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
Vvi16g604 Blo06g01114 . . . . Bpe07g00950 . . . . . . . . . . . . . . . . . . Cla01g00547 Cam01g0572 Cec01g0562 Cco01g0588 Clacu01g0566 Cmu01g0538 Cre09g1969 . . . . . Csa05g00583 Chy09g00923 . . . Bda06g00670 Bda15g00737 . Bpe12g00417 Bma08g00341 . . . . . . . . . . . . . . . . . . . . . . . . Lsi09g00591 . . Cme09g01452
Vvi16g605 . . . . Bpe03g00134 . . Bma14g02062 Cmo16g00151 Cmo18g01251 . . . . Sed07g1061 . Cpe14g00122 Bhi01g01356 Tan01g0284 Cmetu04g3099 . Hepe07g0182 Mch10g0178 . . . . . . . . . Cone5ag0839 . . Lsi05g01256 . . Cme06g00972 . Blo09g00082 . . . . . . . . . Cma16g00144 Cma18g01228 Car16g00125 Car18g01132 Cpe09g00105 . . . . . . . . Cla05g00856 Cam05g0942 Cec05g0947 Cco05g0947 Clacu05g0929 Cmu05g0887 Cre05g0972 . Csa03g01686 Chy06g00919 .
Vvi16g606 . Blo15g00156 . . Bpe03g00135 Bpe07g00949 Bma10g01211 . . . . . . . . . . . . . . . . . Cla01g00545 . . . . . . . Cone5ag0838 . . . Csa05g00580 Chy09g00925 . Blo07g00422 Blo09g00081 Bda06g00671 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi09g00589 . . Cme09g01454
Vvi16g607 . . . . . . . Bma14g02088 Cmo16g00150 Cmo18g01254 . . . . Sed02g1606 . Cpe14g00121 Bhi01g01355 Tan01g0280 Cmetu06g0945 . Hepe07g0181 Mch10g0177 . . . . . . . . . . . . Lsi05g01255 . . Cme06g00973 . . . . . . . . . . . Cma16g00143 Cma18g01231 Car16g00124 Car18g01135 . . . . . . . . . Cla05g00857 Cam05g0943 Cec05g0948 Cco05g0948 Clacu05g0930 Cmu05g0888 Cre05g0973 . Csa03g01687 Chy06g00920 .
Vvi16g608 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g609 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g610 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g611 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g612 . Blo15g00158 Bda05g00058 . Bpe03g00297 . . . Cmo16g00149 . . . . . Sed01g3916 . Cpe14g00120 Bhi01g01353 Tan01g0278 Cmetu09g1857 Lac11g2130 Hepe07g0179 Mch10g0175 . Cla01g00296 Cam01g0307 Cec01g0297 Cco01g0314 Clacu01g0307 Cmu01g0292 Cre09g2216 . . . . Lsi05g01253 Csa05g00319 Chy09g01189 Cme06g00975 . . Bda06g00672 . . . . . . . . Cma16g00142 . . . . . Bhi12g00208 . . Lac11g2130 Hepe06g1578 . Lcy12g1690 Cla05g00859 Cam05g0945 Cec05g0950 Cco05g0950 Clacu05g0932 Cmu05g0890 Cre05g0975 . Csa03g01689 Chy06g00922 .
Vvi16g613 . . . . Bpe03g00136 . . Bma14g02061 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo09g00080 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 3419544 3420581 + Bda020646.1 Bda05g00058 58
6 9308583 9309947 - Bda023957.1 Bda06g00670 670
6 9322506 9323980 + Bda023958.1 Bda06g00671 671
6 9368649 9371387 + Bda023963.1 Bda06g00672 672
15 10864690 10866808 + Bda012593.1 Bda15g00737 737
1 27167088 27170895 - XM_039036649.1 Bhi01g01353 1353
1 27172870 27179606 - XM_039036641.1 Bhi01g01355 1355
1 27218759 27221672 + XM_039022285.1 Bhi01g01356 1356
12 6717987 6721524 + XM_039018762.1 Bhi12g00208 208
6 34551495 34559900 - BLOR17697 Blo06g01114 1114
7 7997571 7999614 - BLOR18354 Blo07g00422 422
9 1433723 1434070 + BLOR20995 Blo09g00080 80
9 1438958 1444092 - BLOR20996 Blo09g00081 81
9 1453631 1455433 + BLOR20997 Blo09g00082 82
15 1591360 1592948 - BLOR06550 Blo15g00156 156
15 1622332 1625479 + BLOR06552 Blo15g00158 158
8 6178067 6180234 + Bma027385.1 Bma08g00341 341
10 42848468 42850014 + Bma005281.1 Bma10g01211 1211
14 43937532 43937894 + Bma012870.1 Bma14g02061 2061
14 43957170 43958242 + Bma012871.1 Bma14g02062 2062
14 44259084 44259464 - Bma012899.1 Bma14g02088 2088
3 1883850 1884853 - Bpe011979.1 Bpe03g00134 134
3 1886480 1889258 + Bpe011980.1 Bpe03g00135 135
3 1890324 1890671 - Bpe011981.1 Bpe03g00136 136
3 4078013 4080796 - Bpe012149.1 Bpe03g00297 297
7 15321266 15322846 - Bpe021793.1 Bpe07g00949 949
7 15326283 15328093 + Bpe021794.1 Bpe07g00950 950
12 9747206 9749287 - Bpe005673.1 Bpe12g00417 417
1 3400418 3403555 - CaPI482276_01g003070.1 Cam01g0307 307
1 6072655 6075126 + CaPI482276_01g005720.1 Cam01g0572 572
5 8530158 8532858 - CaPI482276_05g009420.1 Cam05g0942 942
5 8537655 8542961 + CaPI482276_05g009430.1 Cam05g0943 943
5 8546707 8549942 + CaPI482276_05g009450.1 Cam05g0945 945
16 724428 727190 - Carg16695-RA Car16g00124 124
16 728369 731067 + Carg16696-RA Car16g00125 125
18 11282508 11285258 - Carg22080-RA Car18g01132 1132
18 11299190 11302974 + Carg22083-RA Car18g01135 1135
1 3037665 3040781 - CcPI632755_01g003140.1 Cco01g0314 314
1 5794430 5796985 + CcPI632755_01g005880.1 Cco01g0588 588
5 8297274 8299975 - CcPI632755_05g009470.1 Cco05g0947 947
5 8304689 8310015 + CcPI632755_05g009480.1 Cco05g0948 948
5 8313810 8316983 + CcPI632755_05g009500.1 Cco05g0950 950
1 3005520 3008669 - CePI673135_01g002970.1 Cec01g0297 297
1 5835485 5838040 + CePI673135_01g005620.1 Cec01g0562 562
5 8278577 8281259 - CePI673135_05g009470.1 Cec05g0947 947
5 8286077 8291448 + CePI673135_05g009480.1 Cec05g0948 948
5 8294342 8297565 + CePI673135_05g009500.1 Cec05g0950 950
6 6763719 6768925 - Chy6G114470.1 Chy06g00919 919
6 6769047 6773709 + Chy6G114480.1 Chy06g00920 920
6 6776475 6779786 + Chy6G114500.1 Chy06g00922 922
9 12005737 12006286 - Chy9G166390.1 Chy09g00923 923
9 12052701 12054908 - Chy9G166410.1 Chy09g00925 925
9 14103579 14106620 + Chy9G169050.1 Chy09g01189 1189
1 3016313 3019467 - ClG42_01g0030700.10 Clacu01g0307 307
1 5706068 5708460 + ClG42_01g0056600.10 Clacu01g0566 566
5 8233589 8236259 - ClG42_05g0092900.10 Clacu05g0929 929
5 8249942 8255320 + ClG42_05g0093000.10 Clacu05g0930 930
5 8259146 8262386 + ClG42_05g0093200.10 Clacu05g0932 932
1 3090662 3094638 - ClCG01G003070.1 Cla01g00296 296
1 5940377 5943563 + ClCG01G005560.1 Cla01g00545 545
1 5994790 5997388 + ClCG01G005600.1 Cla01g00547 547
5 8479093 8482071 - ClCG05G007860.1 Cla05g00856 856
5 8496715 8503869 + ClCG05G007870.1 Cla05g00857 857
5 8507408 8511481 + ClCG05G007880.2 Cla05g00859 859
16 624748 629151 - CmaCh16G001420.1 Cma16g00142 142
16 629275 632233 - CmaCh16G001430.1 Cma16g00143 143
16 632794 635467 + CmaCh16G001440.1 Cma16g00144 144
18 9666120 9668983 - CmaCh18G012280.1 Cma18g01228 1228
18 9683488 9687410 + CmaCh18G012310.1 Cma18g01231 1231
6 6909135 6911741 - MELO3C006881.2.1 Cme06g00972 972
6 6917975 6923169 + MELO3C006882.2.1 Cme06g00973 973
6 6925325 6928919 + MELO3C006884.2.1 Cme06g00975 975
9 19729634 19731007 - MELO3C005373.2.1 Cme09g01452 1452
9 19782493 19785044 - MELO3C005375.2.1 Cme09g01454 1454
4 30030223 30033815 + PI0010232.1 Cmetu04g3099 3099
6 6967330 6972085 + PI0024002.1 Cmetu06g0945 945
9 2282829 2286383 - PI0010833.1 Cmetu09g1857 1857
16 675398 678954 - CmoCh16G001490.1 Cmo16g00149 149
16 680084 682847 - CmoCh16G001500.1 Cmo16g00150 150
16 683803 686723 + CmoCh16G001510.1 Cmo16g00151 151
18 12279148 12281839 - CmoCh18G012510.1 Cmo18g01251 1251
18 12299837 12303679 + CmoCh18G012540.1 Cmo18g01254 1254
1 2972367 2975516 - CmPI595203_01g002920.1 Cmu01g0292 292
1 5662868 5665260 + CmPI595203_01g005380.1 Cmu01g0538 538
5 8082425 8085099 - CmPI595203_05g008870.1 Cmu05g0887 887
5 8098873 8104249 + CmPI595203_05g008880.1 Cmu05g0888 888
5 8108070 8111310 + CmPI595203_05g008900.1 Cmu05g0890 890
5 3592009 3593470 - Conep05aG0086400.1 Cone5ag0838 838
5 3595140 3596116 + Conep05aG0086500.1 Cone5ag0839 839
9 604431 607315 + Cp4.1LG09g01070.1 Cpe09g00105 105
14 648979 652756 - Cp4.1LG14g05970.1 Cpe14g00120 120
14 653832 655568 - Cp4.1LG14g05960.1 Cpe14g00121 121
14 657848 660873 + Cp4.1LG14g06060.1 Cpe14g00122 122
5 8969338 8972026 - CrPI670011_05g009720.1 Cre05g0972 972
5 8976779 8982170 + CrPI670011_05g009730.1 Cre05g0973 973
5 8986077 8989317 + CrPI670011_05g009750.1 Cre05g0975 975
9 38664491 38667041 - CrPI670011_09g019690.1 Cre09g1969 1969
9 41337421 41340541 + CrPI670011_09g022160.1 Cre09g2216 2216
3 12644135 12648967 - CsaV3_3G016860.1 Csa03g01686 1686
3 12651314 12655349 + CsaV3_3G016870.1 Csa03g01687 1687
3 12657495 12661787 + CsaV3_3G016890.1 Csa03g01689 1689
5 1981018 1986144 - CsaV3_5G003190.1 Csa05g00319 319
5 3804954 3812938 + CsaV3_5G005800.1 Csa05g00580 580
5 3849339 3852975 + CsaV3_5G005830.1 Csa05g00583 583
6 66523925 66527244 - Hsped.06g15780.1 Hepe06g1578 1578
7 1595942 1599166 - Hsped.07g01790.1 Hepe07g0179 179
7 1603105 1608619 - Hsped.07g01810.1 Hepe07g0181 181
7 1617062 1619956 + Hsped.07g01820.1 Hepe07g0182 182
11 37332617 37335797 - Lag0032768.1 Lac11g2130 2130
12 37375438 37379515 - Maker00003051 Lcy12g1690 1690
5 20312916 20316671 - Lsi05G012530.1 Lsi05g01253 1253
5 20318940 20323221 - Lsi05G012550.1 Lsi05g01255 1255
5 20328665 20331455 + Lsi05G012560.1 Lsi05g01256 1256
9 6325428 6328126 + Lsi09G005890.1 Lsi09g00589 589
9 6373555 6375592 + Lsi09G005910.1 Lsi09g00591 591
10 1049417 1053575 - MC10g0144 Mch10g0175 175
10 1055547 1059208 - MC10g0146 Mch10g0177 177
10 1062560 1065724 + MC10g0147 Mch10g0178 178
1 68346925 68350701 - Sed0005254.1 Sed01g3916 3916
2 51548353 51549039 - Sed0006114.1 Sed02g1606 1606
7 7629822 7633167 + Sed0012084.1 Sed07g1061 1061
1 2341564 2345625 - Tan0003320.2 Tan01g0278 278
1 2350341 2355308 - Tan0001711.1 Tan01g0280 280
1 2405691 2408939 + Tan0001051.1 Tan01g0284 284
16 16005952 16008324 - Vvi16g604 Vvi16g604 604
16 16017971 16022823 - Vvi16g605 Vvi16g605 605
16 16027555 16046231 + Vvi16g606 Vvi16g606 606
16 16062536 16066034 + Vvi16g607 Vvi16g607 607
16 16080848 16081797 + Vvi16g608 Vvi16g608 608
16 16082632 16085131 + Vvi16g609 Vvi16g609 609
16 16088471 16095546 + Vvi16g610 Vvi16g610 610
16 16096084 16099561 + Vvi16g611 Vvi16g611 611
16 16113211 16117083 + Vvi16g612 Vvi16g612 612
16 16121437 16122777 - Vvi16g613 Vvi16g613 613
       

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