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
Vvi19g644 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g645 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g646 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g647 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone9ag0013 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g648 . . . . . . . . . . Cma01g01081 Cma09g01002 Car01g00956 Car09g00913 Sed07g2743 Cpe06g00810 Cpe02g00817 Bhi09g01749 Tan01g3181 Cmetu01g1982 . . Mch11g1259 . . . . . . . . . . Cone14ag1212 Cone15ag1233 Lsi02g01842 Csa07g00939 . . . . . . Bpe11g00582 . . Bma14g00172 . Cmo01g01127 Cmo09g01002 . . . . . . . . . . . . . Cla09g02063 Cam09g2152 Cec09g2217 . . . . . . Chy01g01165 Cme01g00930
Vvi19g649 . Blo03g01480 . . . Bpe08g01095 . . . . . Cma09g01003 . Car09g00914 . Cpe06g00811 . Bhi09g01751 . . . . Mch11g1260 . . . . . . . . . . . . Lsi02g01841 Csa07g00937 . . . . . . . . Bma07g01249 . . . Cmo09g01003 . . . . . . . . . . . . . Cla09g02064 Cam09g2153 Cec09g2218 . . . . . . Chy01g01164 Cme01g00928
Vvi19g650 . . . Bda09g00436 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0013 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g651 . . . . . Bpe08g01094 . . . . Cma01g01079 Cma09g01005 Car01g00954 Car09g00916 . . Cpe02g00819 . . . . . . . . . . . . . . . Cone9ag0012 . . Lsi02g01840 . . . . . . . . . Bma07g01248 . . Cmo01g01125 . . . . . . . . . . . . . . Cla09g02066 Cam09g2155 Cec09g2220 . . . . . . Chy01g01154 Cme01g00925
Vvi19g652 . . . . . . . . . . . . . . Sed01g1398 Cpe06g00814 . Bhi09g01755 Tan01g3185 Cmetu01g2316 . . Mch11g1262 . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo09g01006 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g653 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
9 5782644 5783868 + Bda031024.1 Bda09g00436 436
9 47524841 47532707 - XM_039041667.1 Bhi09g01749 1749
9 47540524 47549680 + XM_039043868.1 Bhi09g01751 1751
9 47758867 47762131 + XM_039040207.1 Bhi09g01755 1755
3 41585099 41588432 - BLOR12661 Blo03g01480 1480
7 47466945 47468169 - Bma026502.1 Bma07g01248 1248
7 47470520 47473557 + Bma026503.1 Bma07g01249 1249
14 2296110 2299361 + Bma010582.1 Bma14g00172 172
8 13015500 13016724 - Bpe023219.1 Bpe08g01094 1094
8 13021137 13024262 + Bpe023220.1 Bpe08g01095 1095
11 4432647 4435898 - Bpe003947.1 Bpe11g00582 582
9 36051201 36056586 - CaPI482276_09g021520.1 Cam09g2152 2152
9 36059010 36062439 + CaPI482276_09g021530.1 Cam09g2153 2153
9 36084890 36086132 + CaPI482276_09g021550.1 Cam09g2155 2155
1 9161999 9165350 - Carg22409-RA Car01g00954 954
1 9170356 9174561 + Carg22407-RA Car01g00956 956
9 5619643 5624511 - Carg12868-RA Car09g00913 913
9 5625825 5628708 + Carg12869-RA Car09g00914 914
9 5642024 5643487 + Carg12871-RA Car09g00916 916
9 39077252 39083951 - CePI673135_09g022170.1 Cec09g2217 2217
9 39086428 39089860 + CePI673135_09g022180.1 Cec09g2218 2218
9 39112448 39113690 + CePI673135_09g022200.1 Cec09g2220 2220
1 13481172 13482412 - Chy1G011540.1 Chy01g01154 1154
1 13542400 13544461 - Chy1G011640.1 Chy01g01164 1164
1 13550000 13554911 + Chy1G011650.1 Chy01g01165 1165
9 38201580 38207199 - ClCG09G021200.1 Cla09g02063 2063
9 38210273 38213065 + ClCG09G021210.2 Cla09g02064 2064
9 38236836 38239858 + ClCG09G021230.1 Cla09g02066 2066
1 7960855 7964255 - CmaCh01G010790.1 Cma01g01079 1079
1 7968801 7973053 + CmaCh01G010810.1 Cma01g01081 1081
9 5107184 5111781 - CmaCh09G010020.1 Cma09g01002 1002
9 5112831 5116781 + CmaCh09G010030.1 Cma09g01003 1003
9 5128133 5133645 + CmaCh09G010050.1 Cma09g01005 1005
1 10731582 10735026 + MELO3C024926.2.1 Cme01g00925 925
1 10792987 10802166 - MELO3C024924.2.1 Cme01g00928 928
1 10814974 10820762 + MELO3C024922.2.1 Cme01g00930 930
1 13148126 13154144 - PI0003187.2 Cmetu01g1982 1982
1 13231037 13232273 + PI0011932.1 Cmetu01g2316 2316
1 9286483 9289732 - CmoCh01G011250.1 Cmo01g01125 1125
1 9297060 9301200 + CmoCh01G011270.1 Cmo01g01127 1127
9 5331187 5335806 - CmoCh09G010020.1 Cmo09g01002 1002
9 5337349 5340265 + CmoCh09G010030.1 Cmo09g01003 1003
9 5354417 5356098 + CmoCh09G010060.1 Cmo09g01006 1006
6 94055 96320 - Conep06aG0001300.1 Cone6ag0013 13
9 59796 62396 - Conep09aG0001200.1 Cone9ag0012 12
9 83220 85691 + Conep09aG0001300.1 Cone9ag0013 13
14 9862882 9865976 - Conep14aG0124400.1 Cone14ag1212 1212
15 9773620 9776655 - Conep15aG0126200.1 Cone15ag1233 1233
2 5226847 5231196 - Cp4.1LG02g00590.1 Cpe02g00817 817
2 5237600 5240821 + Cp4.1LG02g00510.1 Cpe02g00819 819
6 5182864 5187246 - Cp4.1LG06g08480.1 Cpe06g00810 810
6 5188664 5189994 + Cp4.1LG06g08590.1 Cpe06g00811 811
6 5207894 5209800 + Cp4.1LG06g08420.1 Cpe06g00814 814
7 8118753 8143617 - CsaV3_7G018280.1 Csa07g00937 937
7 8178093 8184039 + CsaV3_7G018300.1 Csa07g00939 939
2 24163922 24167473 - Lsi02G018400.1 Lsi02g01840 1840
2 24187748 24191376 - Lsi02G018410.1 Lsi02g01841 1841
2 24192984 24200569 + Lsi02G018420.1 Lsi02g01842 1842
11 8933813 8942207 - MC11g1040 Mch11g1259 1259
11 8945555 8949095 + MC11g1041 Mch11g1260 1260
11 8963483 8967117 + MC11g1043 Mch11g1262 1262
1 10376157 10377320 + Sed0023919.1 Sed01g1398 1398
7 42525466 42531318 - Sed0002134.3 Sed07g2743 2743
1 85455364 85469012 - Tan0006451.1 Tan01g3181 3181
1 85590895 85594567 + Tan0002464.1 Tan01g3185 3185
19 8231329 8232084 + Vvi19g644 Vvi19g644 644
19 8232991 8235393 - Vvi19g645 Vvi19g645 645
19 8237519 8237662 + Vvi19g646 Vvi19g646 646
19 8237666 8239566 - Vvi19g647 Vvi19g647 647
19 8241014 8247039 - Vvi19g648 Vvi19g648 648
19 8278979 8284207 - Vvi19g649 Vvi19g649 649
19 8297132 8299782 + Vvi19g650 Vvi19g650 650
19 8304201 8305387 + Vvi19g651 Vvi19g651 651
19 8315681 8317995 + Vvi19g652 Vvi19g652 652
19 8329804 8330017 + Vvi19g653 Vvi19g653 653
       

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