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
Vvi5g1139 . . . . . Bpe14g01046 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1140 . . . . . . . Bma05g01241 Cmo08g00086 . Cma06g01635 Cma14g01489 Car06g01390 Car14g01325 . Cpe08g00093 Cpe03g01253 Bhi01g02647 . . . . . . . . . . . . . . . Cone18ag0891 . . . . Cme07g01866 Blo02g00458 Blo07g00096 Bda11g00468 Bda13g00238 . Bpe13g00714 Bma02g00954 Bma06g01451 . Cmo06g01634 Cmo14g01526 . . Car08g00069 . . Cpe17g00994 . . . . . . . . . . . . . . . . . .
Vvi5g1141 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1142 . . . . . . . Bma05g01242 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1143 . . . . . . . Bma05g01243 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1144 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1145 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1146 . . . . . . . . . Cmo17g00570 . . . . . . . . . . . . . . Cla08g00440 Cam08g0873 Cec08g0452 Cco08g0574 Clacu08g0589 . Cre08g0412 . . . . . . . . . . . . . . . . . . . . Cma17g00588 . Car17g00544 Cpe12g00501 . . . . . . . . . . . . . . . . . . .
Vvi5g1147 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1148 . . . . . . . . . . Cma06g01664 . Car06g01406 . . . . Bhi01g02696 . . . . . . . . . . . . . . . . . . . . . . Blo07g00189 . . . . . . . Cmo06g01658 . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 4929788 4932265 - Bda005206.1 Bda11g00468 468
13 2968627 2970560 + Bda001118.3 Bda13g00238 238
1 65804504 65810377 - XM_039042011.1 Bhi01g02647 2647
1 66727539 66735149 - XM_039041289.1 Bhi01g02696 2696
2 6465576 6489489 - BLOR10188 Blo02g00458 458
7 1376738 1391962 - BLOR18028 Blo07g00096 96
7 2361335 2364435 + BLOR18121 Blo07g00189 189
2 49575252 49577187 + Bma015752.1 Bma02g00954 954
5 51791420 51794016 - Bma022432.1 Bma05g01241 1241
5 51798059 51803078 - Bma022433.1 Bma05g01242 1242
5 51804480 51807025 - Bma022434.1 Bma05g01243 1243
6 51205616 51207998 - Bma024565.1 Bma06g01451 1451
13 13690340 13692800 + Bpe010413.1 Bpe13g00714 714
14 7816666 7820930 - Bpe014420.1 Bpe14g01046 1046
8 12745989 12753574 + CaPI482276_08g008730.1 Cam08g0873 873
6 9994531 9998232 - Carg15486-RA Car06g01390 1390
6 10085450 10086480 - Carg15470-RA Car06g01406 1406
8 404266 408988 - Carg04911-RA Car08g00069 69
14 11207128 11211324 + Carg22436-RA Car14g01325 1325
17 5056961 5061340 + Carg22614-RA Car17g00544 544
8 14764234 14768914 + CcPI632755_08g005740.1 Cco08g0574 574
8 13250389 13255065 + CePI673135_08g004520.1 Cec08g0452 452
8 12978985 12986182 + ClG42_08g0058900.10 Clacu08g0589 589
8 13458074 13464054 + ClCG08G004220.2 Cla08g00440 440
6 10181522 10185501 - CmaCh06G016350.1 Cma06g01635 1635
6 10283073 10284212 - CmaCh06G016640.1 Cma06g01664 1664
14 11296614 11299447 + CmaCh14G014890.1 Cma14g01489 1489
17 4853841 4857125 + CmaCh17G005880.1 Cma17g00588 588
7 24085083 24090649 - MELO3C017693.2.1 Cme07g01866 1866
6 11395678 11399030 - CmoCh06G016340.1 Cmo06g01634 1634
6 11494315 11496384 - CmoCh06G016580.1 Cmo06g01658 1658
8 442225 446934 - CmoCh08G000860.1 Cmo08g00086 86
14 12203277 12206065 + CmoCh14G015260.1 Cmo14g01526 1526
17 5853506 5856705 + CmoCh17G005700.1 Cmo17g00570 570
18 6286726 6290490 - Conep18aG0091700.1 Cone18ag0891 891
3 10153402 10157661 + Cp4.1LG03g12600.1 Cpe03g01253 1253
8 579297 582882 + Cp4.1LG08g05990.1 Cpe08g00093 93
12 4900558 4905091 + Cp4.1LG12g04950.1 Cpe12g00501 501
17 7541379 7546196 - Cp4.1LG17g10050.1 Cpe17g00994 994
8 13810356 13815035 + CrPI670011_08g004120.1 Cre08g0412 412
5 20915174 20938514 - Vvi5g1139 Vvi5g1139 1139
5 20953221 20959005 - Vvi5g1140 Vvi5g1140 1140
5 20962433 20963774 + Vvi5g1141 Vvi5g1141 1141
5 20967341 21013412 - Vvi5g1142 Vvi5g1142 1142
5 21017107 21042799 - Vvi5g1143 Vvi5g1143 1143
5 21044651 21052561 - Vvi5g1144 Vvi5g1144 1144
5 21065719 21066532 + Vvi5g1145 Vvi5g1145 1145
5 21078965 21081956 - Vvi5g1146 Vvi5g1146 1146
5 21087893 21093137 + Vvi5g1147 Vvi5g1147 1147
5 21093926 21098316 - Vvi5g1148 Vvi5g1148 1148
       

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