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
Vvi3g906 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g907 . . . . . . . . Cmo19g00505 . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi03g00683 Csa07g00618 . Cme01g00183 . . . . . . . . . . . . Cma19g00488 . Car19g00365 . . . . . . . . . . . . . . . . . . Chy01g00191 .
Vvi3g908 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g909 . . . . . Bpe12g00712 . . . . . . . . . . . Bhi05g00942 . . . . . . Cla10g00921 Cam10g0941 Cec10g0980 Cco10g0939 Clacu10g0966 Cmu10g1749 Cre10g1125 . . . . . . . . . . Bda15g00490 . . . . Bma08g00038 . . Cmo16g00296 . . . . Cpe14g00230 Cpe01g00370 . . . . . . . . . . . . . . . . . Cme07g02236
Vvi3g910 . . Bda06g01119 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi03g00684 Csa07g00613 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy01g00192 .
Vvi3g911 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g912 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g913 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g914 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g915 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 39851201 39853336 + Bda022914.2 Bda06g01119 1119
15 8043975 8049436 - Bda012318.1 Bda15g00490 490
5 33019057 33078997 + XM_039030934.1 Bhi05g00942 942
8 560062 565607 - Bma027033.1 Bma08g00038 38
12 12675896 12681429 + Bpe005973.1 Bpe12g00712 712
10 21328192 21336326 + CaPI482276_10g009410.1 Cam10g0941 941
19 5520194 5522356 + Carg22799-RA Car19g00365 365
10 20524499 20532949 + CcPI632755_10g009390.1 Cco10g0939 939
10 22215785 22223131 + CePI673135_10g009800.1 Cec10g0980 980
1 1293004 1295040 + Chy1G001910.1 Chy01g00191 191
1 1296575 1298704 + Chy1G001920.1 Chy01g00192 192
10 20956602 20963858 + ClG42_10g0096600.10 Clacu10g0966 966
10 21905135 21911124 + ClCG10G009620.1 Cla10g00921 921
19 5816049 5818238 + CmaCh19G004880.1 Cma19g00488 488
1 1269220 1271760 - MELO3C018582.2.1 Cme01g00183 183
7 26497289 26507994 - MELO3C018049.2.1 Cme07g02236 2236
16 1342335 1346091 + CmoCh16G002960.1 Cmo16g00296 296
19 6001254 6003473 + CmoCh19G005050.1 Cmo19g00505 505
10 21565469 21572692 + CmPI595203_10g017490.1 Cmu10g1749 1749
1 2125778 2134856 + Cp4.1LG01g02990.1 Cpe01g00370 370
14 1323554 1327231 + Cp4.1LG14g04960.1 Cpe14g00230 230
10 23271488 23279480 + CrPI670011_10g011250.1 Cre10g1125 1125
7 4466391 4469312 + CsaV3_7G007120.1 Csa07g00613 613
7 4492517 4494949 - CsaV3_7G007170.1 Csa07g00618 618
3 8669570 8671693 - Lsi03G006830.1 Lsi03g00683 683
3 8688781 8690907 + Lsi03G006840.1 Lsi03g00684 684
3 12208527 12209070 + Vvi3g906 Vvi3g906 906
3 12209634 12212696 - Vvi3g907 Vvi3g907 907
3 12215288 12216459 + Vvi3g908 Vvi3g908 908
3 12256603 12295018 - Vvi3g909 Vvi3g909 909
3 12333545 12335687 - Vvi3g910 Vvi3g910 910
3 12363480 12378235 + Vvi3g911 Vvi3g911 911
3 12421539 12422888 - Vvi3g912 Vvi3g912 912
3 12485371 12485512 + Vvi3g913 Vvi3g913 913
3 12486814 12487788 - Vvi3g914 Vvi3g914 914
3 12541257 12542643 - Vvi3g915 Vvi3g915 915
       

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