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
Vvi4g352 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g353 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g354 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g355 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g356 . . . . . . . Bma01g02489 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g357 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g358 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g359 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g360 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g361 Blo01g01711 . . . . Bpe02g00232 . Bma01g02490 . . Cma01g01593 . Car09g00478 . . . Cpe06g00414 . . . . . . . . . . . . . . Cone4ag1541 . . . Lsi04g02217 . . . . . . . . . . . Sed05g1617 Cmo01g01641 Cmo09g00537 . . Car01g01212 . . Cpe02g00384 Bhi09g02408 Tan01g3769 Cmetu04g2116 . Hepe01g2111 Mch11g0649 . . . . . . . . . . . Cme04g00306
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
9 65520437 65531453 - XM_039042984.1 Bhi09g02408 2408
1 56869106 56872409 + BLOR01711 Blo01g01711 1711
1 82633704 82634974 + Bma003367.1 Bma01g02489 2489
1 82639312 82646269 + Bma003368.3 Bma01g02490 2490
2 1586414 1593686 - Bpe008076.1 Bpe02g00232 232
1 11163561 11171423 - Carg21193-RA Car01g01212 1212
9 2668192 2674297 - Carg02960-RA Car09g00478 478
1 11001845 11009863 - CmaCh01G015930.1 Cma01g01593 1593
4 2382541 2391881 + MELO3C003593.2.1 Cme04g00306 306
4 13758218 13764947 + PI0015932.1 Cmetu04g2116 2116
1 12455169 12463062 - CmoCh01G016410.1 Cmo01g01641 1641
9 2549346 2557602 - CmoCh09G005370.1 Cmo09g00537 537
4 11892738 11902602 + Conep04aG0159300.1 Cone4ag1541 1541
2 2116826 2125029 + Cp4.1LG02g04990.1 Cpe02g00384 384
6 2362533 2369082 - Cp4.1LG06g04480.1 Cpe06g00414 414
1 85742671 85756256 - Hsped.01g21110.1 Hepe01g2111 2111
4 29225680 29236595 - Lsi04G022170.1 Lsi04g02217 2217
11 4226907 4234741 - MC11g0541 Mch11g0649 649
5 30072119 30081373 + Sed0003524.1 Sed05g1617 1617
1 102527891 102538266 - Tan0003334.1 Tan01g3769 3769
4 3401676 3401950 + Vvi4g352 Vvi4g352 352
4 3427249 3438858 + Vvi4g353 Vvi4g353 353
4 3439923 3441644 + Vvi4g354 Vvi4g354 354
4 3442164 3442402 - Vvi4g355 Vvi4g355 355
4 3443681 3465344 + Vvi4g356 Vvi4g356 356
4 3465416 3465608 + Vvi4g357 Vvi4g357 357
4 3466050 3471214 + Vvi4g358 Vvi4g358 358
4 3478069 3480238 + Vvi4g359 Vvi4g359 359
4 3503996 3512108 + Vvi4g360 Vvi4g360 360
4 3516690 3537291 + Vvi4g361 Vvi4g361 361
       

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