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
Vvi4g242 . . . . . . . . . . Cma01g01586 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo01g01634 . Cma09g00540 . . . . Cpe02g00392 . . . . . . . . . . . . . . . . . Cme04g00318
Vvi4g243 . . . . . . . . . . . . . . Sed03g1519 . . Bhi04g01112 Tan02g2600 Cmetu03g0813 . Hepe10g0329 . Lcy13g1703 . . . . . . . . . . . . . . Cme03g01709 . . . . . . . . . . . . . . . . . . . . . . . . Cla08g01253 Cam08g1710 Cec08g1290 Cco08g1411 Clacu08g1407 . Cre08g1192 Lsi08g01115 Csa02g02306 . .
Vvi4g244 . . . . . . . . . . . . . . . . . Bhi04g01111 . . . . . Lcy13g1363 . . . . . . . . . . Cone20ag0623 . . . Cme03g01708 . . . . Bpe14g00541 . . . . . . . . . . . . . . . . . . . Cla08g01254 . . . . . . Lsi08g01116 Csa02g02307 . Cme04g00319
Vvi4g245 . . . . . Bpe02g00227 . . . . Cma01g01585 . . . . . . Bhi04g01107 Tan02g2604 . . . . . . . . . . . . . . . . . . . Cme03g01706 . . . . . . . . . Cmo01g01633 . Cma09g00539 . . . . . . . . . . . . Cla08g01256 . . . . . . Lsi08g01117 Csa02g02310 . Cme04g00320
Vvi4g246 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g247 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone20ag0627 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g248 . . . . . Bpe02g00226 . . . . Cma01g01584 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo01g01631 . Cma09g00537 . . . . . . . . . . . . . . . . . . . . . . Cme04g00321
Vvi4g249 . . . . . Bpe02g00220 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g250 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car01g01137 . . . . . . . . . . . . . . . . . . . . .
Vvi4g251 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 27122321 27127807 - XM_039030085.1 Bhi04g01107 1107
4 27148831 27155274 - XM_039030431.1 Bhi04g01111 1111
4 27191260 27196374 + XM_039028435.1 Bhi04g01112 1112
2 1529844 1531959 + Bpe008066.1 Bpe02g00220 220
2 1559948 1571752 + Bpe008072.1 Bpe02g00226 226
2 1572515 1575485 - Bpe008073.1 Bpe02g00227 227
14 4701524 4704125 + Bpe007191.2 Bpe14g00541 541
8 23398255 23408896 - CaPI482276_08g017100.1 Cam08g1710 1710
1 10528698 10534573 - Carg24712-RA Car01g01137 1137
8 26035507 26046059 - CcPI632755_08g014110.1 Cco08g1411 1411
8 24879870 24890262 - CePI673135_08g012900.1 Cec08g1290 1290
8 24149714 24160286 - ClG42_08g0140700.10 Clacu08g1407 1407
8 25451778 25456938 - ClCG08G012550.2 Cla08g01253 1253
8 25459986 25465572 + ClCG08G012560.1 Cla08g01254 1254
8 25473806 25487201 + ClCG08G012580.1 Cla08g01256 1256
1 10927593 10935387 + CmaCh01G015840.1 Cma01g01584 1584
1 10935651 10941910 - CmaCh01G015850.1 Cma01g01585 1585
1 10943665 10946054 - CmaCh01G015860.1 Cma01g01586 1586
9 2394093 2408201 + CmaCh09G005370.1 Cma09g00537 537
9 2408437 2413525 - CmaCh09G005390.1 Cma09g00539 539
9 2414500 2420338 - CmaCh09G005400.1 Cma09g00540 540
3 25705404 25707408 - MELO3C011177.2.1 Cme03g01706 1706
3 25715727 25719526 - MELO3C011175.2.1 Cme03g01708 1708
3 25721380 25723303 + MELO3C011174.2.1 Cme03g01709 1709
4 2493520 2496187 + MELO3C003604.2.1 Cme04g00318 318
4 2496731 2500638 + MELO3C003605.2.1 Cme04g00319 319
4 2501637 2507092 + MELO3C003606.2.1 Cme04g00320 320
4 2530797 2551424 - MELO3C003609.2.1 Cme04g00321 321
3 3718274 3721788 - PI0016569.2 Cmetu03g0813 813
1 12389885 12391638 + CmoCh01G016310.1 Cmo01g01631 1631
1 12395026 12401462 - CmoCh01G016330.1 Cmo01g01633 1633
1 12402863 12404688 - CmoCh01G016340.1 Cmo01g01634 1634
20 3723995 3726618 + Conep20aG0064100.1 Cone20ag0623 623
20 3745018 3749133 - Conep20aG0064500.1 Cone20ag0627 627
2 2176128 2179140 + Cp4.1LG02g04810.1 Cpe02g00392 392
8 25196293 25200566 - CrPI670011_08g011920.1 Cre08g1192 1192
2 20573767 20576209 - CsaV3_2G031250.1 Csa02g02306 2306
2 20577187 20580919 + CsaV3_2G031260.1 Csa02g02307 2307
2 20598002 20602959 + CsaV3_2G031290.1 Csa02g02310 2310
10 3531327 3546651 + Hsped.10g03290.1 Hepe10g0329 329
13 31701227 31708181 - Maker00025703 Lcy13g1363 1363
13 36015940 36019083 + Maker00033862 Lcy13g1703 1703
8 19789873 19794395 - Lsi08G011150.1 Lsi08g01115 1115
8 19798175 19811107 + Lsi08G011160.1 Lsi08g01116 1116
8 19813869 19825354 + Lsi08G011170.1 Lsi08g01117 1117
3 9686906 9691421 - Sed0011404.1 Sed03g1519 1519
2 94638255 94647608 - Tan0010023.1 Tan02g2600 2600
2 94669874 94673483 + Tan0005031.1 Tan02g2604 2604
4 2385159 2387738 + Vvi4g242 Vvi4g242 242
4 2388544 2390093 - Vvi4g243 Vvi4g243 243
4 2391521 2397246 + Vvi4g244 Vvi4g244 244
4 2397245 2404845 + Vvi4g245 Vvi4g245 245
4 2404930 2406318 - Vvi4g246 Vvi4g246 246
4 2407999 2428839 - Vvi4g247 Vvi4g247 247
4 2431146 2462039 - Vvi4g248 Vvi4g248 248
4 2470500 2472631 + Vvi4g249 Vvi4g249 249
4 2476207 2484277 - Vvi4g250 Vvi4g250 250
4 2484775 2491888 - Vvi4g251 Vvi4g251 251
       

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