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
Vvi2g762 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g763 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g764 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g765 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g766 . . Bda06g01237 . . Bpe07g00242 . . Cmo06g00622 Cmo16g01247 . . . . . Cpe14g00993 . . . . . . . . Cla10g00119 Cam10g0117 Cec10g0126 Cco10g0126 Clacu10g0123 Cmu10g0970 Cre10g0380 . . . . Lsi07g01152 . . Cme06g02431 . . . . . . . Bma12g00244 . . . Cma06g00615 Cma16g01199 Car06g00548 Car16g01130 . . . . . . . . . . . . . . . . . Csa03g00123 Chy06g02182 .
Vvi2g767 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g768 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g769 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone16ag0496 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla09g01071 . . . . . . . . . .
Vvi2g770 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g771 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 42463805 42468113 - Bda023068.2 Bda06g01237 1237
12 3136008 3140975 + Bma007135.1 Bma12g00244 244
7 1728375 1731976 + Bpe021053.1 Bpe07g00242 242
10 2758792 2762824 - CaPI482276_10g001170.1 Cam10g0117 117
6 3114425 3118593 - Carg23415-RA Car06g00548 548
16 9678208 9679494 + Carg23579-RA Car16g01130 1130
10 1166478 1170486 - CcPI632755_10g001260.1 Cco10g0126 126
10 1180998 1185113 - CePI673135_10g001260.1 Cec10g0126 126
6 26075824 26080374 + Chy6G127100.1 Chy06g02182 2182
10 1481955 1486068 - ClG42_10g0012300.10 Clacu10g0123 123
9 11338359 11341100 + ClCG09G011460.1 Cla09g01071 1071
10 1208046 1218797 - ClCG10G001180.2 Cla10g00119 119
6 2998499 3002654 - CmaCh06G006150.1 Cma06g00615 615
16 9123316 9127933 + CmaCh16G011990.1 Cma16g01199 1199
6 31385391 31390019 - MELO3C013812.2.1 Cme06g02431 2431
6 3091299 3095881 - CmoCh06G006220.1 Cmo06g00622 622
16 8903263 8908366 + CmoCh16G012470.1 Cmo16g01247 1247
10 1633239 1637336 - CmPI595203_10g009700.1 Cmu10g0970 970
16 7043650 7045092 - Conep16aG0285400.1 Cone16ag0496 496
14 8371986 8382457 + Cp4.1LG14g09920.1 Cpe14g00993 993
10 2593889 2597944 - CrPI670011_10g003800.1 Cre10g0380 380
3 964639 969255 - CsaV3_3G001230.1 Csa03g00123 123
7 16985749 16989277 - Lsi07G011520.1 Lsi07g01152 1152
2 10508819 10511615 - Vvi2g762 Vvi2g762 762
2 10573743 10587530 + Vvi2g763 Vvi2g763 763
2 10591346 10591814 + Vvi2g764 Vvi2g764 764
2 10594830 10608680 + Vvi2g765 Vvi2g765 765
2 10652274 10716631 - Vvi2g766 Vvi2g766 766
2 10785022 10786852 - Vvi2g767 Vvi2g767 767
2 10833511 10835788 - Vvi2g768 Vvi2g768 768
2 10849882 10851759 + Vvi2g769 Vvi2g769 769
2 10872892 10872997 + Vvi2g770 Vvi2g770 770
2 11554980 11575642 - Vvi2g771 Vvi2g771 771
       

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