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
Vvi18g850 . Blo12g00927 . Bda03g00236 . . Bma04g00188 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g01616 Csa03g04161 Chy04g00555 . . . . . . . . . . . Cmo09g00183 . . . . . . Bhi09g02035 . . . . . . Cla05g01983 . . . . . . . . . Cme04g00662
Vvi18g851 . Blo12g00926 . . . . . . . . . Cma09g00186 . . . . . . . . . . . . . . . . . . . . . . . . Csa03g04162 Chy04g00553 . . . . . . . . . . Cmo01g01941 . . . . . . . Bhi09g02039 . . . . . . Cla05g01982 . . . . . . . . . Cme04g00661
Vvi18g852 . . . Bda03g00237 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g01618 Csa03g04163 Chy04g00552 . . . . . . . . . . . Cmo09g00180 . . . . . . Bhi09g02046 . . . . . . Cla05g01981 . . . . . . . . . Cme04g00654
Vvi18g853 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g854 . . Bda01g00557 . . . . . . . . Cma09g00185 . . . . . . . . . . . . . . . . . . . . . . . Lsi04g01620 Csa03g04164 Chy04g00550 . . . . . . . . . . Cmo01g01942 . . . . . . . . . . . . . . . . . . . . . . . . Cme04g00651
Vvi18g855 . Blo12g00924 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g01622 Csa03g04165 . . . . . . . . . . . . . . . . . . . Bhi09g02052 . . . . . . Cla05g01973 . . . . . . . . . Cme04g00638
Vvi18g856 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g857 . Blo12g00923 Bda01g00555 Bda03g00240 Bpe02g00413 . . . . . . Cma09g00183 . . . . . . . . . . . . . . . . . . . . . . . Lsi04g01624 Csa03g04166 Chy04g00549 . . . . . . . . . . Cmo01g01943 Cmo09g00179 . . . Car09g00162 . . Bhi09g02056 . . . . . . . . . . . . . . . . Cme04g00637
Vvi18g858 . Blo12g00922 . Bda03g00241 . . Bma04g00191 . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1876 . . . Lsi04g01627 Csa03g04169 Chy04g00548 . . . . . . . . . . . Cmo09g00178 . . . . . . Bhi09g02057 . . . . . . . . . . . . . . . . .
Vvi18g859 . Blo12g00921 . Bda03g00242 . Bpe04g00201 Bma04g00192 . . . . Cma09g00181 . . . Cpe06g00130 . . . . . . . . . . . . . . . Cone4ag1878 Cone7ag1787 . . Lsi04g01631 Csa03g04172 Chy04g00545 . . . . . . Bpe05g00345 . . . . Cmo09g00177 . . . Car09g00161 . . . . . . . . . Cla05g01971 . . . . . . . . . Cme04g00634
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 32480229 32481885 - Bda002569.1 Bda01g00555 555
1 32502486 32504278 - Bda002571.1 Bda01g00557 557
3 1825868 1827413 - Bda016179.1 Bda03g00236 236
3 1834645 1836418 - Bda016180.1 Bda03g00237 237
3 1910604 1912259 + Bda016183.1 Bda03g00240 240
3 1928684 1930464 + Bda016184.1 Bda03g00241 241
3 1931658 1935534 + Bda016185.1 Bda03g00242 242
9 57203416 57206752 + XM_039042616.1 Bhi09g02035 2035
9 57277052 57279747 + XM_039041401.1 Bhi09g02039 2039
9 57806242 57815388 - XM_039043811.1 Bhi09g02046 2046
9 58171240 58174156 + XM_039041053.1 Bhi09g02052 2052
9 58486504 58488324 - XM_039043456.1 Bhi09g02056 2056
9 58607632 58609695 - XM_039041270.1 Bhi09g02057 2057
12 27373890 27377890 - BLOR04940 Blo12g00921 921
12 27405958 27407633 - BLOR04941 Blo12g00922 922
12 27421071 27422732 - BLOR04942 Blo12g00923 923
12 27426084 27427745 - BLOR04943 Blo12g00924 924
12 27455219 27456880 + BLOR04945 Blo12g00926 926
12 27460601 27462941 - BLOR04946 Blo12g00927 927
4 1642580 1644060 - Bma018637.1 Bma04g00188 188
4 1696104 1712662 + Bma018640.1 Bma04g00191 191
4 1714569 1718507 + Bma018641.1 Bma04g00192 192
2 2687103 2688760 - Bpe008254.1 Bpe02g00413 413
4 1363947 1367788 + Bpe014919.1 Bpe04g00201 201
5 17406581 17409193 - Bpe017760.2 Bpe05g00345 345
9 758697 765492 - Carg08745-RA Car09g00161 161
9 765120 769480 - Carg08746-RA Car09g00162 162
4 5499304 5503423 - Chy4G072630.1 Chy04g00545 545
4 5586023 5588716 - Chy4G072660.1 Chy04g00548 548
4 5605933 5607841 - Chy4G072670.1 Chy04g00549 549
4 5634131 5637290 + Chy4G072680.1 Chy04g00550 550
4 5660245 5662650 - Chy4G072700.1 Chy04g00552 552
4 5677724 5678832 - Chy4G072710.1 Chy04g00553 553
4 5698404 5704012 + Chy4G072730.1 Chy04g00555 555
5 31514001 31519182 - ClCG05G019280.2 Cla05g01971 1971
5 31531719 31556403 - ClCG05G019300.1 Cla05g01973 1973
5 31623812 31627119 - ClCG05G019340.1 Cla05g01981 1981
5 31638218 31640203 - ClCG05G019350.2 Cla05g01982 1982
5 31648354 31651356 - ClCG05G019360.1 Cla05g01983 1983
9 763087 767299 - CmaCh09G001810.1 Cma09g00181 181
9 770192 771820 - CmaCh09G001830.1 Cma09g00183 183
9 775094 777828 - CmaCh09G001850.1 Cma09g00185 185
9 778159 779676 - CmaCh09G001860.1 Cma09g00186 186
4 6199318 6204483 - MELO3C003898.2.1 Cme04g00634 634
4 6323767 6326765 - MELO3C003902.2.1 Cme04g00637 637
4 6323797 6326548 - MELO3C003899.2.1 Cme04g00638 638
4 6588915 6593509 + MELO3C026486.2.1 Cme04g00651 651
4 6652981 6656558 + MELO3C026488.2.1 Cme04g00654 654
4 6859592 6861708 + MELO3C026491.2.1 Cme04g00661 661
4 6890499 6893155 + MELO3C026492.2.1 Cme04g00662 662
1 13838099 13840035 + CmoCh01G019410.1 Cmo01g01941 1941
1 13841183 13843091 + CmoCh01G019420.1 Cmo01g01942 1942
1 13844429 13846252 + CmoCh01G019430.1 Cmo01g01943 1943
9 788703 792889 - CmoCh09G001770.1 Cmo09g00177 177
9 792951 797509 - CmoCh09G001780.1 Cmo09g00178 178
9 798867 800572 - CmoCh09G001790.1 Cmo09g00179 179
9 801207 805655 - CmoCh09G001800.1 Cmo09g00180 180
9 816745 818608 - CmoCh09G001830.1 Cmo09g00183 183
4 13422523 13424360 + Conep04aG0193500.1 Cone4ag1876 1876
4 13429540 13433234 + Conep04aG0193700.1 Cone4ag1878 1878
7 11729437 11730823 + Conep07aG0184000.1 Cone7ag1787 1787
6 641243 646416 - Cp4.1LG06g01280.1 Cpe06g00130 130
3 36557638 36560240 + CsaV3_3G044670.1 Csa03g04161 4161
3 36561588 36566219 - CsaV3_3G044680.1 Csa03g04162 4162
3 36571830 36574000 + CsaV3_3G044690.1 Csa03g04163 4163
3 36576709 36579608 + CsaV3_3G044700.1 Csa03g04164 4164
3 36583366 36586076 + CsaV3_3G044710.1 Csa03g04165 4165
3 36594231 36596608 + CsaV3_3G044720.1 Csa03g04166 4166
3 36603782 36606536 + CsaV3_3G044750.1 Csa03g04169 4169
3 36622788 36626898 + CsaV3_3G044780.1 Csa03g04172 4172
4 23651418 23654689 + Lsi04G016160.1 Lsi04g01616 1616
4 23666265 23671105 + Lsi04G016180.1 Lsi04g01618 1618
4 23688152 23690139 + Lsi04G016200.1 Lsi04g01620 1620
4 23705834 23708632 + Lsi04G016220.1 Lsi04g01622 1622
4 23738506 23740949 + Lsi04G016240.1 Lsi04g01624 1624
4 23764211 23766763 + Lsi04G016270.1 Lsi04g01627 1627
4 23798960 23806421 + Lsi04G016310.1 Lsi04g01631 1631
18 9762402 9784663 + Vvi18g850 Vvi18g850 850
18 9787514 9794746 + Vvi18g851 Vvi18g851 851
18 9794861 9802663 + Vvi18g852 Vvi18g852 852
18 9802984 9804462 - Vvi18g853 Vvi18g853 853
18 9804912 9814683 + Vvi18g854 Vvi18g854 854
18 9816438 9818721 + Vvi18g855 Vvi18g855 855
18 9819459 9824402 + Vvi18g856 Vvi18g856 856
18 9828011 9838662 + Vvi18g857 Vvi18g857 857
18 9846631 9858576 + Vvi18g858 Vvi18g858 858
18 9884659 9889936 + Vvi18g859 Vvi18g859 859
       

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