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
Vvi4g912 . . Bda04g00320 Bda10g00321 . . Bma09g00354 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1347 . Lsi01g01053 . . . . . . . . Bpe06g00247 Bma03g01058 . Sed01g0082 . . . . . . . . Bhi10g02232 Tan07g1029 Cmetu11g0018 . Hepe10g0829 . . . . . . . . . . . Chy02g00973 .
Vvi4g913 Blo04g00953 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma03g01018 . Sed01g0084 . . . . . . . . Bhi10g02231 Tan07g1031 Cmetu11g0453 . Hepe10g0832 . . . . . . . . . . . . .
Vvi4g914 . . . . . . . . Cmo04g00791 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g915 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g916 . . . . . . Bma09g00356 . . . . Cma07g00754 . Car07g00741 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe06g00249 . . . . Cmo07g00777 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g917 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed01g0317 . . . Cma20g00871 . . . . Bhi10g02052 Tan05g1354 Cmetu11g2314 . Hepe08g1041 . . . . . . . . . . . . .
Vvi4g918 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g919 . . . . . . . Bma15g01011 Cmo04g00845 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy07g01301 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g920 . . . . . . Bma09g00060 . . . Cma03g00775 Cma07g00508 Car03g00704 Car07g00444 Sed14g1094 . . Bhi03g01260 Tan03g1950 Cmetu08g1008 . Hepe04g1483 . . . . . . . . . Cone8ag0795 . . . Lsi01g00704 . . . . Blo06g00124 . . . Bpe06g00056 . . . Cmo03g00806 Cmo07g00506 . . . . . . . . . . . . . . . . . . . . . . Chy02g00673 .
Vvi4g921 . . Bda04g00323 Bda10g00314 . . Bma09g00361 . . . . . . . . Cpe19g00768 Cpe10g00565 . . . . . . . Cla01g01843 Cam01g1930 Cec04g1582 Cco04g1646 Clacu01g1952 Cmu01g1826 Cre04g1504 . . Cone6ag1344 Cone9ag1489 . . . Cme08g00775 . . . . Bpe10g00087 Bpe06g00254 . . . . . . . . . . . . . . . . . . . . . . . . . . Csa06g03164 . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 47141986 47143228 - Bda019199.1 Bda04g00320 320
4 47248458 47249928 - Bda019202.1 Bda04g00323 323
10 32668551 32670098 - Bda007088.1 Bda10g00314 314
10 33137469 33138574 + Bda007104.1 Bda10g00321 321
3 25803108 25805775 + XM_039026216.1 Bhi03g01260 1260
10 51322198 51327286 - XM_039046988.1 Bhi10g02052 2052
10 57844365 57847868 + XM_039046057.1 Bhi10g02231 2231
10 57960178 57963229 + XM_039044942.1 Bhi10g02232 2232
4 11596760 11602332 + BLOR13865 Blo04g00953 953
6 4857397 4858669 + BLOR16707 Blo06g00124 124
3 11295011 11297954 + Bma017367.1 Bma03g01018 1018
3 12801962 12803721 + Bma017427.2 Bma03g01058 1058
9 1447336 1448472 + Bma028739.1 Bma09g00060 60
9 30484278 30485527 - Bma029268.2 Bma09g00354 354
9 30503049 30504179 - Bma029270.1 Bma09g00356 356
9 30650651 30652165 - Bma029277.1 Bma09g00361 361
15 39706813 39708477 + Bma014298.1 Bma15g01011 1011
6 673237 674337 - Bpe019503.1 Bpe06g00056 56
6 12946797 12948033 - Bpe019737.1 Bpe06g00247 247
6 12956622 12957758 - Bpe019739.1 Bpe06g00249 249
6 13085631 13087127 - Bpe019744.1 Bpe06g00254 254
10 1307349 1309063 + Bpe002388.1 Bpe10g00087 87
1 32714602 32718920 - CaPI482276_01g019300.1 Cam01g1930 1930
3 6143695 6145391 - Carg00664-RA Car03g00704 704
7 2261078 2263146 - Carg16031-RA Car07g00444 444
7 3820575 3821693 + Carg05263-RA Car07g00741 741
4 31728678 31733296 - CcPI632755_04g016460.1 Cco04g1646 1646
4 35236912 35241565 - CePI673135_04g015820.1 Cec04g1582 1582
2 4095543 4097052 - Chy2G029400.1 Chy02g00673 673
2 6481323 6482492 - Chy2G032400.1 Chy02g00973 973
7 17672714 17675184 - Chy7G141310.1 Chy07g01301 1301
1 31559070 31561275 - ClG42_01g0195200.10 Clacu01g1952 1952
1 33296436 33300591 - ClCG01G018840.2 Cla01g01843 1843
3 6022602 6029709 - CmaCh03G007750.1 Cma03g00775 775
7 2196728 2199203 - CmaCh07G005080.1 Cma07g00508 508
7 3347502 3348371 + CmaCh07G007540.1 Cma07g00754 754
20 4172857 4177499 - CmaCh20G008710.1 Cma20g00871 871
8 5170429 5173247 - MELO3C007763.2.1 Cme08g00775 775
8 21494058 21496960 + PI0001816.3 Cmetu08g1008 1008
11 29687980 29690443 + PI0005606.1 Cmetu11g0018 18
11 29671094 29674437 + PI0020555.1 Cmetu11g0453 453
11 27040863 27046639 + PI0025330.1 Cmetu11g2314 2314
3 6530547 6533260 - CmoCh03G008060.1 Cmo03g00806 806
4 3953402 3955854 - CmoCh04G007910.1 Cmo04g00791 791
4 4220651 4222504 - CmoCh04G008450.1 Cmo04g00845 845
7 2298841 2300921 - CmoCh07G005060.1 Cmo07g00506 506
7 3511881 3512999 + CmoCh07G007770.1 Cmo07g00777 777
1 31903533 31909755 - CmPI595203_01g018260.1 Cmu01g1826 1826
6 10834649 10836116 + Conep06aG0139900.1 Cone6ag1344 1344
6 10845260 10847690 + Conep06aG0140300.1 Cone6ag1347 1347
8 7987106 7989386 + Conep08aG0082100.1 Cone8ag0795 795
9 10938914 10941272 - Conep09aG0153400.1 Cone9ag1489 1489
10 3315727 3318625 - Cp4.1LG10g01200.1 Cpe10g00565 565
19 5869262 5872451 - Cp4.1LG19g09690.1 Cpe19g00768 768
4 33748768 33751005 - CrPI670011_04g015040.1 Cre04g1504 1504
6 26950656 26954198 - CsaV3_6G045500.1 Csa06g03164 3164
4 70471002 70473876 + Hsped.04g14830.1 Hepe04g1483 1483
8 10027517 10032997 - Hsped.08g10410.1 Hepe08g1041 1041
10 17381009 17383493 - Hsped.10g08290.1 Hepe10g0829 829
10 17632294 17634946 - Hsped.10g08320.1 Hepe10g0832 832
1 5623250 5629639 - Lsi01G007040.1 Lsi01g00704 704
1 8723465 8725276 - Lsi01G010530.1 Lsi01g01053 1053
1 753586 756580 - Sed0015273.1 Sed01g0082 82
1 763561 766113 - Sed0022143.2 Sed01g0084 84
1 2411093 2416191 - Sed0006655.1 Sed01g0317 317
14 20448004 20450782 + Sed0002715.1 Sed14g1094 1094
3 74643878 74646926 + Tan0002851.1 Tan03g1950 1950
5 17995122 18001020 - Tan0013041.1 Tan05g1354 1354
7 26935636 26938171 - Tan0010273.1 Tan07g1029 1029
7 27186817 27188698 - Tan0016732.1 Tan07g1031 1031
4 17573395 17575463 - Vvi4g912 Vvi4g912 912
4 17578958 17583726 - Vvi4g913 Vvi4g913 913
4 17584685 17588252 - Vvi4g914 Vvi4g914 914
4 17597611 17601315 + Vvi4g915 Vvi4g915 915
4 17612787 17614321 - Vvi4g916 Vvi4g916 916
4 17615877 17627150 - Vvi4g917 Vvi4g917 917
4 17631051 17631501 - Vvi4g918 Vvi4g918 918
4 17638952 17641872 - Vvi4g919 Vvi4g919 919
4 17661358 17664518 - Vvi4g920 Vvi4g920 920
4 17674973 17681364 + Vvi4g921 Vvi4g921 921
       

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