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
Vvi4g842 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g843 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag0934 Cone1ag1688 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g844 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme05g01150 . . . . . . . . . . . . . . Car05g00711 . . . . . . . . . . . . . . . . . . . .
Vvi4g845 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla03g01032 Cam03g1080 Cec03g1084 Cco03g1075 Clacu03g1054 Cmu03g1642 Cre03g1342 Lsi06g00705 . . Cme02g00916
Vvi4g846 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag0936 Cone1ag1690 . . . . . . . . . . . . . . . . . . . . Car05g00712 . . . . . . . . . . . . . . . . . . . .
Vvi4g847 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla03g01026 Cam03g1077 Cec03g1081 Cco03g1073 Clacu03g1046 Cmu03g1637 Cre03g1338 Lsi06g00702 . . Cme02g00915
Vvi4g848 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag0938 Cone1ag1692 Cone10ag0604 Cone3ag0630 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla03g01025 Cam03g1074 Cec03g1079 Cco03g1072 Clacu03g1045 Cmu03g1635 Cre03g1335 Lsi06g00701 . . Cme02g00913
Vvi4g849 Blo04g00958 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme05g01162 . . . Bda14g01224 . . . . . . . . . . Car05g00713 . . . . . . . . . . . . . . . . . . . .
Vvi4g850 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag0939 . Cone10ag0603 Cone3ag0629 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla03g01024 Cam03g1073 Cec03g1078 Cco03g1071 Clacu03g1044 Cmu03g1634 Cre03g1334 Lsi06g00700 . . .
Vvi4g851 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag1693 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla03g01019 Cam03g1071 Cec03g1072 Cco03g1064 Clacu03g1043 Cmu03g1633 Cre03g1333 Lsi06g00696 . . Cme02g00910
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
14 12345572 12347712 + Bda028088.1 Bda14g01224 1224
4 11695906 11697306 - BLOR13870 Blo04g00958 958
3 19788186 19789617 + CaPI482276_03g010710.1 Cam03g1071 1071
3 19826360 19837861 + CaPI482276_03g010730.1 Cam03g1073 1073
3 19860330 19860647 - CaPI482276_03g010740.1 Cam03g1074 1074
3 19925367 19927051 - CaPI482276_03g010770.1 Cam03g1077 1077
3 20118941 20121696 + CaPI482276_03g010800.1 Cam03g1080 1080
5 4892405 4899775 + Carg19840-RA Car05g00711 711
5 4900007 4901989 - Carg19841-RA Car05g00712 712
5 4907389 4910985 + Carg19842-RA Car05g00713 713
3 18614193 18616762 + CcPI632755_03g010640.1 Cco03g1064 1064
3 18674904 18680855 + CcPI632755_03g010710.1 Cco03g1071 1071
3 18713104 18713421 - CcPI632755_03g010720.1 Cco03g1072 1072
3 18766671 18768379 - CcPI632755_03g010730.1 Cco03g1073 1073
3 18921494 18924240 + CcPI632755_03g010750.1 Cco03g1075 1075
3 22301070 22302500 + CePI673135_03g010720.1 Cec03g1072 1072
3 22360113 22367671 + CePI673135_03g010780.1 Cec03g1078 1078
3 22379941 22380510 - CePI673135_03g010790.1 Cec03g1079 1079
3 22447885 22449569 - CePI673135_03g010810.1 Cec03g1081 1081
3 22643007 22645781 + CePI673135_03g010840.1 Cec03g1084 1084
3 18625529 18626959 + ClG42_03g0104300.10 Clacu03g1043 1043
3 18665081 18674857 + ClG42_03g0104400.10 Clacu03g1044 1044
3 18698859 18699176 - ClG42_03g0104500.10 Clacu03g1045 1045
3 18753412 18755117 - ClG42_03g0104600.10 Clacu03g1046 1046
3 18941969 18944681 + ClG42_03g0105400.10 Clacu03g1054 1054
3 19435236 19436748 + ClCG03G010670.1 Cla03g01019 1019
3 19476497 19487578 + ClCG03G010700.2 Cla03g01024 1024
3 19510804 19511121 - ClCG03G010710.1 Cla03g01025 1025
3 19567511 19569348 - ClCG03G010730.1 Cla03g01026 1026
3 19777577 19780301 + ClCG03G010790.1 Cla03g01032 1032
2 12586348 12587983 + MELO3C010056.2.1 Cme02g00910 910
2 12635657 12637480 - MELO3C010059.2.1 Cme02g00913 913
2 12679571 12681639 - MELO3C010061.2.1 Cme02g00915 915
2 12712156 12715130 - MELO3C010062.2.1 Cme02g00916 916
5 18430594 18444046 - MELO3C008734.2.1 Cme05g01150 1150
5 18662622 18663027 - MELO3C001206.2.1 Cme05g01162 1162
3 19009776 19011206 + CmPI595203_03g016330.1 Cmu03g1633 1633
3 19049389 19060949 + CmPI595203_03g016340.1 Cmu03g1634 1634
3 19083175 19083492 - CmPI595203_03g016350.1 Cmu03g1635 1635
3 19133120 19139298 - CmPI595203_03g016370.1 Cmu03g1637 1637
3 19326277 19328992 + CmPI595203_03g016420.1 Cmu03g1642 1642
1 57936990 57940922 + Conep01aG0175100.1 Cone1ag1688 1688
1 57941707 57943616 - Conep01aG0175300.1 Cone1ag1690 1690
1 57948472 57949274 + Conep01aG0175500.1 Cone1ag1692 1692
1 57952472 57953944 + Conep01aG0175600.1 Cone1ag1693 1693
3 3107909 3111419 + Conep03aG0064700.1 Cone3ag0629 629
3 3112399 3113284 - Conep03aG0064800.1 Cone3ag0630 630
5 3997724 4004236 + Conep05aG0096000.1 Cone5ag0934 934
5 4006071 4007363 - Conep05aG0096200.1 Cone5ag0936 936
5 4011942 4012739 + Conep05aG0096400.1 Cone5ag0938 938
5 4013009 4016281 - Conep05aG0096500.1 Cone5ag0939 939
10 2835417 2838930 + Conep10aG0062000.1 Cone10ag0603 603
10 2839418 2840708 - Conep10aG0062100.1 Cone10ag0604 604
3 23658389 23659820 + CrPI670011_03g013330.1 Cre03g1333 1333
3 23710873 23720536 + CrPI670011_03g013340.1 Cre03g1334 1334
3 23745298 23745615 - CrPI670011_03g013350.1 Cre03g1335 1335
3 23821375 23823008 - CrPI670011_03g013380.1 Cre03g1338 1338
3 24024016 24026659 + CrPI670011_03g013420.1 Cre03g1342 1342
6 11056237 11056980 + Lsi06G006960.1 Lsi06g00696 696
6 11115700 11120378 + Lsi06G007000.1 Lsi06g00700 700
6 11135490 11136925 - Lsi06G007010.1 Lsi06g00701 701
6 11192637 11195196 - Lsi06G007020.1 Lsi06g00702 702
6 11302593 11305428 - Lsi06G007050.1 Lsi06g00705 705
4 16577017 16579760 - Vvi4g842 Vvi4g842 842
4 16599412 16607622 + Vvi4g843 Vvi4g843 843
4 16608368 16610633 + Vvi4g844 Vvi4g844 844
4 16612722 16613548 + Vvi4g845 Vvi4g845 845
4 16613621 16615440 - Vvi4g846 Vvi4g846 846
4 16630134 16632757 + Vvi4g847 Vvi4g847 847
4 16642151 16645742 + Vvi4g848 Vvi4g848 848
4 16649309 16652943 - Vvi4g849 Vvi4g849 849
4 16664475 16666741 - Vvi4g850 Vvi4g850 850
4 16695326 16700045 + Vvi4g851 Vvi4g851 851
       

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