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
Vvi17g1006 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1 . . . . . . Bma04g00311 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1483 . Lsi04g02441 . . . . . Bda11g00988 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g3 Blo01g01664 . . Bda03g00342 Bpe02g00277 Bpe04g00302 Bma04g00311 Bma01g02435 . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1483 . Lsi04g02441 Csa04g02758 . . . . . Bda01g01580 Bpe02g01770 . . . . . . . . . . . . . . . . . . . Cla11g01868 Cam11g1938 Cec11g1964 . Clacu11g2104 Cmu11g1905 Cre11g2313 . . Chy07g00444 .
Vvi18g4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g5 . . . . . . . . . . Cma01g02055 . Car01g01619 . . . . . . . . . . . . . . . . . . . . . Cone20ag0001 Lsi04g02440 Csa04g02756 . . . . . . . . . . Sed05g3034 Cmo01g02111 . . . . . . . Bhi09g02776 Tan01g5196 Cmetu07g1779 . . Mch11g0004 . Cla11g01867 Cam11g1937 Cec11g1963 Cco11g1977 Clacu11g2102 Cmu11g1904 Cre11g2311 . . Chy07g00443 Cme07g00006
Vvi18g6 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g7 Blo01g01663 . . . Bpe02g00278 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag2039 Cone7ag1952 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g8 . Blo12g00834 . Bda03g00341 Bpe02g00279 Bpe04g00301 Bma04g00310 Bma01g02434 . . . Cma09g00001 . . . . . . . . . . . . . . . . . . . Cone4ag2039 Cone7ag1952 . . . Csa04g02755 . . . . . . . . . . . . Cmo09g00001 . . . Car09g00001 . Cpe02g00001 . . . . . . . Cla11g01866 Cam11g1936 Cec11g1962 Cco11g1976 Clacu11g2101 Cmu11g1903 . . . Chy07g00442 Cme07g00007
Vvi18g9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 51628296 51631668 + Bda003847.1 Bda01g01580 1580
3 2887440 2889991 - Bda016302.1 Bda03g00341 341
3 2893279 2898192 - Bda016303.1 Bda03g00342 342
11 9656516 9662180 + Bda007442.1 Bda11g00988 988
9 73916865 73920002 - XM_039044069.1 Bhi09g02776 2776
1 56383506 56387634 + BLOR01663 Blo01g01663 1663
1 56388186 56393225 - BLOR01664 Blo01g01664 1664
12 26640297 26652460 + BLOR04853 Blo12g00834 834
1 81980603 81983102 - Bma003305.1 Bma01g02434 2434
1 81994324 82003787 - Bma003306.1 Bma01g02435 2435
4 2455936 2457294 - Bma018764.1 Bma04g00310 310
4 2460464 2466947 - Bma018765.1 Bma04g00311 311
2 1856804 1866075 + Bpe008121.1 Bpe02g00277 277
2 1866590 1870749 - Bpe008122.1 Bpe02g00278 278
2 1872126 1874649 + Bpe008123.1 Bpe02g00279 279
2 20017770 20021104 + Bpe009602.1 Bpe02g01770 1770
4 1929764 1931412 - Bpe025601 Bpe04g00301 301
4 1934256 1947232 - Bpe015003.1 Bpe04g00302 302
11 31737318 31745440 - CaPI482276_11g019360.1 Cam11g1936 1936
11 31745467 31750326 - CaPI482276_11g019370.1 Cam11g1937 1937
11 31756108 31770063 - CaPI482276_11g019380.1 Cam11g1938 1938
1 13273254 13276026 + Carg21336-RA Car01g01619 1619
9 473 4780 - Carg08584-RA Car09g00001 1
11 32213105 32221485 - CcPI632755_11g019760.1 Cco11g1976 1976
11 32221512 32226523 - CcPI632755_11g019770.1 Cco11g1977 1977
11 33666855 33675108 - CePI673135_11g019620.1 Cec11g1962 1962
11 33675135 33679873 - CePI673135_11g019630.1 Cec11g1963 1963
11 33687056 33702832 - CePI673135_11g019640.1 Cec11g1964 1964
7 3390292 3393972 - Chy7G132720.1 Chy07g00442 442
7 3397091 3399577 - Chy7G132730.1 Chy07g00443 443
7 3402014 3419767 - Chy7G132740.1 Chy07g00444 444
11 31776092 31784225 - ClG42_11g0210100.10 Clacu11g2101 2101
11 31784252 31789088 - ClG42_11g0210200.10 Clacu11g2102 2102
11 31794872 31819451 - ClG42_11g0210400.10 Clacu11g2104 2104
11 32188724 32194047 - ClCG11G019210.2 Cla11g01866 1866
11 32198683 32203910 - ClCG11G019220.2 Cla11g01867 1867
11 32209662 32234774 - ClCG11G019240.2 Cla11g01868 1868
1 13051705 13054332 + CmaCh01G020550.1 Cma01g02055 2055
9 1232 6043 - CmaCh09G000010.1 Cma09g00001 1
7 81221 84194 + MELO3C017076.2.1 Cme07g00006 6
7 87113 91614 + MELO3C017075.2.1 Cme07g00007 7
7 24723801 24727004 - PI0022513.1 Cmetu07g1779 1779
1 14599240 14602096 + CmoCh01G021110.1 Cmo01g02111 2111
9 751 5556 - CmoCh09G000010.1 Cmo09g00001 1
11 31025546 31033678 - CmPI595203_11g019030.1 Cmu11g1903 1903
11 31033705 31038541 - CmPI595203_11g019040.1 Cmu11g1904 1904
11 31053094 31068900 - CmPI595203_11g019050.1 Cmu11g1905 1905
4 14146157 14149625 + Conep04aG0210400.1 Cone4ag2039 2039
7 12447842 12451561 - Conep07aG0201000.1 Cone7ag1952 1952
17 10006195 10011672 + Conep17aG0152400.1 Cone17ag1483 1483
20 11335 14975 - Conep20aG0000100.1 Cone20ag0001 1
2 6731 9230 - Cp4.1LG02g08520.1 Cpe02g00001 1
11 34709770 34722688 - CrPI670011_11g023110.1 Cre11g2311 2311
11 34742313 34758194 - CrPI670011_11g023130.1 Cre11g2313 2313
4 26394150 26399335 - CsaV3_4G037810.1 Csa04g02755 2755
4 26401469 26404727 - CsaV3_4G037820.1 Csa04g02756 2756
4 26406598 26434108 - CsaV3_4G037840.1 Csa04g02758 2758
4 31477451 31480938 - Lsi04G024400.1 Lsi04g02440 2440
4 31484866 31490573 - Lsi04G024410.1 Lsi04g02441 2441
11 31412 36263 + MC11g0002 Mch11g0004 4
5 40746054 40748720 - Sed0014707.3 Sed05g3034 3034
1 117039879 117043336 - Tan0017324.1 Tan01g5196 5196
17 17077435 17089089 + Vvi17g1006 Vvi17g1006 1006
18 4257 27771 - Vvi18g1 Vvi18g1 1
18 67890 70298 + Vvi18g2 Vvi18g2 2
18 70304 92437 + Vvi18g3 Vvi18g3 3
18 93653 95299 + Vvi18g4 Vvi18g4 4
18 99417 105675 + Vvi18g5 Vvi18g5 5
18 130985 159404 + Vvi18g6 Vvi18g6 6
18 159413 165445 - Vvi18g7 Vvi18g7 7
18 170186 176322 + Vvi18g8 Vvi18g8 8
18 176321 177599 + Vvi18g9 Vvi18g9 9
       

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