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
Vvi4g832 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla03g01043 Cam03g1088 Cec03g1096 Cco03g1087 Clacu03g1066 Cmu03g1649 Cre03g1353 Lsi06g00723 . . .
Vvi4g833 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag0928 Cone1ag1682 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla03g01042 Cam03g1087 Cec03g1095 Cco03g1084 Clacu03g1065 Cmu03g1648 Cre03g1350 . . . Cme02g00927
Vvi4g834 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone10ag0612 Cone3ag0639 . . . . . . . . . . . . . . . . . . Car05g00708 . . . . . . . . . . . . . . . . . . . .
Vvi4g835 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g836 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag0929 Cone1ag1683 Cone10ag0609 Cone3ag0635 . . . Cme05g01140 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g837 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g838 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g839 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone10ag0606 Cone3ag0632 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla03g01039 Cam03g1084 Cec03g1089 Cco03g1078 Clacu03g1058 Cmu03g1645 Cre03g1345 Lsi06g00708 . . Cme02g00925
Vvi4g840 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car05g00710 . . . . . . . . . Cla03g01038 Cam03g1083 Cec03g1088 Cco03g1077 Clacu03g1057 Cmu03g1644 Cre03g1344 Lsi06g00707 . . Cme02g00923
Vvi4g841 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag0933 Cone1ag1687 Cone10ag0605 Cone3ag0631 . . . . . . . . . . . . . . . . . . . . . Bhi10g02240 . . . . . . Cla03g01037 Cam03g1082 Cec03g1087 Cco03g1076 Clacu03g1056 Cmu03g1643 Cre03g1343 Lsi06g00706 . . Cme02g00920
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
10 58292575 58299866 - XM_039044613.1 Bhi10g02240 2240
3 20172643 20184827 + CaPI482276_03g010820.1 Cam03g1082 1082
3 20188437 20188890 + CaPI482276_03g010830.1 Cam03g1083 1083
3 20198032 20203252 - CaPI482276_03g010840.1 Cam03g1084 1084
3 20353909 20356173 + CaPI482276_03g010870.1 Cam03g1087 1087
3 20359822 20377673 - CaPI482276_03g010880.1 Cam03g1088 1088
5 4846604 4849442 + Carg19837-RA Car05g00708 708
5 4888016 4888875 - Carg19839-RA Car05g00710 710
3 18987124 18999193 + CcPI632755_03g010760.1 Cco03g1076 1076
3 19002872 19003349 + CcPI632755_03g010770.1 Cco03g1077 1077
3 19012097 19017234 - CcPI632755_03g010780.1 Cco03g1078 1078
3 19185790 19188054 + CcPI632755_03g010840.1 Cco03g1084 1084
3 19206302 19214397 - CcPI632755_03g010870.1 Cco03g1087 1087
3 22718840 22730917 + CePI673135_03g010870.1 Cec03g1087 1087
3 22734591 22735066 + CePI673135_03g010880.1 Cec03g1088 1088
3 22744109 22749297 - CePI673135_03g010890.1 Cec03g1089 1089
3 22951424 22953688 + CePI673135_03g010950.1 Cec03g1095 1095
3 22962810 22978390 - CePI673135_03g010960.1 Cec03g1096 1096
3 19003619 19015557 + ClG42_03g0105600.10 Clacu03g1056 1056
3 19019189 19019646 + ClG42_03g0105700.10 Clacu03g1057 1057
3 19028702 19033923 - ClG42_03g0105800.10 Clacu03g1058 1058
3 19179979 19182243 + ClG42_03g0106500.10 Clacu03g1065 1065
3 19187543 19207022 - ClG42_03g0106600.10 Clacu03g1066 1066
3 19840153 19852445 + ClCG03G010840.1 Cla03g01037 1037
3 19855626 19857586 + ClCG03G010850.2 Cla03g01038 1038
3 19865503 19871955 - ClCG03G010860.2 Cla03g01039 1039
3 20026988 20029252 + ClCG03G010890.2 Cla03g01042 1042
3 20034197 20054348 - ClCG03G010900.1 Cla03g01043 1043
2 12823681 12836910 + MELO3C010064.2.1 Cme02g00920 920
2 12862229 12865077 + MELO3C010069.2.1 Cme02g00923 923
2 12879216 12883157 - MELO3C010070.2.1 Cme02g00925 925
2 12940214 12949566 + MELO3C010073.2.1 Cme02g00927 927
5 18319598 18325142 - MELO3C008726.2.1 Cme05g01140 1140
3 19387669 19399609 + CmPI595203_03g016430.1 Cmu03g1643 1643
3 19403240 19403698 + CmPI595203_03g016440.1 Cmu03g1644 1644
3 19412759 19417977 - CmPI595203_03g016450.1 Cmu03g1645 1645
3 19563911 19566175 + CmPI595203_03g016480.1 Cmu03g1648 1648
3 19571399 19590960 - CmPI595203_03g016490.1 Cmu03g1649 1649
1 57914692 57917781 - Conep01aG0174500.1 Cone1ag1682 1682
1 57923501 57925384 + Conep01aG0174600.1 Cone1ag1683 1683
1 57933628 57936991 - Conep01aG0175000.1 Cone1ag1687 1687
3 3113517 3117611 + Conep03aG0064900.1 Cone3ag0631 631
3 3120463 3124173 - Conep03aG0065000.1 Cone3ag0632 632
3 3155659 3157215 - Conep03aG0065300.1 Cone3ag0635 635
3 3169650 3172501 - Conep03aG0065700.1 Cone3ag0639 639
5 3976161 3979051 - Conep05aG0095400.1 Cone5ag0928 928
5 3982235 3984299 + Conep05aG0095500.1 Cone5ag0929 929
5 3992290 3996509 - Conep05aG0095900.1 Cone5ag0933 933
10 2840936 2844946 + Conep10aG0062200.1 Cone10ag0605 605
10 2847121 2850830 - Conep10aG0062300.1 Cone10ag0606 606
10 2883716 2885507 - Conep10aG0062600.1 Cone10ag0609 609
10 2904626 2907857 - Conep10aG0062900.1 Cone10ag0612 612
3 24092840 24105027 + CrPI670011_03g013430.1 Cre03g1343 1343
3 24108652 24109118 + CrPI670011_03g013440.1 Cre03g1344 1344
3 24117753 24122804 - CrPI670011_03g013450.1 Cre03g1345 1345
3 24335625 24337889 + CrPI670011_03g013500.1 Cre03g1350 1350
3 24351247 24359563 - CrPI670011_03g013530.1 Cre03g1353 1353
6 11422584 11435226 + Lsi06G007060.1 Lsi06g00706 706
6 11440208 11441154 + Lsi06G007070.1 Lsi06g00707 707
6 11482621 11488578 - Lsi06G007080.1 Lsi06g00708 708
6 12173347 12180657 + Lsi06G007230.1 Lsi06g00723 723
4 16404475 16417806 + Vvi4g832 Vvi4g832 832
4 16418700 16420923 - Vvi4g833 Vvi4g833 833
4 16461699 16467355 + Vvi4g834 Vvi4g834 834
4 16467365 16467554 - Vvi4g835 Vvi4g835 835
4 16483824 16487265 + Vvi4g836 Vvi4g836 836
4 16523400 16527061 + Vvi4g837 Vvi4g837 837
4 16527064 16528699 - Vvi4g838 Vvi4g838 838
4 16545493 16553795 + Vvi4g839 Vvi4g839 839
4 16561322 16562396 - Vvi4g840 Vvi4g840 840
4 16567671 16576903 - Vvi4g841 Vvi4g841 841
       

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