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
Vvi2g382 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g383 . . . Bda08g00528 . . . . . Cmo16g00593 . . . . . Cpe14g00457 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma16g00541 . . . . . . . . . . . . . . . . . . . . . .
Vvi2g384 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g385 . . . . . . . . . . . Cma15g01210 . . . . . . . . . . . . . . . . . . . . . . . . . Chy09g01195 . . . . . . . . . . . Cmo15g01274 . . . . . . . . . . . . . . . . . . . . . . . Cme09g01731
Vvi2g386 . . . . . . . . . . . Cma15g01208 . . . . . . . . . . . . . . . . . . . . . . . . . Chy09g01194 . . . . . . . . . . . Cmo15g01273 . . . . . . . . . . . . . . . . . . . . Lsi09g00292 . . Cme09g01730
Vvi2g387 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g388 . . . . . . . . . . . Cma15g01207 . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00314 . . . . . . . Bpe11g00682 . . . . Cmo15g01272 . . . . . Cpe13g00169 . . . . . . . Cla01g00291 Cam01g0302 Cec01g0294 Cco01g0309 Clacu01g0302 Cmu01g0287 Cre09g2220 Lsi09g00294 . . Cme09g01729
Vvi2g389 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g390 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g391 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 5278490 5280605 + Bda024983.1 Bda08g00528 528
11 5246196 5246873 - Bpe004038.1 Bpe11g00682 682
1 3371306 3372069 - CaPI482276_01g003020.1 Cam01g0302 302
1 3008896 3009658 - CcPI632755_01g003090.1 Cco01g0309 309
1 2976622 2977385 - CePI673135_01g002940.1 Cec01g0294 294
9 14126169 14130082 + Chy9G169100.1 Chy09g01194 1194
9 14132126 14134851 + Chy9G169110.1 Chy09g01195 1195
1 2987440 2988203 - ClG42_01g0030200.10 Clacu01g0302 302
1 3060780 3061689 - ClCG01G003020.2 Cla01g00291 291
15 7635279 7635947 + CmaCh15G012070.1 Cma15g01207 1207
15 7637101 7637766 + CmaCh15G012080.1 Cma15g01208 1208
15 7648476 7651255 + CmaCh15G012100.1 Cma15g01210 1210
16 2769550 2783030 - CmaCh16G005410.1 Cma16g00541 541
9 21886385 21887347 + MELO3C005641.2.1 Cme09g01729 1729
9 21889717 21890793 + MELO3C005642.2.1 Cme09g01730 1730
9 21894879 21895866 + MELO3C005643.2.1 Cme09g01731 1731
15 8705503 8707463 + CmoCh15G012720.1 Cmo15g01272 1272
15 8708248 8710760 + CmoCh15G012730.1 Cmo15g01273 1273
15 8711302 8712935 + CmoCh15G012740.1 Cmo15g01274 1274
16 2870211 2884508 - CmoCh16G005930.1 Cmo16g00593 593
1 2943335 2944098 - CmPI595203_01g002870.1 Cmu01g0287 287
13 1344053 1351764 - Cp4.1LG13g01750.1 Cpe13g00169 169
14 2875980 2881476 - Cp4.1LG14g02610.1 Cpe14g00457 457
9 41366922 41367684 + CrPI670011_09g022200.1 Cre09g2220 2220
5 1961108 1962482 - CsaV3_5G003140.1 Csa05g00314 314
9 3032278 3033587 - Lsi09G002920.1 Lsi09g00292 292
9 3040586 3041751 - Lsi09G002940.1 Lsi09g00294 294
2 3727274 3728813 - Vvi2g382 Vvi2g382 382
2 3729207 3733046 - Vvi2g383 Vvi2g383 383
2 3737144 3744356 - Vvi2g384 Vvi2g384 384
2 3754954 3774888 + Vvi2g385 Vvi2g385 385
2 3775418 3776265 + Vvi2g386 Vvi2g386 386
2 3790320 3791061 + Vvi2g387 Vvi2g387 387
2 3796864 3797720 + Vvi2g388 Vvi2g388 388
2 3799836 3800512 + Vvi2g389 Vvi2g389 389
2 3801947 3805389 - Vvi2g390 Vvi2g390 390
2 3821888 3822828 + Vvi2g391 Vvi2g391 391
       

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