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
Vvi4g712 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g713 . . . . . . . . . . . . . . . . . . . . . . . . Cla01g00841 Cam01g0866 Cec01g0866 Cco01g0893 Clacu01g0855 Cmu01g0824 Cre09g1686 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g714 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g715 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g716 . . . . . . . . . . . . . . . . . . . . . . . . Cla01g00843 Cam01g0869 Cec01g0868 Cco01g0895 Clacu01g0857 Cmu01g0826 Cre09g1684 . . . . . . . . . . . Bda13g01816 Bpe14g00062 . . Bma02g00563 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g717 . . . . . . . . . . . . . . . . . . . . . . . . Cla01g00846 Cam01g0871 Cec01g0869 Cco01g0897 Clacu01g0860 Cmu01g0828 Cre09g1682 . . . . . . . . . . . . Bpe14g00063 . . Bma02g00562 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g718 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g719 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda13g01815 Bpe14g00064 . . Bma02g00561 . . . . . . . . . . . . . . . . . . . . . . . Lsi06g00766 . . .
Vvi4g720 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g721 . . . . . . . . . . . . . . . . . . . . . . . . Cla01g00847 Cam01g0872 Cec01g0872 Cco01g0901 Clacu01g0862 Cmu01g0829 Cre09g1680 . . . . . . . . . . . . Bpe14g00065 . . Bma02g00560 . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
13 42074884 42079955 + Bda000704.1 Bda13g01815 1815
13 42087613 42089393 - Bda000705.2 Bda13g01816 1816
2 11649214 11653711 - Bma015089.1 Bma02g00560 560
2 11674754 11679679 + Bma015090.1 Bma02g00561 561
2 11681493 11685369 - Bma015091.2 Bma02g00562 562
2 11687610 11689292 - Bma015092.2 Bma02g00563 563
14 1002195 1003166 + Bpe024957 Bpe14g00062 62
14 1010579 1014406 + Bpe024958 Bpe14g00063 63
14 1015450 1021342 - Bpe006717.2 Bpe14g00064 64
14 1026114 1028502 + Bpe006718.1 Bpe14g00065 65
1 10047756 10052138 - CaPI482276_01g008660.1 Cam01g0866 866
1 10076696 10078897 + CaPI482276_01g008690.1 Cam01g0869 869
1 10115622 10120237 + CaPI482276_01g008710.1 Cam01g0871 871
1 10177470 10187058 + CaPI482276_01g008720.1 Cam01g0872 872
1 9852810 9857226 - CcPI632755_01g008930.1 Cco01g0893 893
1 9887018 9888657 + CcPI632755_01g008950.1 Cco01g0895 895
1 9919026 9923641 + CcPI632755_01g008970.1 Cco01g0897 897
1 9995233 9998160 + CcPI632755_01g009010.1 Cco01g0901 901
1 9890651 9894873 - CePI673135_01g008660.1 Cec01g0866 866
1 9915351 9922401 + CePI673135_01g008680.1 Cec01g0868 868
1 9968570 9973191 + CePI673135_01g008690.1 Cec01g0869 869
1 10033264 10042600 + CePI673135_01g008720.1 Cec01g0872 872
1 9694199 9698474 - ClG42_01g0085500.10 Clacu01g0855 855
1 9727784 9729457 + ClG42_01g0085700.10 Clacu01g0857 857
1 9766038 9773113 + ClG42_01g0086000.10 Clacu01g0860 860
1 9828393 9837813 + ClG42_01g0086200.10 Clacu01g0862 862
1 10187801 10192465 - ClCG01G008560.2 Cla01g00841 841
1 10215573 10223989 + ClCG01G008580.2 Cla01g00843 843
1 10259894 10267683 + ClCG01G008610.2 Cla01g00846 846
1 10324719 10334497 + ClCG01G008630.1 Cla01g00847 847
1 9658926 9663206 - CmPI595203_01g008240.1 Cmu01g0824 824
1 9692515 9698141 + CmPI595203_01g008260.1 Cmu01g0826 826
1 9730692 9737770 + CmPI595203_01g008280.1 Cmu01g0828 828
1 9793026 9802513 + CmPI595203_01g008290.1 Cmu01g0829 829
9 34561921 34562534 - CrPI670011_09g016800.1 Cre09g1680 1680
9 34639492 34644159 - CrPI670011_09g016820.1 Cre09g1682 1682
9 34679240 34681977 - CrPI670011_09g016840.1 Cre09g1684 1684
9 34701851 34706110 + CrPI670011_09g016860.1 Cre09g1686 1686
6 14692176 14698645 - Lsi06G007660.1 Lsi06g00766 766
4 10884889 10889188 + Vvi4g712 Vvi4g712 712
4 10905014 10909860 + Vvi4g713 Vvi4g713 713
4 10914290 10921085 - Vvi4g714 Vvi4g714 714
4 10997909 11025564 + Vvi4g715 Vvi4g715 715
4 11088567 11103149 + Vvi4g716 Vvi4g716 716
4 11130799 11137368 + Vvi4g717 Vvi4g717 717
4 11138081 11139316 + Vvi4g718 Vvi4g718 718
4 11141527 11206907 - Vvi4g719 Vvi4g719 719
4 11208511 11211508 + Vvi4g720 Vvi4g720 720
4 11271683 11278138 + Vvi4g721 Vvi4g721 721
       

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