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
Vvi3g456 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g457 . . . Bda08g00844 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1114 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g458 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi10g00308 . . . . . . . . . . . Sed05g3657 . . . . . . . . Bhi10g02079 Tan05g1401 Cmetu11g0840 . . . . Cla09g01710 Cam09g1806 . . . . Cre01g0701 . Csa02g01198 . .
Vvi3g459 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone10ag1125 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g460 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1115 . . . . . . . . . . . . . . Cmo02g00447 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g461 . . . . . . . . . . . Cma20g00889 Car02g00299 Car20g00766 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g462 . . Bda06g01042 . . . . . . . Cma02g00440 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo02g00446 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g463 . . . . . . . . Cmo19g00638 . . . . . Sed10g2047 . Cpe15g00502 Bhi05g01139 Tan02g0886 Cmetu01g2178 . Hepe02g0570 . . Cla02g00582 Cam02g0615 Cec02g0614 Cco02g0630 Clacu02g0611 Cmu02g0608 Cre02g0939 Cone12ag1109 Cone8ag1150 . . . Csa07g00779 . Cme01g00032 Blo04g00492 . . Bda14g00522 Bpe15g00892 . Bma03g00523 . . . . . Cma19g00620 . Car19g00472 . . . . . . . . . . . . . . . . Lsi11g01024 . Chy01g00037 .
Vvi3g464 . . . . . Bpe12g00062 . . . Cmo11g01347 . Cma20g00888 . Car20g00765 . Cpe04g00267 . Bhi05g01141 . . . Hepe02g0569 . . Cla02g00581 Cam02g0614 Cec02g0613 Cco02g0629 Clacu02g0610 Cmu02g0607 Cre02g0938 . Cone8ag1151 Cone3ag1116 Cone10ag1127 Lsi10g00310 Csa07g00780 Chy11g00439 Cme01g00031 . Blo13g00569 Bda15g00028 . . . . . Sed05g3656 . Cmo20g00895 Cma11g01765 . Car11g01085 . . . Bhi10g02077 Tan05g1396 Cmetu11g0215 . Hepe08g1064 . . Cla09g01711 Cam09g1807 Cec09g1868 Cco09g1961 . . Cre01g0699 Lsi11g01025 Csa02g01199 Chy01g00036 Cme11g00511
Vvi3g465 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 36667149 36667676 + Bda022790.1 Bda06g01042 1042
8 13891238 13896882 + Bda029411.1 Bda08g00844 844
14 3777752 3781606 + Bda027268.1 Bda14g00522 522
15 1686777 1690488 + Bda011782.1 Bda15g00028 28
5 40841328 40855520 + XM_039031524.1 Bhi05g01139 1139
5 40859054 40864871 - XM_039031993.1 Bhi05g01141 1141
10 52129121 52135342 + XM_039044811.1 Bhi10g02077 2077
10 52141102 52142488 + XM_039046103.1 Bhi10g02079 2079
4 4079159 4083085 + BLOR13404 Blo04g00492 492
13 27805002 27808847 + BLOR19621 Blo13g00569 569
3 4071566 4075504 + Bma016806.1 Bma03g00523 523
12 455099 459073 - Bpe005300.1 Bpe12g00062 62
15 18827825 18831719 - Bpe001812.1 Bpe15g00892 892
2 7016416 7021234 + CaPI482276_02g006140.1 Cam02g0614 614
2 7023237 7027741 - CaPI482276_02g006150.1 Cam02g0615 615
9 32412636 32413680 - CaPI482276_09g018060.1 Cam09g1806 1806
9 32423285 32428579 - CaPI482276_09g018070.1 Cam09g1807 1807
2 2004588 2005407 + Carg22984-RA Car02g00299 299
11 8480080 8483742 + Carg27593-RA Car11g01085 1085
19 6376688 6381614 + Carg22052-RA Car19g00472 472
20 4507994 4513170 + Carg23618-RA Car20g00765 765
20 4514516 4515300 + Carg23617-RA Car20g00766 766
2 6195441 6200309 + CcPI632755_02g006290.1 Cco02g0629 629
2 6202377 6206881 - CcPI632755_02g006300.1 Cco02g0630 630
9 33632575 33637871 - CcPI632755_09g019610.1 Cco09g1961 1961
2 6089652 6094509 + CePI673135_02g006130.1 Cec02g0613 613
2 6096451 6100944 - CePI673135_02g006140.1 Cec02g0614 614
9 35315362 35320646 - CePI673135_09g018680.1 Cec09g1868 1868
1 251024 255904 + Chy1G000360.1 Chy01g00036 36
1 258107 262622 - Chy1G000370.1 Chy01g00037 37
11 4303231 4308712 + Chy11G190190.1 Chy11g00439 439
2 6008250 6013036 + ClG42_02g0061000.10 Clacu02g0610 610
2 6014989 6019489 - ClG42_02g0061100.10 Clacu02g0611 611
2 6286950 6292529 + ClCG02G005740.2 Cla02g00581 581
2 6295879 6302517 - ClCG02G005750.1 Cla02g00582 582
9 34256299 34257461 - ClCG09G017480.2 Cla09g01710 1710
9 34266441 34272298 - ClCG09G017490.1 Cla09g01711 1711
2 2241128 2242767 + CmaCh02G004400.1 Cma02g00440 440
11 11788303 11792565 - CmaCh11G017650.1 Cma11g01765 1765
19 6712161 6716524 + CmaCh19G006200.1 Cma19g00620 620
20 4269420 4274017 + CmaCh20G008880.1 Cma20g00888 888
20 4274521 4275914 + CmaCh20G008890.1 Cma20g00889 889
1 247613 253267 + MELO3C018433.2.1 Cme01g00031 31
1 253788 258826 - MELO3C018434.2.1 Cme01g00032 32
11 5225399 5231445 + MELO3C021912.2.1 Cme11g00511 511
1 302427 307040 - PI0018384.1 Cmetu01g2178 2178
11 26769443 26776213 - PI0008802.1 Cmetu11g0215 215
11 26762149 26763791 - PI0022804.1 Cmetu11g0840 840
2 2337790 2339757 + CmoCh02G004460.1 Cmo02g00446 446
2 2341520 2342014 - CmoCh02G004470.1 Cmo02g00447 447
11 9353349 9357072 + CmoCh11G013470.1 Cmo11g01347 1347
19 6917399 6921903 + CmoCh19G006380.1 Cmo19g00638 638
20 4540672 4546334 + CmoCh20G008950.1 Cmo20g00895 895
2 5915159 5919944 + CmPI595203_02g006070.1 Cmu02g0607 607
2 5921904 5926386 - CmPI595203_02g006080.1 Cmu02g0608 608
3 29715065 29717213 - Conep03aG0161800.1 Cone3ag1114 1114
3 29722883 29723825 - Conep03aG0161900.1 Cone3ag1115 1115
3 29737320 29741748 - Conep03aG0162000.1 Cone3ag1116 1116
8 10035336 10037312 + Conep08aG0118200.1 Cone8ag1150 1150
8 10037488 10039500 - Conep08aG0118300.1 Cone8ag1151 1151
10 8087268 8088186 - Conep10aG0115600.1 Cone10ag1125 1125
10 8096310 8100150 - Conep10aG0115800.1 Cone10ag1127 1127
12 8991435 8994174 + Conep12aG0114500.1 Cone12ag1109 1109
4 3341512 3345786 + Cp4.1LG04g08180.1 Cpe04g00267 267
15 5958496 5964689 + Cp4.1LG15g04930.1 Cpe15g00502 502
1 6650472 6655754 + CrPI670011_01g006990.1 Cre01g0699 699
1 6666017 6666613 + CrPI670011_01g007010.1 Cre01g0701 701
2 6535836 6540580 + CrPI670011_02g009380.1 Cre02g0938 938
2 6542629 6547123 - CrPI670011_02g009390.1 Cre02g0939 939
2 11776684 11778286 - CsaV3_2G014140.1 Csa02g01198 1198
2 11781859 11788137 - CsaV3_2G014150.1 Csa02g01199 1199
7 5469048 5474579 + CsaV3_7G008780.1 Csa07g00779 779
7 5474811 5481426 - CsaV3_7G008790.1 Csa07g00780 780
2 5764401 5768378 + Hsped.02g05690.1 Hepe02g0569 569
2 5769872 5773723 - Hsped.02g05700.1 Hepe02g0570 570
8 10335887 10341470 + Hsped.08g10640.1 Hepe08g1064 1064
10 4934157 4936890 - Lsi10G003080.1 Lsi10g00308 308
10 4944910 4951350 - Lsi10G003100.1 Lsi10g00310 310
11 17424517 17430518 + Lsi11G010240.1 Lsi11g01024 1024
11 17432350 17437941 - Lsi11G010250.1 Lsi11g01025 1025
5 44761409 44768485 + Sed0025422.1 Sed05g3656 3656
5 44774214 44776053 + Sed0012283.1 Sed05g3657 3657
10 36991033 36995490 + Sed0027300.2 Sed10g2047 2047
2 10067079 10079799 - Tan0001396.1 Tan02g0886 886
5 19945076 19951403 + Tan0010676.1 Tan05g1396 1396
5 20009224 20010800 + Tan0015207.1 Tan05g1401 1401
3 4405631 4406580 + Vvi3g456 Vvi3g456 456
3 4415090 4420009 - Vvi3g457 Vvi3g457 457
3 4422526 4423196 - Vvi3g458 Vvi3g458 458
3 4427052 4429871 - Vvi3g459 Vvi3g459 459
3 4430289 4430939 - Vvi3g460 Vvi3g460 460
3 4433889 4442649 - Vvi3g461 Vvi3g461 461
3 4445630 4446279 - Vvi3g462 Vvi3g462 462
3 4450820 4454744 + Vvi3g463 Vvi3g463 463
3 4455952 4467024 - Vvi3g464 Vvi3g464 464
3 4473081 4476262 - Vvi3g465 Vvi3g465 465
       

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