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
Vvi17g946 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g947 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g948 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g949 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g950 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g951 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g952 . . . . . . . . . Cmo18g00079 . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00276 Csa01g00754 . Cme12g01789 . . . . . . . . . . . . Cma18g00102 . Car18g00092 Cpe09g01088 . Bhi08g01351 Tan05g2137 . . . . . Cla01g01459 Cam01g1526 Cec01g1567 Cco01g1614 Clacu01g1550 Cmu01g1440 Cre01g1362 . . . .
Vvi17g953 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g954 . . . . . . . . . Cmo18g00078 . . . . . Cpe20g00180 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed08g2805 . . Cma13g00959 Cma18g00101 Car13g00795 Car18g00091 . . Bhi08g01350 Tan05g2138 Cmetu04g2126 Lac10g0326 Hepe07g2321 . . . . . . . . . . . . .
Vvi17g955 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 40655594 40660463 - XM_039038570.1 Bhi08g01350 1350
8 40663726 40674006 - XM_039038727.1 Bhi08g01351 1351
1 28805019 28819111 + CaPI482276_01g015260.1 Cam01g1526 1526
13 8800119 8804630 + Carg04877-RA Car13g00795 795
18 486222 491305 - Carg06656-RA Car18g00091 91
18 492931 500458 - Carg06657-RA Car18g00092 92
1 28830747 28838153 + CcPI632755_01g016140.1 Cco01g1614 1614
1 30249645 30257056 + CePI673135_01g015670.1 Cec01g1567 1567
1 27595072 27602025 + ClG42_01g0155000.10 Clacu01g1550 1550
1 29093131 29107731 + ClCG01G014780.2 Cla01g01459 1459
13 7510416 7514832 + CmaCh13G009590.1 Cma13g00959 959
18 476546 481516 - CmaCh18G001010.1 Cma18g00101 101
18 482755 492318 - CmaCh18G001020.1 Cma18g00102 102
12 24422249 24427363 + MELO3C002172.2.1 Cme12g01789 1789
4 11463821 11467116 + PI0026752.1 Cmetu04g2126 2126
18 522094 527184 - CmoCh18G000780.1 Cmo18g00078 78
18 529027 536700 - CmoCh18G000790.1 Cmo18g00079 79
1 27937604 27944997 + CmPI595203_01g014400.1 Cmu01g1440 1440
9 9416892 9424278 + Cp4.1LG09g10800.1 Cpe09g01088 1088
20 1021726 1026248 - Cp4.1LG20g01820.1 Cpe20g00180 180
1 26811091 26818516 + CrPI670011_01g013620.1 Cre01g1362 1362
1 4792892 4801697 - CsaV3_1G007540.1 Csa01g00754 754
7 67542858 67547855 + Hsped.07g23210.1 Hepe07g2321 2321
10 2528675 2535523 - Lag0024371.1 Lac10g0326 326
2 2340063 2354580 - Lsi02G002760.1 Lsi02g00276 276
8 39517631 39522328 - Sed0011947.3 Sed08g2805 2805
5 72106706 72115640 + Tan0007456.2 Tan05g2137 2137
5 72119501 72124233 + Tan0022478.1 Tan05g2138 2138
17 14091300 14091438 + Vvi17g946 Vvi17g946 946
17 14092767 14094314 - Vvi17g947 Vvi17g947 947
17 14120526 14120715 + Vvi17g948 Vvi17g948 948
17 14123815 14125018 - Vvi17g949 Vvi17g949 949
17 14190488 14191260 - Vvi17g950 Vvi17g950 950
17 14209989 14211405 - Vvi17g951 Vvi17g951 951
17 14285203 14293195 - Vvi17g952 Vvi17g952 952
17 14377188 14378419 + Vvi17g953 Vvi17g953 953
17 14425929 14430764 + Vvi17g954 Vvi17g954 954
17 14461860 14465916 - Vvi17g955 Vvi17g955 955
       

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