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
Vvi1g551 . . . . . . Bma14g01891 . . . . . . . . . . Bhi07g00104 . . . . . . . . . . . . . Cone13ag0720 . . . . . . . . Blo11g00958 Bda07g01731 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00990 . .
Vvi1g552 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g553 . . . . . . Bma14g01890 . . . . Cma04g00026 . Car04g00035 . . . Bhi07g00107 . . . . . . . . . . . . . . . . . . . . . . Blo11g00959 Bda07g01710 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00988 . .
Vvi1g554 . . . . . . . . . . . . . . . . Cpe01g01864 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo04g02245 Cmo15g00916 Cma04g02151 Cma15g00880 Car04g02085 Car15g00827 Cpe13g00435 . Bhi12g00980 . . . Hepe02g2589 . . Cla01g00663 Cam01g0694 Cec01g0686 Cco01g0714 Clacu01g0682 Cmu01g0657 Cre09g1849 Lsi09g00717 Csa05g01290 . Cme09g01290
Vvi1g555 . . . . . . . . . . . . . . Sed04g3065 . . Bhi07g00146 Tan04g1690 Cmetu08g1955 Lac13g1666 . . . . . . . . . . . Cone19ag0716 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g556 Blo01g00789 . Bda01g01773 . . . . . . . . . . . . . Cpe01g01865 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe02g01952 Bma01g00505 . . Cmo04g02246 Cmo15g00913 Cma04g02152 Cma15g00878 . Car15g00826 Cpe13g00436 . Bhi12g00981 . . . Hepe02g2586 . Lcy10g1583 Cla01g00664 Cam01g0695 Cec01g0687 Cco01g0715 Clacu01g0683 Cmu01g0658 Cre09g1848 Lsi09g00719 Csa05g01292 . Cme09g01288
Vvi1g557 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0332 Cone9ag0368 . . . . . . . . . . . Bma06g01143 . Cmo04g02248 Cmo15g00912 Cma04g02153 Cma15g00877 Car04g02087 Car15g00825 Cpe13g00437 . Bhi12g00982 . . . . . Lcy10g1582 Cla01g00665 . . . . . . Lsi09g00720 Csa05g01293 . Cme09g01287
Vvi1g558 . . . . . . Bma14g01967 . . . . Cma04g00024 . Car04g00033 . . . Bhi07g00153 . . . Hepe01g0358 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g559 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g560 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 53969933 53971646 - Bda004062.1 Bda01g01773 1773
7 32005008 32014744 + Bda033991 Bda07g01710 1710
7 32436716 32437762 + Bda028637.1 Bda07g01731 1731
7 6477137 6491304 + XM_039036474.1 Bhi07g00104 104
7 6624521 6626351 + XM_039037072.1 Bhi07g00107 107
7 7830170 7837365 + XM_039035640.1 Bhi07g00146 146
7 8162452 8165743 + XM_039037287.1 Bhi07g00153 153
12 29769150 29771605 - XM_039019814.1 Bhi12g00980 980
12 29828061 29830637 + XM_039019415.1 Bhi12g00981 981
12 29901157 29905551 - XM_039019349.1 Bhi12g00982 982
1 11529792 11531481 + BLOR00789 Blo01g00789 789
11 21221941 21224841 + BLOR03834 Blo11g00958 958
11 21287153 21288353 + BLOR03835 Blo11g00959 959
1 4159786 4161270 + Bma000684.2 Bma01g00505 505
6 48354489 48357896 + Bma024242.1 Bma06g01143 1143
14 40410243 40411309 - Bma012676.1 Bma14g01890 1890
14 40423517 40433755 - Bma012677.1 Bma14g01891 1891
14 42560430 42562311 + Bma012775.1 Bma14g01967 1967
2 21439405 21441100 - Bpe009777.2 Bpe02g01952 1952
1 7762291 7771516 - CaPI482276_01g006940.1 Cam01g0694 694
1 7792728 7794507 + CaPI482276_01g006950.1 Cam01g0695 695
4 154899 156065 - Carg21981-RA Car04g00033 33
4 159789 165086 - Carg21983-RA Car04g00035 35
4 16986664 16991077 - Carg25259-RA Car04g02085 2085
4 17006651 17010037 - Carg25261-RA Car04g02087 2087
15 4698262 4701669 + Carg01330-RA Car15g00825 825
15 4705386 4706742 - Carg01329-RA Car15g00826 826
15 4712996 4720233 + Carg01328-RA Car15g00827 827
1 7554551 7562299 - CcPI632755_01g007140.1 Cco01g0714 714
1 7584910 7586666 + CcPI632755_01g007150.1 Cco01g0715 715
1 7617962 7626113 - CePI673135_01g006860.1 Cec01g0686 686
1 7648167 7649957 + CePI673135_01g006870.1 Cec01g0687 687
1 7438124 7448343 - ClG42_01g0068200.10 Clacu01g0682 682
1 7468551 7470336 + ClG42_01g0068300.10 Clacu01g0683 683
1 7830640 7838541 - ClCG01G006800.1 Cla01g00663 663
1 7864149 7865934 + ClCG01G006810.1 Cla01g00664 664
1 7877610 7883271 - ClCG01G006820.2 Cla01g00665 665
4 121228 122720 - CmaCh04G000240.1 Cma04g00024 24
4 126329 127877 - CmaCh04G000260.1 Cma04g00026 26
4 15042263 15052622 - CmaCh04G021510.1 Cma04g02151 2151
4 15062482 15064603 + CmaCh04G021520.1 Cma04g02152 2152
4 15068257 15071637 - CmaCh04G021530.1 Cma04g02153 2153
15 4444583 4447990 + CmaCh15G008770.1 Cma15g00877 877
15 4451639 4453460 - CmaCh15G008780.1 Cma15g00878 878
15 4464667 4468518 + CmaCh15G008800.1 Cma15g00880 880
9 17788528 17791998 + MELO3C005236.2.1 Cme09g01287 1287
9 17800861 17803457 - MELO3C005237.2.1 Cme09g01288 1288
9 17834599 17836630 + MELO3C005239.2.1 Cme09g01290 1290
8 2130127 2133991 + PI0028164.2 Cmetu08g1955 1955
4 16789695 16793331 - CmoCh04G022450.1 Cmo04g02245 2245
4 16801358 16802185 + CmoCh04G022460.1 Cmo04g02246 2246
4 16807180 16810566 - CmoCh04G022480.1 Cmo04g02248 2248
15 4628864 4632271 + CmoCh15G009120.1 Cmo15g00912 912
15 4635933 4637660 - CmoCh15G009130.1 Cmo15g00913 913
15 4648073 4653689 + CmoCh15G009160.1 Cmo15g00916 916
1 7413277 7421709 - CmPI595203_01g006570.1 Cmu01g0657 657
1 7441831 7443616 + CmPI595203_01g006580.1 Cmu01g0658 658
6 1569748 1573178 + Conep06aG0033800.1 Cone6ag0332 332
9 1634768 1638286 + Conep09aG0037600.1 Cone9ag0368 368
13 6974738 6978408 - Conep13aG0074400.1 Cone13ag0720 720
19 5921912 5924200 - Conep19aG0073700.1 Cone19ag0716 716
1 15958613 15967147 - Cp4.1LG01g18660.1 Cpe01g01864 1864
1 15978666 15980953 + Cp4.1LG01g18590.1 Cpe01g01865 1865
13 4680757 4685643 - Cp4.1LG13g06450.1 Cpe13g00435 435
13 4697519 4699328 + Cp4.1LG13g06460.1 Cpe13g00436 436
13 4702710 4706117 - Cp4.1LG13g06430.1 Cpe13g00437 437
9 36885334 36887130 - CrPI670011_09g018480.1 Cre09g1848 1848
9 36915193 36924503 + CrPI670011_09g018490.1 Cre09g1849 1849
5 9193962 9195944 - CsaV3_5G012940.1 Csa05g00988 988
5 9220449 9241621 - CsaV3_5G012960.1 Csa05g00990 990
5 13700427 13703021 - CsaV3_5G017130.1 Csa05g01290 1290
5 13726487 13728350 + CsaV3_5G017150.1 Csa05g01292 1292
5 13737132 13741182 - CsaV3_5G017160.1 Csa05g01293 1293
1 53254698 53262411 + Hsped.01g03580.1 Hepe01g0358 358
2 72942126 72944374 - Hsped.02g25860.1 Hepe02g2586 2586
2 72986404 72987243 + Hsped.02g25890.1 Hepe02g2589 2589
13 18299354 18307188 + Lag0041462.1 Lac13g1666 1666
10 40180458 40183865 + Maker00039167 Lcy10g1582 1582
10 40193461 40195955 - Maker00039909 Lcy10g1583 1583
9 8228722 8234770 - Lsi09G007170.1 Lsi09g00717 717
9 8267896 8269723 + Lsi09G007190.1 Lsi09g00719 719
9 8278768 8282175 - Lsi09G007200.1 Lsi09g00720 720
4 41679001 41684387 + Sed0019363.1 Sed04g3065 3065
4 36687788 36692879 - Tan0011511.1 Tan04g1690 1690
1 6138233 6155954 + Vvi1g551 Vvi1g551 551
1 6158390 6160886 - Vvi1g552 Vvi1g552 552
1 6168518 6169676 + Vvi1g553 Vvi1g553 553
1 6173132 6176111 - Vvi1g554 Vvi1g554 554
1 6187967 6190575 + Vvi1g555 Vvi1g555 555
1 6214540 6217236 + Vvi1g556 Vvi1g556 556
1 6226979 6230660 - Vvi1g557 Vvi1g557 557
1 6241007 6248273 - Vvi1g558 Vvi1g558 558
1 6248925 6263935 - Vvi1g559 Vvi1g559 559
1 6264419 6272529 - Vvi1g560 Vvi1g560 560
       

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