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
Vvi18g1240 . . . . . . . . . . . Cma09g01112 . . . . Cpe13g00716 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo09g01118 . . . . . Cpe02g00910 Bhi09g01524 . . . . Mch11g1474 . . . . . . . . . . . .
Vvi18g1241 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo17g00219 Blo18g00219 . Bda13g01527 Bpe02g01602 Bpe14g00334 Bma01g00868 Bma02g00277 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1242 . . . . . . . . . . Cma01g00990 . Car01g00881 . . Cpe06g00895 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed10g1573 Cmo01g01027 . . . . Car09g00993 . . Bhi09g01502 Tan01g3380 Cmetu01g2157 . . . . Cla09g00923 Cam09g0975 Cec09g0980 Cco09g0986 . . Cre09g0944 . . . .
Vvi18g1243 . . . . . . . . Cmo04g02550 . . . . . Sed11g1334 . . Bhi04g01803 Tan11g1171 Cmetu03g1357 . Hepe02g2779 . Lcy10g1329 Cla08g00676 Cam08g1106 Cec08g0691 Cco08g0800 Clacu08g0812 . Cre08g0616 . . Cone17ag0795 Cone20ag0392 . . . Cme03g01094 Blo17g00218 Blo18g00217 . Bda13g01526 Bpe02g01604 Bpe14g00335 Bma01g00866 Bma02g00276 . . . . . Car04g02347 . Cpe01g02106 . . . . . . . . . . . . . . . Lsi08g00608 . Chy03g00543 .
Vvi18g1244 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1245 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1246 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1247 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1248 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1249 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
13 38311150 38312334 + Bda000374.1 Bda13g01526 1526
13 38328754 38329341 - Bda000376.1 Bda13g01527 1527
4 44423560 44426457 + XM_039029467.1 Bhi04g01803 1803
9 39254163 39263569 + XM_039043487.1 Bhi09g01502 1502
9 40484192 40492598 + XM_039043090.1 Bhi09g01524 1524
17 2241950 2243242 + BLOR16039 Blo17g00218 218
17 2248200 2248925 - BLOR16040 Blo17g00219 219
18 2144376 2145572 + BLOR08705 Blo18g00217 217
18 2150628 2151362 - BLOR08707 Blo18g00219 219
1 8135595 8136791 + Bma001087.1 Bma01g00866 866
1 8142111 8142824 - Bma001089.1 Bma01g00868 868
2 3196651 3197817 + Bma014727.1 Bma02g00276 276
2 3201246 3201977 - Bma014728.1 Bma02g00277 277
2 18921230 18921937 + Bpe009448.1 Bpe02g01602 1602
2 18925594 18926790 - Bpe009450.1 Bpe02g01604 1604
14 3240991 3241716 + Bpe006987.1 Bpe14g00334 334
14 3244967 3246121 - Bpe006988.1 Bpe14g00335 335
8 17429182 17431549 - CaPI482276_08g011060.1 Cam08g1106 1106
9 10079348 10085454 - CaPI482276_09g009750.1 Cam09g0975 975
1 8081487 8087116 + Carg25044-RA Car01g00881 881
4 18856135 18858627 - Carg15781-RA Car04g02347 2347
9 6420450 6427383 - Carg27265-RA Car09g00993 993
8 19839261 19840445 - CcPI632755_08g008000.1 Cco08g0800 800
9 9337132 9343200 - CcPI632755_09g009860.1 Cco09g0986 986
8 18646944 18649319 - CePI673135_08g006910.1 Cec08g0691 691
9 9366301 9372366 - CePI673135_09g009800.1 Cec09g0980 980
3 7647164 7648339 + Chy3G055230.1 Chy03g00543 543
8 18161369 18163736 - ClG42_08g0081200.10 Clacu08g0812 812
8 19028997 19030181 - ClCG08G006600.1 Cla08g00676 676
9 9607706 9613758 - ClCG09G009890.2 Cla09g00923 923
1 7109821 7115175 + CmaCh01G009900.1 Cma01g00990 990
9 6098294 6103921 - CmaCh09G011120.1 Cma09g01112 1112
3 20367852 20374128 - MELO3C019943.2.1 Cme03g01094 1094
1 17494371 17507594 + PI0017507.2 Cmetu01g2157 2157
3 9949710 9952567 + PI0004301.3 Cmetu03g1357 1357
1 8044477 8049465 + CmoCh01G010270.1 Cmo01g01027 1027
4 18688147 18690107 - CmoCh04G025500.1 Cmo04g02550 2550
9 6352818 6358473 - CmoCh09G011180.1 Cmo09g01118 1118
17 6242703 6244966 + Conep17aG0081300.1 Cone17ag0795 795
20 1876488 1879585 + Conep20aG0040600.1 Cone20ag0392 392
1 17815269 17816438 - Cp4.1LG01g21140.1 Cpe01g02106 2106
2 6679039 6684466 - Cp4.1LG02g09100.1 Cpe02g00910 910
6 6019481 6028558 - Cp4.1LG06g07600.1 Cpe06g00895 895
13 6625699 6628764 - Cp4.1LG13g10780.1 Cpe13g00716 716
8 19081475 19083843 - CrPI670011_08g006160.1 Cre08g0616 616
9 9575852 9581986 - CrPI670011_09g009440.1 Cre09g0944 944
2 76381790 76384514 - Hsped.02g27790.1 Hepe02g2779 2779
10 36148416 36149582 - Maker00008559 Lcy10g1329 1329
8 14384684 14406476 - Lsi08G006080.1 Lsi08g00608 608
11 11480596 11487660 - MC11g1195 Mch11g1474 1474
10 32345792 32354778 + Sed0006161.1 Sed10g1573 1573
11 29090661 29096655 - Sed0024209.1 Sed11g1334 1334
1 95345045 95362675 - Tan0020142.1 Tan01g3380 3380
11 9667764 9671078 + Tan0008539.1 Tan11g1171 1171
18 14023103 14027197 - Vvi18g1240 Vvi18g1240 1240
18 14033383 14034350 + Vvi18g1241 Vvi18g1241 1241
18 14041067 14042290 - Vvi18g1242 Vvi18g1242 1242
18 14075967 14077515 - Vvi18g1243 Vvi18g1243 1243
18 14095988 14097108 + Vvi18g1244 Vvi18g1244 1244
18 14109273 14109357 + Vvi18g1245 Vvi18g1245 1245
18 14116296 14117427 + Vvi18g1246 Vvi18g1246 1246
18 14122251 14123294 + Vvi18g1247 Vvi18g1247 1247
18 14130866 14134399 + Vvi18g1248 Vvi18g1248 1248
18 14136505 14140433 + Vvi18g1249 Vvi18g1249 1249
       

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