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
Vvi4g82 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g83 . . Bda01g00625 . . . . . . . . . . . Sed08g1775 . . Bhi04g00529 Tan02g1620 Cmetu03g0019 . Hepe08g1401 . Lcy13g2193 . . . . . . . . . . . . . . . . . Bda01g01046 . . . Bma01g00919 Bma02g00351 . . . . . . . . . . . . . . . . . . . . . . . Lsi08g01587 . . .
Vvi4g84 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo17g00284 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy03g01655 .
Vvi4g85 Blo01g01460 Blo12g01017 Bda01g00627 . Bpe02g01543 . . Bma01g02209 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone20ag0275 . . . . . . . . . . . . . . . . . Car01g01342 . . Cpe02g00266 . . . . . . . . . . . . . . . . . .
Vvi4g86 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g01419 . . . . . . . . Bpe04g00123 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g87 . . . Bda03g00139 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda01g01076 . . . . . . . . Cma09g00342 . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g88 . . . . . . . . Cmo05g00096 . . Cma05g00089 . . . . . . . . . . . . . . . . . . . . . . Cone20ag0274 . . . . . . . Bda13g01599 . . . . . . . . . . Car05g00076 Cpe11g00071 . . . . . . . . . . . . . . . Lsi08g01589 Csa02g01831 . .
Vvi4g89 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g90 Blo01g01462 . . . . . Bma04g00124 . . Cmo12g00580 . . . . . Cpe07g00561 . . . . . . . . . . . . . . . . . . Cone20ag0273 . . . . . . . . . . . . . . . . Cma12g00641 . Car05g00075 Cpe11g00070 . . . . . . . . . . . . . . . Lsi08g01591 . Chy03g01656 .
Vvi4g91 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe02g00264 . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 33257992 33260328 + Bda032909 Bda01g00625 625
1 33266195 33268002 - Bda002648.1 Bda01g00627 627
1 44575451 44577963 - Bda003211.1 Bda01g01046 1046
1 45403356 45410705 + Bda003254.1 Bda01g01076 1076
3 1205149 1206728 - Bda016080.1 Bda03g00139 139
13 39540740 39541861 - Bda000470.1 Bda13g01599 1599
4 13027789 13031518 - XM_039030778.1 Bhi04g00529 529
1 53769300 53771160 + BLOR01460 Blo01g01460 1460
1 53797698 53799827 - BLOR01462 Blo01g01462 1462
12 28111644 28113705 - BLOR05036 Blo12g01017 1017
17 3011091 3017966 + BLOR16105 Blo17g00284 284
1 8963981 8978761 + Bma001150.3 Bma01g00919 919
1 79004323 79006139 + Bma003055.1 Bma01g02209 2209
2 5634615 5637100 + Bma014822.1 Bma02g00351 351
4 990477 992748 - Bma018572.1 Bma04g00124 124
2 18514597 18515977 - Bpe009395.1 Bpe02g01543 1543
4 835877 838563 - Bpe014843.2 Bpe04g00123 123
1 11925877 11928711 + Carg10695-RA Car01g01342 1342
5 395205 397243 + Carg11931-RA Car05g00075 75
5 398325 399897 - Carg11930-RA Car05g00076 76
3 18352236 18354312 - Chy3G066350.1 Chy03g01655 1655
3 18355708 18358111 - Chy3G066360.1 Chy03g01656 1656
5 384437 385977 - CmaCh05G000890.1 Cma05g00089 89
9 1407434 1411966 + CmaCh09G003420.1 Cma09g00342 342
12 3411411 3414278 + CmaCh12G006410.1 Cma12g00641 641
3 552952 555662 + PI0018043.1 Cmetu03g0019 19
5 393383 395093 - CmoCh05G000960.1 Cmo05g00096 96
12 3589821 3592918 + CmoCh12G005800.1 Cmo12g00580 580
20 1212621 1215297 + Conep20aG0028400.1 Cone20ag0273 273
20 1220134 1222471 + Conep20aG0028500.1 Cone20ag0274 274
20 1221713 1223603 - Conep20aG0028600.1 Cone20ag0275 275
2 1367373 1370620 + Cp4.1LG02g06120.1 Cpe02g00264 264
2 1377504 1381318 - Cp4.1LG02g06000.1 Cpe02g00266 266
7 3728764 3731823 + Cp4.1LG07g06050.1 Cpe07g00561 561
11 384510 389038 + Cp4.1LG11g00300.1 Cpe11g00070 70
11 386896 390077 - Cp4.1LG11g00150.1 Cpe11g00071 71
2 17542329 17543717 - CsaV3_2G025510.1 Csa02g01831 1831
8 16531412 16535157 - Hsped.08g14010.1 Hepe08g1401 1401
13 40858276 40864099 - Maker00025449 Lcy13g2193 2193
4 21949301 21952797 - Lsi04G014190.1 Lsi04g01419 1419
8 23875337 23878000 + Lsi08G015870.1 Lsi08g01587 1587
8 23892060 23896892 + Lsi08G015890.1 Lsi08g01589 1589
8 23897733 23900335 - Lsi08G015910.1 Lsi08g01591 1591
8 32566537 32571064 - Sed0017388.1 Sed08g1775 1775
2 75317965 75329546 + Tan0011971.2 Tan02g1620 1620
4 890765 891570 - Vvi4g82 Vvi4g82 82
4 896111 901069 + Vvi4g83 Vvi4g83 83
4 905618 908738 + Vvi4g84 Vvi4g84 84
4 912017 914578 + Vvi4g85 Vvi4g85 85
4 914900 915869 - Vvi4g86 Vvi4g86 86
4 915979 921064 - Vvi4g87 Vvi4g87 87
4 921551 923881 - Vvi4g88 Vvi4g88 88
4 931994 932896 - Vvi4g89 Vvi4g89 89
4 935961 939236 - Vvi4g90 Vvi4g90 90
4 941253 945402 - Vvi4g91 Vvi4g91 91
       

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