240
15 9801560 9803059 + Conep15aG0127000.1 Cone15ag1241 1241
15 9806022 9810112 + Conep15aG0127100.1 Cone15ag1242 1242
15 10138307 10142141 - Conep15aG0132400.1 Cone15ag1295 1295
2 5272936 5274183 + Cp4.1LG02g00470.1 Cpe02g00823 823
6 5249329 5250576 + Cp4.1LG06g08390.1 Cpe06g00821 821
6 5253622 5269630 - Cp4.1LG06g08300.1 Cpe06g00822 822
14 6208777 6209253 + Cp4.1LG14g07850.1 Cpe14g00788 788
14 6211978 6212637 - Cp4.1LG14g07940.1 Cpe14g00789 789
10 6228589 6229116 + CrPI670011_10g006570.1 Cre10g0657 657
10 6259357 6260118 + CrPI670011_10g006610.1 Cre10g0661 661
3 3604442 3607034 + CsaV3_3G004250.1 Csa03g00425 425
3 3617539 3618171 + CsaV3_3G004260.1 Csa03g00426 426
2 24057474 24065767 + Lsi02G018230.1 Lsi02g01823 1823
2 24079021 24080271 - Lsi02G018250.1 Lsi02g01825 1825
5 6245182 6245718 + Lsi05G004940.1 Lsi05g00494 494
5 6261900 6265688 + Lsi05G004960.1 Lsi05g00496 496
5 6269061 6269693 + Lsi05G004970.1 Lsi05g00497 497
5 6272711 6273472 + Lsi05G004980.1 Lsi05g00498 498
11 9020783 9021973 + MC11g1057 Mch11g1277 1277
11 9034956 9062975 - MC11g1059 Mch11g1279 1279
4 45610126 45623812 + Sed0001626.1 Sed04g3651 3651
7 42571293 42573374 + Sed0015897.1 Sed07g2749 2749
1 85758064 85759683 + Tan0021457.1 Tan01g3193 3193
1 85804435 85862720 - Tan0019627.2 Tan01g3196 3196
19 8525024 8558949 - Vvi19g664 Vvi19g664 664
19 8566311 8585299 + Vvi19g665 Vvi19g665 665
19 8585324 8587301 - Vvi19g666 Vvi19g666 666
19 8590710 8591677 + Vvi19g667 Vvi19g667 667
19 8597169 8601079 + Vvi19g668 Vvi19g668 668
19 8601630 8609299 - Vvi19g669 Vvi19g669 669
19 8623966 8624827 + Vvi19g670 Vvi19g670 670
19 8637607 8659887 + Vvi19g671 Vvi19g671 671
19 8666962 8668364 + Vvi19g672 Vvi19g672 672
19 8672302 8673839 + Vvi19g673 Vvi19g673 673
       

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