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
Vvi5g1229 Blo01g00198 . . Bda08g00155 . . . Bma05g01168 . . . . . . . . . . . . . . . . . . . . . . . . . Cone18ag0844 Cone11ag0664 . . . . . . . . Bpe05g00977 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1230 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1231 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1232 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1233 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1234 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1235 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1236 . . . . . Bpe14g01055 . . . . Cma06g01737 . . . Sed02g0957 . . Bhi01g03729 Tan10g1382 Cmetu07g1340 . Hepe05g1091 . Lcy11g0995 . . . . . . . . . . . . . . Cme07g01976 . Blo07g00110 Bda11g00474 . . . . Bma06g01436 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1237 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1238 Blo01g00197 Blo12g00260 Bda03g00976 . Bpe04g00903 . . . Cmo08g00204 Cmo17g00583 . . . . . . . . . . . . . . Cla06g00083 Cam06g0141 Cec06g0090 Cco06g0087 Clacu06g0090 Cmu06g0088 Cre06g0861 . . . . . . . . . . . . Bpe05g00976 . . . Sed09g0418 . . . Cma17g00603 Car08g00178 Car17g00570 Cpe12g00513 Cpe17g01091 Bhi12g02522 Tan06g1586 Cmetu11g0190 . Hepe03g1051 . . . . . . . . . . . . Cme11g02461
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 8815365 8827867 - Bda016987.1 Bda03g00976 976
8 1445376 1447352 - Bda024563.1 Bda08g00155 155
11 4983610 4984936 - Bda033033 Bda11g00474 474
1 95846375 95854673 - XM_039042790.1 Bhi01g03729 3729
12 78787192 78791162 - XM_039020281.1 Bhi12g02522 2522
1 2619799 2621848 - BLOR00197 Blo01g00197 197
1 2625603 2626664 + BLOR00198 Blo01g00198 198
7 1550333 1559532 - BLOR18042 Blo07g00110 110
12 15929557 15931906 + BLOR04279 Blo12g00260 260
5 50734983 50735612 + Bma022357.1 Bma05g01168 1168
6 51075372 51076510 - Bma024551.1 Bma06g01436 1436
4 6049220 6051535 - Bpe015567.2 Bpe04g00903 903
5 22607354 22612685 - Bpe018388.1 Bpe05g00976 976
5 22614500 22616503 + Bpe018389.1 Bpe05g00977 977
14 7901769 7907124 - Bpe014429.1 Bpe14g01055 1055
6 3316974 3320256 - CaPI482276_06g001410.1 Cam06g0141 141
8 1098345 1101804 - Carg05024-RA Car08g00178 178
17 5324122 5325908 + Carg28163-RA Car17g00570 570
6 823468 826803 + CcPI632755_06g000870.1 Cco06g0087 87
6 849407 852739 + CePI673135_06g000900.1 Cec06g0090 90
6 1030671 1033910 + ClG42_06g0009000.10 Clacu06g0090 90
6 857171 860493 + ClCG06G000890.1 Cla06g00083 83
6 10622119 10624585 - CmaCh06G017370.1 Cma06g01737 1737
17 5079298 5081715 + CmaCh17G006030.1 Cma17g00603 603
7 24884149 24889768 - MELO3C017801.2.1 Cme07g01976 1976
11 31305727 31309427 - MELO3C022452.2.1 Cme11g02461 2461
7 2003106 2009462 + PI0016739.1 Cmetu07g1340 1340
11 668876 672429 + PI0014306.1 Cmetu11g0190 190
8 1189194 1192772 - CmoCh08G002040.1 Cmo08g00204 204
17 6100653 6102521 + CmoCh17G005830.1 Cmo17g00583 583
6 820206 823445 + CmPI595203_06g000880.1 Cmu06g0088 88
11 4431038 4435175 + Conep11aG0068100.1 Cone11ag0664 664
18 5764174 5768474 - Conep18aG0087000.1 Cone18ag0844 844
12 5094584 5096640 + Cp4.1LG12g05050.1 Cpe12g00513 513
17 8268654 8272073 - Cp4.1LG17g10940.1 Cpe17g01091 1091
6 1916615 1919978 + CrPI670011_06g008610.1 Cre06g0861 861
3 57624635 57628776 + Hsped.03g10510.1 Hepe03g1051 1051
5 53040391 53046845 - Hsped.05g10910.1 Hepe05g1091 1091
11 30321427 30329517 + Maker00030867 Lcy11g0995 995
2 47101711 47108235 + Sed0001495.1 Sed02g0957 957
9 4143143 4147283 - Sed0022515.1 Sed09g0418 418
6 25406435 25410696 - Tan0020467.1 Tan06g1586 1586
10 17730552 17739175 + Tan0009567.1 Tan10g1382 1382
5 22500902 22503567 + Vvi5g1229 Vvi5g1229 1229
5 22523022 22538810 + Vvi5g1230 Vvi5g1230 1230
5 22545645 22549350 + Vvi5g1231 Vvi5g1231 1231
5 22549435 22551788 - Vvi5g1232 Vvi5g1232 1232
5 22562077 22564255 + Vvi5g1233 Vvi5g1233 1233
5 22567121 22573980 - Vvi5g1234 Vvi5g1234 1234
5 22578398 22579963 - Vvi5g1235 Vvi5g1235 1235
5 22582036 22588193 - Vvi5g1236 Vvi5g1236 1236
5 22606843 22611712 + Vvi5g1237 Vvi5g1237 1237
5 22616260 22620249 + Vvi5g1238 Vvi5g1238 1238
       

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