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
Vvi2g902 . . . . . . . . Cmo06g00603 . . . . . . . . . . . . . . . Cla10g00096 Cam10g0094 Cec10g0099 Cco10g0100 Clacu10g0095 Cmu10g0942 Cre10g0356 Cone8ag0546 . . . Lsi07g01124 . . Cme06g02405 . . . . . . Bma05g00686 . . . . Cma06g00596 . Car06g00531 . . . . . . . . . . . . . . . . . . Csa03g00100 Chy06g02205 .
Vvi2g903 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0538 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g904 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g905 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g906 . . . . . . . . . Cmo16g01266 . . . . . Cpe14g01009 . . . . . . . . Cla10g00093 Cam10g0093 Cec10g0097 Cco10g0099 Clacu10g0094 Cmu10g0941 Cre10g0355 . Cone12ag0548 . . Lsi07g01122 . . Cme06g02403 . . . . . . . . . . . . Cma16g01223 . Car16g01150 . . . . . . . . . . . . . . . . . Csa03g00098 Chy06g02209 .
Vvi2g907 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g908 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g909 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g910 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g911 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 39918907 39922999 + Bma021745.1 Bma05g00686 686
10 2512313 2523713 - CaPI482276_10g000930.1 Cam10g0093 93
10 2530197 2537949 + CaPI482276_10g000940.1 Cam10g0094 94
6 2986491 2989661 + Carg16283-RA Car06g00531 531
16 9799670 9811776 + Carg19491-RA Car16g01150 1150
10 918695 930106 - CcPI632755_10g000990.1 Cco10g0099 99
10 933154 941245 + CcPI632755_10g001000.1 Cco10g0100 100
10 944780 956194 - CePI673135_10g000970.1 Cec10g0097 97
10 963046 970646 + CePI673135_10g000990.1 Cec10g0099 99
6 26253854 26257212 - Chy6G127330.1 Chy06g02205 2205
6 26266196 26277667 + Chy6G127370.1 Chy06g02209 2209
10 1235010 1246609 - ClG42_10g0009400.10 Clacu10g0094 94
10 1253024 1260676 + ClG42_10g0009500.10 Clacu10g0095 95
10 956954 968647 - ClCG10G000900.1 Cla10g00093 93
10 979357 982657 + ClCG10G000930.2 Cla10g00096 96
6 2881162 2884562 + CmaCh06G005960.1 Cma06g00596 596
16 9237095 9249589 + CmaCh16G012230.1 Cma16g01223 1223
6 31201575 31213186 - MELO3C013786.2.1 Cme06g02403 2403
6 31218042 31221978 + MELO3C013790.2.1 Cme06g02405 2405
6 2972044 2975927 + CmoCh06G006030.1 Cmo06g00603 603
16 9018713 9030986 + CmoCh16G012660.1 Cmo16g01266 1266
10 1386706 1398115 - CmPI595203_10g009410.1 Cmu10g0941 941
10 1408884 1412184 + CmPI595203_10g009420.1 Cmu10g0942 942
8 4038403 4043094 + Conep08aG0056700.1 Cone8ag0546 546
12 3778653 3780188 - Conep12aG0055900.1 Cone12ag0538 538
12 3901492 3904691 + Conep12aG0056900.1 Cone12ag0548 548
14 8493295 8505745 + Cp4.1LG14g10050.1 Cpe14g01009 1009
10 2354890 2366020 - CrPI670011_10g003550.1 Cre10g0355 355
10 2369994 2378224 + CrPI670011_10g003560.1 Cre10g0356 356
3 768618 780125 - CsaV3_3G000980.1 Csa03g00098 98
3 787997 792095 + CsaV3_3G001000.1 Csa03g00100 100
7 16656788 16668882 - Lsi07G011220.1 Lsi07g01122 1122
7 16678311 16682740 + Lsi07G011240.1 Lsi07g01124 1124
2 16879683 16884544 - Vvi2g902 Vvi2g902 902
2 16900111 16901615 + Vvi2g903 Vvi2g903 903
2 16903455 16903928 - Vvi2g904 Vvi2g904 904
2 16903939 16905266 - Vvi2g905 Vvi2g905 905
2 16907059 16934249 - Vvi2g906 Vvi2g906 906
2 17046629 17048115 - Vvi2g907 Vvi2g907 907
2 17048116 17048305 - Vvi2g908 Vvi2g908 908
2 17048304 17049219 - Vvi2g909 Vvi2g909 909
2 17064623 17065595 - Vvi2g910 Vvi2g910 910
2 17073635 17095499 - Vvi2g911 Vvi2g911 911
       

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