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
Vvi4g752 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g753 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g754 . . . . . . . . . . . . . . . . . . . . . . . . Cla01g00850 . Cec01g0875 Cco01g0905 Clacu01g0866 Cmu01g0832 Cre09g1675 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g755 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g756 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g757 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g758 . . . . . . . . . . . . . . . . . . . . . . . . Cla01g00857 Cam01g0883 Cec01g0882 Cco01g0915 Clacu01g0873 Cmu01g0839 Cre09g1668 . . . . . . . . . . . . . . . Bma02g00558 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g759 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda13g01813 . . . Bma02g00557 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g760 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g761 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
13 42044070 42047686 + Bda000701.1 Bda13g01813 1813
2 11508272 11510254 + Bma015083.1 Bma02g00557 557
2 11542073 11543531 - Bma015084.1 Bma02g00558 558
1 10342523 10346364 - CaPI482276_01g008830.1 Cam01g0883 883
1 10044031 10048352 + CcPI632755_01g009050.1 Cco01g0905 905
1 10175821 10180039 - CcPI632755_01g009150.1 Cco01g0915 915
1 10090771 10095041 + CePI673135_01g008750.1 Cec01g0875 875
1 10241353 10245215 - CePI673135_01g008820.1 Cec01g0882 882
1 9890299 9894552 + ClG42_01g0086600.10 Clacu01g0866 866
1 10013540 10017606 - ClG42_01g0087300.10 Clacu01g0873 873
1 10385781 10390223 + ClCG01G008660.2 Cla01g00850 850
1 10512347 10516573 - ClCG01G008740.1 Cla01g00857 857
1 9855643 9859895 + CmPI595203_01g008320.1 Cmu01g0832 832
1 9978984 9983052 - CmPI595203_01g008390.1 Cmu01g0839 839
9 34381806 34385628 + CrPI670011_09g016680.1 Cre09g1668 1668
9 34499937 34504241 - CrPI670011_09g016750.1 Cre09g1675 1675
4 13400787 13400892 - Vvi4g752 Vvi4g752 752
4 13438817 13455736 - Vvi4g753 Vvi4g753 753
4 13511539 13532182 - Vvi4g754 Vvi4g754 754
4 13532932 13535281 - Vvi4g755 Vvi4g755 755
4 13548758 13552463 - Vvi4g756 Vvi4g756 756
4 13618565 13620032 - Vvi4g757 Vvi4g757 757
4 13620069 13635746 + Vvi4g758 Vvi4g758 758
4 13640929 13649842 - Vvi4g759 Vvi4g759 759
4 13912799 13914204 - Vvi4g760 Vvi4g760 760
4 13932083 13938476 + Vvi4g761 Vvi4g761 761
       

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