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
Vvi5g979 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g980 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g981 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g982 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe05g01081 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g983 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme06g00865 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme11g02227
Vvi5g984 . . . . Bpe04g01004 . . . . . Cma06g01743 . Car06g01478 . . Cpe08g00119 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g985 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g986 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed01g4000 . . . . . . . . Bhi12g02125 Tan06g1925 Cmetu09g0227 Lac12g1461 Hepe03g0639 . Lcy13g0912 . . . . . . . Lsi09g01624 . . .
Vvi5g987 . . . . . . . . Cmo08g00108 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma02g01013 . . . . . . Car08g00086 . . Cpe17g01010 . . . . . . . . . . . . . . . . . .
Vvi5g988 . Blo12g00109 Bda03g01133 . Bpe04g01076 . Bma04g01169 . Cmo08g00975 Cmo17g00088 . . . . . . . . . . . . . . Cla06g00783 Cam06g0836 Cec06g0851 Cco06g0861 Clacu06g0840 Cmu06g0811 Cre06g1592 . . . . . Csa02g00899 . . . . . Bda13g00306 . . . . Sed09g0166 . . Cma08g01002 Cma17g00081 Car08g00884 Car17g00076 Cpe12g00075 Cpe17g00269 Bhi12g01468 Tan06g2267 Cmetu05g1273 . . . . . . . . . . . Lsi09g01115 . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 11932993 11937468 - Bda017183.1 Bda03g01133 1133
13 3895062 3898171 + Bda001196.1 Bda13g00306 306
12 47567326 47574576 - XM_039051087.1 Bhi12g01468 1468
12 66277665 66284048 + XM_039018868.1 Bhi12g02125 2125
12 7915852 7925119 + BLOR04128 Blo12g00109 109
2 51288901 51289194 - Bma015830.1 Bma02g01013 1013
4 30210055 30214564 + Bma019905.1 Bma04g01169 1169
4 7013803 7015248 + Bpe015671.1 Bpe04g01004 1004
4 8241063 8245524 - Bpe015748.1 Bpe04g01076 1076
5 23291457 23298208 + Bpe018496.1 Bpe05g01081 1081
6 11801263 11807995 + CaPI482276_06g008360.1 Cam06g0836 836
6 10446964 10456149 + Carg23330-RA Car06g01478 1478
8 526081 528324 + Carg04929-RA Car08g00086 86
8 5927431 5933932 + Carg11040-RA Car08g00884 884
17 439428 444561 - Carg10156-RA Car17g00076 76
6 10618927 10625810 + CcPI632755_06g008610.1 Cco06g0861 861
6 10681807 10688607 + CePI673135_06g008510.1 Cec06g0851 851
6 10437982 10444625 + ClG42_06g0084000.10 Clacu06g0840 840
6 10756218 10763215 + ClCG06G008030.1 Cla06g00783 783
6 10644563 10655273 + CmaCh06G017430.1 Cma06g01743 1743
8 6289986 6295890 + CmaCh08G010020.1 Cma08g01002 1002
17 406935 412820 - CmaCh17G000810.1 Cma17g00081 81
6 5925532 5931182 + MELO3C006784.2.1 Cme06g00865 865
11 29499556 29502640 + MELO3C021144.2.1 Cme11g02227 2227
5 10599438 10606203 - PI0003037.1 Cmetu05g1273 1273
9 3159304 3162987 - PI0019762.1 Cmetu09g0227 227
8 567199 569731 + CmoCh08G001080.1 Cmo08g00108 108
8 6341071 6347168 + CmoCh08G009750.1 Cmo08g00975 975
17 472643 479010 - CmoCh17G000880.1 Cmo17g00088 88
6 10254514 10261199 + CmPI595203_06g008110.1 Cmu06g0811 811
8 771146 777665 - Cp4.1LG08g05570.1 Cpe08g00119 119
12 447150 454260 - Cp4.1LG12g00760.1 Cpe12g00075 75
17 1775864 1782230 - Cp4.1LG17g03050.1 Cpe17g00269 269
17 7663505 7666086 + Cp4.1LG17g10080.1 Cpe17g01010 1010
6 11325533 11334205 + CrPI670011_06g015920.1 Cre06g1592 1592
2 8371045 8378010 - CsaV3_2G011150.1 Csa02g00899 899
3 13210025 13221865 + Hsped.03g06390.1 Hepe03g0639 639
12 26519509 26531271 - Lag0015833.1 Lac12g1461 1461
13 16607827 16619799 + Maker00026352 Lcy13g0912 912
9 17883804 17891211 - Lsi09G011150.1 Lsi09g01115 1115
9 24456632 24461245 + Lsi09G016240.1 Lsi09g01624 1624
1 69055964 69059452 + Sed0004190.2 Sed01g4000 4000
9 1291269 1299662 - Sed0019285.2 Sed09g0166 166
6 57701137 57713485 - Tan0015512.1 Tan06g1925 1925
6 73639715 73646346 - Tan0016103.1 Tan06g2267 2267
5 16816046 16822301 - Vvi5g979 Vvi5g979 979
5 16833127 16833499 - Vvi5g980 Vvi5g980 980
5 16854401 16867092 + Vvi5g981 Vvi5g981 981
5 16868287 16900139 - Vvi5g982 Vvi5g982 982
5 16908331 16927779 - Vvi5g983 Vvi5g983 983
5 16931579 16942505 - Vvi5g984 Vvi5g984 984
5 16958915 16960436 + Vvi5g985 Vvi5g985 985
5 16964100 16966907 - Vvi5g986 Vvi5g986 986
5 16975517 16977637 + Vvi5g987 Vvi5g987 987
5 16983725 16990038 - Vvi5g988 Vvi5g988 988
       

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