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
Vvi18g1290 . . . . . . . . . . . . . . . . Cpe13g00715 . . . . . . . . . . . . . . . . . . . . . Cme03g01093 . . . Bda01g01467 . . . . . . . . . . Car15g00518 . . . . . . . . . . . . . . . . Lsi08g00607 . . .
Vvi18g1291 Blo01g01753 Blo12g00766 . Bda03g00416 . Bpe04g00382 Bma04g00393 Bma01g02536 . . Cma01g00940 Cma09g01164 . . . Cpe06g00922 . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g00848 . . . . . Sed10g1778 Cmo01g00980 Cmo09g01166 . . . Car09g01041 . . Bhi09g01567 Tan01g2976 Cmetu01g1498 . . . . Cla09g00962 Cam09g1014 Cec09g1017 Cco09g1029 . . Cre09g0977 . . . .
Vvi18g1292 . Blo12g00767 . Bda03g00415 Bpe02g00189 Bpe04g00381 Bma04g00392 . . . . . Car01g00844 . . Cpe06g00923 . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g00849 . . . . . Sed10g1776 Cmo01g00976 . . . . . . . Bhi09g01569 Tan01g2978 Cmetu01g1659 . . . . . . . . . . . . . . Cme01g00754
Vvi18g1293 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1294 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1295 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma01g00789 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1296 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1297 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone20ag0657 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1298 Blo01g01371 Blo12g01087 Bda01g00869 Bda03g00060 Bpe02g00579 Bpe04g00047 Bma04g00059 Bma01g02155 . Cmo12g00266 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1299 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 41505619 41506403 + Bda003003.1 Bda01g00869 869
1 50584800 50586509 - Bda003714.1 Bda01g01467 1467
3 702498 703716 + Bda015996.1 Bda03g00060 60
3 3613285 3613587 - Bda016380.1 Bda03g00415 415
3 3615890 3617351 + Bda016381.1 Bda03g00416 416
11 8354495 8356237 - Bda005598.2 Bda11g00848 848
11 8361125 8361427 + Bda005599.1 Bda11g00849 849
9 42061012 42068401 - XM_039041411.1 Bhi09g01567 1567
9 42122165 42126060 + XM_039042548.1 Bhi09g01569 1569
1 51935608 51937039 + BLOR01371 Blo01g01371 1371
1 57307896 57309799 + BLOR01753 Blo01g01753 1753
12 26014996 26030534 - BLOR04785 Blo12g00766 766
12 26019807 26020106 + BLOR04786 Blo12g00767 767
12 28532149 28533412 - BLOR05106 Blo12g01087 1087
1 7378549 7380537 - Bma030207 Bma01g00789 789
1 78151121 78152551 + Bma002999.1 Bma01g02155 2155
1 83063773 83065507 + Bma003417.1 Bma01g02536 2536
4 546526 547817 + Bma018510.2 Bma04g00059 59
4 3209964 3210272 - Bma018854.1 Bma04g00392 392
4 3213383 3214846 + Bma018855.1 Bma04g00393 393
2 1315524 1315823 + Bpe025061 Bpe02g00189 189
2 3744542 3745979 - Bpe008421.1 Bpe02g00579 579
4 432678 433967 + Bpe025570 Bpe04g00047 47
4 2400763 2401062 - Bpe025617 Bpe04g00381 381
4 2404290 2405620 + Bpe015069.1 Bpe04g00382 382
9 10542227 10547228 - CaPI482276_09g010140.1 Cam09g1014 1014
1 6707108 6707795 - Carg28127-RA Car01g00844 844
9 7736597 7740700 + Carg15269-RA Car09g01041 1041
15 2806904 2809426 + Carg01639-RA Car15g00518 518
9 9840037 9845047 - CcPI632755_09g010290.1 Cco09g1029 1029
9 9849412 9854350 - CePI673135_09g010170.1 Cec09g1017 1017
9 10108705 10113913 - ClCG09G010300.2 Cla09g00962 962
1 5963191 5965211 + CmaCh01G009400.1 Cma01g00940 940
9 6911870 6915156 + CmaCh09G011640.1 Cma09g01164 1164
1 7578186 7582455 - MELO3C023649.2.1 Cme01g00754 754
3 20353179 20356003 - MELO3C019944.2.1 Cme03g01093 1093
1 15940527 15944621 + PI0014458.1 Cmetu01g1498 1498
1 15876900 15881093 - PI0026555.1 Cmetu01g1659 1659
1 6336407 6339862 - CmoCh01G009760.1 Cmo01g00976 976
1 6473143 6475179 + CmoCh01G009800.1 Cmo01g00980 980
9 7592037 7596007 + CmoCh09G011660.1 Cmo09g01166 1166
12 1716019 1717687 + CmoCh12G002660.1 Cmo12g00266 266
20 4002259 4004514 + Conep20aG0067700.1 Cone20ag0657 657
6 6619299 6623638 - Cp4.1LG06g09230.1 Cpe06g00922 922
6 6780204 6786656 + Cp4.1LG06g09210.1 Cpe06g00923 923
13 6620524 6623073 - Cp4.1LG13g10740.1 Cpe13g00715 715
9 10048804 10053896 - CrPI670011_09g009770.1 Cre09g0977 977
8 14377769 14380327 - Lsi08G006070.1 Lsi08g00607 607
10 34831550 34836166 - Sed0021533.1 Sed10g1776 1776
10 34863660 34869370 + Sed0021546.1 Sed10g1778 1778
1 69838804 69841926 - Tan0016822.2 Tan01g2976 2976
1 69964123 69969139 + Tan0008103.1 Tan01g2978 2978
18 17409919 17427601 - Vvi18g1290 Vvi18g1290 1290
18 17448716 17452527 - Vvi18g1291 Vvi18g1291 1291
18 17494097 17503316 + Vvi18g1292 Vvi18g1292 1292
18 17510946 17512912 + Vvi18g1293 Vvi18g1293 1293
18 17544606 17552354 - Vvi18g1294 Vvi18g1294 1294
18 17598950 17599277 + Vvi18g1295 Vvi18g1295 1295
18 17624788 17625250 + Vvi18g1296 Vvi18g1296 1296
18 17736460 17738276 - Vvi18g1297 Vvi18g1297 1297
18 17738304 17740132 - Vvi18g1298 Vvi18g1298 1298
18 17811874 17813214 + Vvi18g1299 Vvi18g1299 1299
       

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