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
Vvi3g286 . . . . . . . . . . . . . . Sed05g2175 . . Bhi05g01588 Tan02g0581 Cmetu01g0188 Lac12g0483 Hepe02g0372 . . Cla02g00351 Cam02g0359 Cec02g0360 Cco02g0366 Clacu02g0351 Cmu02g0348 Cre02g0679 Cone12ag1274 . . . . Csa07g00182 . Cme01g01150 Blo04g00604 . . Bda14g00645 Bpe15g00786 . Bma03g00636 . . . . . . . Car19g00612 . . . . . . . . . . . . . . . . Lsi11g01282 . Chy01g00597 .
Vvi3g287 . Blo15g00712 Bda06g00441 Bda08g00947 Bpe07g00674 . . Bma12g00880 . . Cma02g00298 Cma20g00716 Car02g00178 Car20g00615 . . . . . . . . . . . . . . . . . . . . Cone10ag1214 Lsi10g00829 . . . . . . . . . . . . Cmo02g00293 . . . . . . Cpe05g01338 . . . . . . . . . . . . . . . . . Cme11g00154
Vvi3g288 Blo02g00813 . . . . . . . . Cmo11g01784 . . . . . Cpe04g00629 . Bhi05g01586 Tan02g0578 . . . . . Cla02g00349 Cam02g0358 Cec02g0359 Cco02g0365 Clacu02g0350 Cmu02g0347 . Cone12ag1275 Cone8ag1328 . . Lsi10g00865 Csa07g00184 . Cme01g01149 Blo04g00605 . . Bda14g00646 Bpe15g00785 . . . Sed01g0685 . . Cma11g01335 . Car11g01411 . Cpe16g00265 . Bhi10g01176 Tan05g0810 Cmetu08g0460 . Hepe08g0513 . . . . . . . . . Lsi11g01283 . Chy01g00596 .
Vvi3g289 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g290 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g291 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g292 . . . . . . . . . Cmo11g01785 . . . . . Cpe04g00630 . Bhi05g01584 . . . . . . Cla02g00348 . . . . . . Cone12ag1276 Cone8ag1330 Cone3ag1248 . . Csa07g00185 . Cme01g01148 . Blo13g00474 . . . . . Bma08g00718 . . . Cma11g01334 Cma19g00797 Car11g01412 . . . . . . . . . . . . . . . . . Lsi11g01284 . Chy01g00595 Cme11g01308
Vvi3g293 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g294 . . . . . Bpe12g00149 . . Cmo19g00818 Cmo11g01786 . . . . . Cpe04g00631 Cpe15g00642 Bhi05g01248 Tan02g0781 . . . . . Cla02g00347 Cam02g0356 Cec02g0357 Cco02g0363 Clacu02g0348 Cmu02g0345 Cre02g0677 . . . . . Csa07g00186 . Cme01g01147 Blo04g00606 Blo13g00473 . Bda14g00648 Bpe15g00784 . Bma03g00637 Bma08g00717 . . . Cma11g01333 Cma19g00798 Car11g01413 Car19g00614 . . . . . . . . . . . . . . . . Lsi11g01285 . Chy01g00594 .
Vvi3g295 . Blo15g00423 Bda06g00442 . Bpe07g00675 . . Bma12g00881 . . Cma02g00299 . Car02g00180 . . . . . . . . . . . . . . . . . . . . . Cone10ag1212 . . . . . . . . . . . . . Cmo02g00294 . . . . . . Cpe05g01337 . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 6509817 6511922 - Bda023686.1 Bda06g00441 441
6 6512698 6514155 + Bda023687.1 Bda06g00442 442
8 17789171 17794262 + Bda029593.1 Bda08g00947 947
14 4840940 4843495 - Bda027402.1 Bda14g00645 645
14 4844111 4846628 - Bda027403.1 Bda14g00646 646
14 4851309 4855957 - Bda027405.1 Bda14g00648 648
5 45295517 45298752 + XM_039031765.1 Bhi05g01248 1248
5 52663060 52666780 + XM_039030933.1 Bhi05g01584 1584
5 52678306 52683424 + XM_039032907.1 Bhi05g01586 1586
5 52711749 52716331 + XM_039032362.1 Bhi05g01588 1588
10 25029607 25032445 - XM_039046044.1 Bhi10g01176 1176
2 28708115 28719119 + BLOR10543 Blo02g00813 813
4 5227869 5230935 - BLOR13516 Blo04g00604 604
4 5231534 5237970 - BLOR13517 Blo04g00605 605
4 5238852 5243426 - BLOR13518 Blo04g00606 606
13 25617984 25622885 + BLOR05754 Blo13g00473 473
13 25624794 25627468 + BLOR05755 Blo13g00474 474
15 6111074 6113319 - BLOR06817 Blo15g00423 423
15 23101189 23112084 + BLOR07106 Blo15g00712 712
3 5256021 5259120 - Bma016929.1 Bma03g00636 636
3 5268865 5273535 - Bma016930.2 Bma03g00637 637
8 43014428 43019168 + Bma028081.1 Bma08g00717 717
8 43020846 43023059 + Bma028082.1 Bma08g00718 718
12 40020565 40022661 - Bma008204.1 Bma12g00880 880
12 40023458 40027578 + Bma008205.1 Bma12g00881 881
7 13453064 13455157 - Bpe021524.2 Bpe07g00674 674
7 13455927 13457382 + Bpe026071 Bpe07g00675 675
12 1086321 1091023 - Bpe005386.1 Bpe12g00149 149
15 18097867 18102501 + Bpe001711.2 Bpe15g00784 784
15 18105503 18109598 + Bpe001712.1 Bpe15g00785 785
15 18115540 18118638 + Bpe001713.1 Bpe15g00786 786
2 4313985 4318665 + CaPI482276_02g003560.1 Cam02g0356 356
2 4334562 4339261 + CaPI482276_02g003580.1 Cam02g0358 358
2 4348567 4353003 + CaPI482276_02g003590.1 Cam02g0359 359
2 1062502 1079472 - Carg19767-RA Car02g00178 178
2 1084018 1085787 + Carg19769-RA Car02g00180 180
11 11553328 11557736 - Carg18120-RA Car11g01411 1411
11 11558882 11563368 - Carg18119-RA Car11g01412 1412
11 11567020 11571933 - Carg18118-RA Car11g01413 1413
19 7592421 7595685 - Carg04093-RA Car19g00612 612
19 7603348 7607938 - Carg04095-RA Car19g00614 614
20 3447151 3449659 + Carg16135-RA Car20g00615 615
2 3315858 3320538 + CcPI632755_02g003630.1 Cco02g0363 363
2 3335189 3339890 + CcPI632755_02g003650.1 Cco02g0365 365
2 3349606 3354108 + CcPI632755_02g003660.1 Cco02g0366 366
2 3323109 3327773 + CePI673135_02g003570.1 Cec02g0357 357
2 3344867 3349566 + CePI673135_02g003590.1 Cec02g0359 359
2 3357720 3362129 + CePI673135_02g003600.1 Cec02g0360 360
1 4253076 4257758 + Chy1G005940.1 Chy01g00594 594
1 4266202 4269522 + Chy1G005950.1 Chy01g00595 595
1 4273664 4278189 + Chy1G005960.1 Chy01g00596 596
1 4279417 4282686 + Chy1G005970.1 Chy01g00597 597
2 3189986 3194672 + ClG42_02g0034800.10 Clacu02g0348 348
2 3210552 3221397 + ClG42_02g0035000.10 Clacu02g0350 350
2 3225497 3229930 + ClG42_02g0035100.10 Clacu02g0351 351
2 3401811 3406760 + ClCG02G003450.1 Cla02g00347 347
2 3415405 3418800 + ClCG02G003460.1 Cla02g00348 348
2 3424296 3429199 + ClCG02G003470.1 Cla02g00349 349
2 3438928 3443361 + ClCG02G003480.2 Cla02g00351 351
2 1390594 1410066 - CmaCh02G002980.1 Cma02g00298 298
2 1410943 1414159 + CmaCh02G002990.1 Cma02g00299 299
11 8836654 8842061 + CmaCh11G013330.1 Cma11g01333 1333
11 8844329 8849713 + CmaCh11G013340.1 Cma11g01334 1334
11 8850169 8855063 + CmaCh11G013350.1 Cma11g01335 1335
19 7706257 7709595 - CmaCh19G007970.1 Cma19g00797 797
19 7712954 7717659 - CmaCh19G007980.1 Cma19g00798 798
20 3303633 3305864 + CmaCh20G007160.1 Cma20g00716 716
1 14755047 14760243 + MELO3C013253.2.1 Cme01g01147 1147
1 14770045 14774053 + MELO3C013254.2.1 Cme01g01148 1148
1 14776780 14781884 + MELO3C013255.2.1 Cme01g01149 1149
1 14782739 14790102 + MELO3C013256.2.1 Cme01g01150 1150
11 1651284 1656057 - MELO3C023333.2.1 Cme11g00154 154
11 19865237 19870556 + MELO3C025912.2.1 Cme11g01308 1308
1 4571308 4574585 + PI0019345.1 Cmetu01g0188 188
8 9195523 9197993 + PI0022676.1 Cmetu08g0460 460
2 1453968 1472230 - CmoCh02G002930.1 Cmo02g00293 293
2 1473073 1476674 + CmoCh02G002940.1 Cmo02g00294 294
11 12547518 12551821 - CmoCh11G017840.1 Cmo11g01784 1784
11 12551860 12556496 - CmoCh11G017850.1 Cmo11g01785 1785
11 12559458 12564640 - CmoCh11G017860.1 Cmo11g01786 1786
19 8058986 8070005 - CmoCh19G008180.1 Cmo19g00818 818
2 3182686 3187372 + CmPI595203_02g003450.1 Cmu02g0345 345
2 3203266 3218222 + CmPI595203_02g003470.1 Cmu02g0347 347
2 3218223 3222656 + CmPI595203_02g003480.1 Cmu02g0348 348
3 31298386 31301358 - Conep03aG0175500.1 Cone3ag1248 1248
8 10748264 10749812 - Conep08aG0136700.1 Cone8ag1328 1328
8 10751564 10754058 - Conep08aG0136900.1 Cone8ag1330 1330
10 9025223 9029126 - Conep10aG0124700.1 Cone10ag1212 1212
10 9041922 9044150 + Conep10aG0124900.1 Cone10ag1214 1214
12 9746364 9751646 - Conep12aG0131500.1 Cone12ag1274 1274
12 9751820 9755801 - Conep12aG0131600.1 Cone12ag1275 1275
12 9756176 9758875 - Conep12aG0131700.1 Cone12ag1276 1276
4 6518025 6522710 - Cp4.1LG04g04540.1 Cpe04g00629 629
4 6523974 6528518 - Cp4.1LG04g04550.1 Cpe04g00630 630
4 6530445 6537259 - Cp4.1LG04g04530.1 Cpe04g00631 631
5 9404254 9407661 - Cp4.1LG05g13430.1 Cpe05g01337 1337
5 9408661 9427922 + Cp4.1LG05g13350.1 Cpe05g01338 1338
15 7130332 7135132 - Cp4.1LG15g06410.1 Cpe15g00642 642
16 4649470 4654725 - Cp4.1LG16g02670.1 Cpe16g00265 265
2 3731255 3735934 + CrPI670011_02g006770.1 Cre02g0677 677
2 3776691 3781123 + CrPI670011_02g006790.1 Cre02g0679 679
7 1487933 1494173 - CsaV3_7G001820.1 Csa07g00182 182
7 1495003 1500130 - CsaV3_7G001840.1 Csa07g00184 184
7 1503161 1507568 - CsaV3_7G001850.1 Csa07g00185 185
7 1513850 1519128 - CsaV3_7G001860.1 Csa07g00186 186
2 3479020 3482418 + Hsped.02g03720.1 Hepe02g0372 372
8 4507451 4509570 + Hsped.08g05130.1 Hepe08g0513 513
12 5252597 5256954 + Lag0014855.1 Lac12g0483 483
10 11637112 11701458 - Lsi10G008290.1 Lsi10g00829 829
10 12823024 12826323 + Lsi10G008650.1 Lsi10g00865 865
11 21425773 21430707 - Lsi11G012820.1 Lsi11g01282 1282
11 21434214 21439483 - Lsi11G012830.1 Lsi11g01283 1283
11 21445174 21448859 - Lsi11G012840.1 Lsi11g01284 1284
11 21456314 21461549 - Lsi11G012850.1 Lsi11g01285 1285
1 4990711 4993703 - Sed0025066.1 Sed01g0685 685
5 34594770 34600070 + Sed0027220.1 Sed05g2175 2175
2 5124023 5129097 + Tan0011609.2 Tan02g0578 578
2 5131179 5134448 + Tan0019143.1 Tan02g0581 581
2 7444629 7449096 - Tan0021793.3 Tan02g0781 781
5 6145926 6149125 - Tan0013394.1 Tan05g0810 810
3 2676550 2679781 - Vvi3g286 Vvi3g286 286
3 2681128 2731911 - Vvi3g287 Vvi3g287 287
3 2732047 2737839 - Vvi3g288 Vvi3g288 288
3 2749511 2751111 - Vvi3g289 Vvi3g289 289
3 2751840 2755856 - Vvi3g290 Vvi3g290 290
3 2757522 2758963 + Vvi3g291 Vvi3g291 291
3 2759561 2764805 - Vvi3g292 Vvi3g292 292
3 2766207 2771472 - Vvi3g293 Vvi3g293 293
3 2771958 2805318 - Vvi3g294 Vvi3g294 294
3 2811713 2814381 + Vvi3g295 Vvi3g295 295
       

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