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
Vvi5g229 . . . . . Bpe14g01079 . . . . . . Car06g01343 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma02g00946 . . Cmo06g01576 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g230 . . . . . . . . . . . Cma14g01569 . Car14g01383 . . Cpe03g01311 Bhi01g01116 . . . . . . . . . . . . . . Cone15ag0699 . . Lsi05g01397 . . Cme06g00821 . . . . . . . . . . Cmo14g01603 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g231 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone11ag0715 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g232 . . . Bda08g00377 . . . . . . . . . . . . . . . . . . . . Cla06g00440 Cam06g0465 Cec06g0471 Cco06g0470 Clacu06g0452 Cmu06g0453 Cre06g1229 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g233 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g234 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g235 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0730 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi09g01477 . . .
Vvi5g236 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone15ag0741 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi09g01476 . . .
Vvi5g237 . . . . . . . . . . . . Car06g01345 . . Cpe08g00135 Cpe03g01306 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g238 . . . . . Bpe14g01078 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda13g00237 . . Bma02g00953 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 3858565 3863025 - Bda024819.1 Bda08g00377 377
13 2957285 2965002 + Bda001117.1 Bda13g00237 237
1 21808831 21812648 + XM_039021395.1 Bhi01g01116 1116
2 49337514 49343982 - Bma015740.1 Bma02g00946 946
2 49543564 49551185 + Bma015750.1 Bma02g00953 953
14 8073258 8081074 - Bpe014452.1 Bpe14g01078 1078
14 8087953 8093459 + Bpe014453.1 Bpe14g01079 1079
6 6785854 6793440 + CaPI482276_06g004650.1 Cam06g0465 465
6 9628898 9634769 - Carg25652-RA Car06g01343 1343
6 9649713 9651428 + Carg25654-RA Car06g01345 1345
14 11636042 11640530 - Carg19604-RA Car14g01383 1383
6 5184741 5192476 + CcPI632755_06g004700.1 Cco06g0470 470
6 5314867 5322495 + CePI673135_06g004710.1 Cec06g0471 471
6 5320742 5328475 + ClG42_06g0045200.10 Clacu06g0452 452
6 5357290 5364925 + ClCG06G004710.2 Cla06g00440 440
14 11759598 11762444 - CmaCh14G015690.1 Cma14g01569 1569
6 5624870 5627883 + MELO3C006743.2.1 Cme06g00821 821
6 11088080 11094229 - CmoCh06G015760.1 Cmo06g01576 1576
14 12683302 12687555 - CmoCh14G016030.1 Cmo14g01603 1603
6 5123327 5130928 + CmPI595203_06g004530.1 Cmu06g0453 453
11 4928701 4931246 - Conep11aG0073300.1 Cone11ag0715 715
14 4060717 4064408 + Conep14aG0074600.1 Cone14ag0730 730
15 3802527 3804935 - Conep15aG0071300.1 Cone15ag0699 699
15 4253021 4257200 + Conep15aG0075600.1 Cone15ag0741 741
3 10585651 10590361 - Cp4.1LG03g12110.1 Cpe03g01306 1306
3 10613913 10618183 - Cp4.1LG03g11980.1 Cpe03g01311 1311
8 874056 876996 - Cp4.1LG08g05420.1 Cpe08g00135 135
6 6179212 6186675 + CrPI670011_06g012290.1 Cre06g1229 1229
5 21810658 21812588 - Lsi05G013970.1 Lsi05g01397 1397
9 22800506 22801048 - Lsi09G014760.1 Lsi09g01476 1476
9 22814717 22822673 - Lsi09G014770.1 Lsi09g01477 1477
5 2390890 2394802 - Vvi5g229 Vvi5g229 229
5 2399528 2403126 + Vvi5g230 Vvi5g230 230
5 2403216 2408128 + Vvi5g231 Vvi5g231 231
5 2410854 2411857 + Vvi5g232 Vvi5g232 232
5 2411937 2413331 + Vvi5g233 Vvi5g233 233
5 2414687 2417615 - Vvi5g234 Vvi5g234 234
5 2419710 2422722 - Vvi5g235 Vvi5g235 235
5 2429183 2432197 + Vvi5g236 Vvi5g236 236
5 2435657 2438610 - Vvi5g237 Vvi5g237 237
5 2439088 2450560 + Vvi5g238 Vvi5g238 238
       

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