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
Vvi4g872 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag1701 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla03g01013 Cam03g1067 Cec03g1064 Cco03g1059 Clacu03g1038 Cmu03g1628 Cre03g1329 Lsi06g00691 . Chy02g00677 Cme02g00904
Vvi4g873 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag0943 Cone1ag1702 . . Lsi01g00707 . Chy07g01304 . . . . . . . . . . . . . Cma20g00873 . Car05g00767 . . . . . . . . . Cla03g01012 Cam03g1066 Cec03g1062 Cco03g1057 Clacu03g1036 Cmu03g1626 Cre03g1328 Lsi06g00689 . . .
Vvi4g874 . . . . Bpe15g00448 . . . Cmo04g00855 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe06g00067 . . . . . . . . . . . . . . . . . . . . . . . . . Lsi06g00688 . . Cme02g00903
Vvi4g875 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag0944 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g876 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone10ag0596 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme02g00860
Vvi4g877 . . . . . Bpe13g00456 . Bma15g01028 . . . Cma07g00510 . Car07g00446 . . . . . . . . . . . . . . . . . . . . Cone3ag0624 . . . . . . . . . . . . . . Cmo07g00508 . . . Car05g00768 . . Bhi10g02053 Tan05g1355 . . Hepe10g1418 . . . . . . . . . . Csa04g00525 . Cme02g00859
Vvi4g878 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag0945 Cone1ag1703 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g879 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag0946 Cone1ag1704 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g880 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone2ag0281 Cone16ag0756 . . . . . . . . . . . . . . . . . . . . Car05g00770 . . . . . . . . . . . . . . . . . . . .
Vvi4g881 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag0948 Cone1ag1705 . . . . . . . . Bda11g01879 . . . . Bma06g00134 . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 53829927 53837441 + Bda008817.1 Bda11g01879 1879
10 51357301 51360867 + XM_039045261.1 Bhi10g02053 2053
6 1767080 1767612 + Bma022752.1 Bma06g00134 134
15 40935444 40936982 - Bma014322.1 Bma15g01028 1028
6 777670 780958 + Bpe019514.1 Bpe06g00067 67
13 12060772 12068587 + Bpe006581.1 Bpe13g00456 456
15 15932620 15933134 + Bpe001383.1 Bpe15g00448 448
3 19505095 19509527 + CaPI482276_03g010660.1 Cam03g1066 1066
3 19535848 19543201 - CaPI482276_03g010670.1 Cam03g1067 1067
5 5959827 5963157 + Carg25821-RA Car05g00767 767
5 5965855 5970924 - Carg25820-RA Car05g00768 768
5 5981959 5985049 + Carg25818-RA Car05g00770 770
7 2269673 2276242 + Carg16029-RA Car07g00446 446
3 18342714 18350959 + CcPI632755_03g010570.1 Cco03g1057 1057
3 18371123 18378464 - CcPI632755_03g010590.1 Cco03g1059 1059
3 21930953 21933602 + CePI673135_03g010620.1 Cec03g1062 1062
3 21989813 21997174 - CePI673135_03g010640.1 Cec03g1064 1064
2 4117155 4126318 + Chy2G029440.1 Chy02g00677 677
7 17710286 17714369 + Chy7G141340.1 Chy07g01304 1304
3 18360288 18362945 + ClG42_03g0103600.10 Clacu03g1036 1036
3 18396327 18403665 - ClG42_03g0103800.10 Clacu03g1038 1038
3 19168090 19173576 + ClCG03G010590.1 Cla03g01012 1012
3 19204767 19213237 - ClCG03G010600.2 Cla03g01013 1013
7 2206266 2214377 + CmaCh07G005100.1 Cma07g00510 510
20 4181204 4182490 + CmaCh20G008730.1 Cma20g00873 873
2 11378519 11384524 + MELO3C010007.2.1 Cme02g00859 859
2 11385556 11390463 - MELO3C010008.2.1 Cme02g00860 860
2 12364157 12375445 + MELO3C010046.2.1 Cme02g00903 903
2 12381738 12392921 - MELO3C010048.2.1 Cme02g00904 904
4 4274350 4277037 + CmoCh04G008550.1 Cmo04g00855 855
7 2307932 2326676 + CmoCh07G005080.1 Cmo07g00508 508
3 18742968 18745625 + CmPI595203_03g016260.1 Cmu03g1626 1626
3 18779009 18786350 - CmPI595203_03g016280.1 Cmu03g1628 1628
1 57967179 57971042 + Conep01aG0176400.1 Cone1ag1701 1701
1 57974327 57978309 + Conep01aG0176500.1 Cone1ag1702 1702
1 57981556 57982386 + Conep01aG0176600.1 Cone1ag1703 1703
1 57982645 57985254 - Conep01aG0176700.1 Cone1ag1704 1704
1 57986181 57988197 + Conep01aG0176800.1 Cone1ag1705 1705
2 1460697 1461337 - Conep02aG0029100.1 Cone2ag0281 281
3 3084087 3087735 + Conep03aG0064200.1 Cone3ag0624 624
5 4036801 4040881 + Conep05aG0096900.1 Cone5ag0943 943
5 4041034 4043669 - Conep05aG0097000.1 Cone5ag0944 944
5 4048574 4049966 + Conep05aG0097100.1 Cone5ag0945 945
5 4050083 4053105 - Conep05aG0097200.1 Cone5ag0946 946
5 4058585 4061468 + Conep05aG0097400.1 Cone5ag0948 948
10 2808033 2809856 - Conep10aG0061300.1 Cone10ag0596 596
16 8559921 8561567 + Conep16aG0311800.1 Cone16ag0756 756
3 23326276 23328922 + CrPI670011_03g013280.1 Cre03g1328 1328
3 23367535 23374893 - CrPI670011_03g013290.1 Cre03g1329 1329
4 3460824 3463406 + CsaV3_4G005250.1 Csa04g00525 525
10 50844336 50849027 + Hsped.10g14180.1 Hepe10g1418 1418
1 5651700 5659953 + Lsi01G007070.1 Lsi01g00707 707
6 10864102 10880403 + Lsi06G006880.1 Lsi06g00688 688
6 10884609 10889220 + Lsi06G006890.1 Lsi06g00689 689
6 10918550 10926026 - Lsi06G006910.1 Lsi06g00691 691
5 18005902 18009320 + Tan0018430.1 Tan05g1355 1355
4 16994788 17002116 + Vvi4g872 Vvi4g872 872
4 17021548 17026738 + Vvi4g873 Vvi4g873 873
4 17037832 17057049 - Vvi4g874 Vvi4g874 874
4 17057536 17060722 - Vvi4g875 Vvi4g875 875
4 17078979 17094658 + Vvi4g876 Vvi4g876 876
4 17094879 17107573 - Vvi4g877 Vvi4g877 877
4 17127762 17132342 + Vvi4g878 Vvi4g878 878
4 17142612 17150031 + Vvi4g879 Vvi4g879 879
4 17151855 17154684 + Vvi4g880 Vvi4g880 880
4 17179502 17200164 + Vvi4g881 Vvi4g881 881
       

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