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
Vvi3g826 . . . . . . . . Cmo19g00526 Cmo11g01441 . . . . Sed10g1926 Cpe04g00344 Cpe15g00409 Bhi05g00987 Tan02g1087 Cmetu01g1268 Lac12g0126 Hepe02g0676 . . Cla02g00729 Cam02g0775 Cec02g0773 Cco02g0802 Clacu02g0770 Cmu02g0763 Cre02g1077 . Cone8ag1047 . . Lsi03g00644 Csa07g00647 . Cme01g00155 . . . . . . . . . . . . Cma19g00513 Car11g01157 Car19g00388 . . . . . . . . . . . . . . . . . . Chy01g00164 .
Vvi3g827 . . . . . . . . Cmo19g00525 . . . . . . . Cpe15g00407 Bhi05g00984 . . . . . . Cla02g00730 Cam02g0776 Cec02g0774 Cco02g0803 Clacu02g0771 Cmu02g0764 Cre02g1078 Cone12ag1017 Cone8ag1046 . . Lsi03g00645 . . . . . . . . . . . . . . . Cma19g00512 . Car19g00386 . . . . . . . . . . . . . . . . . . . .
Vvi3g828 . . . . . . . . Cmo19g00523 . . . . . . . Cpe15g00405 Bhi05g00980 Tan02g1093 . Lac12g0121 . . . Cla02g00732 Cam02g0777 Cec02g0776 Cco02g0805 Clacu02g0772 Cmu02g0765 Cre02g1079 Cone12ag1016 Cone8ag1045 . . Lsi03g00647 . . . . . . . . . . . . . . . Cma19g00510 . Car19g00384 . . . . . . . . . . . . . . . . . . . .
Vvi3g829 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g830 . Blo03g00046 Bda06g01142 . Bpe07g00302 . Bma05g00627 Bma12g00318 Cmo19g00522 Cmo11g01443 . . . . Sed06g0813 Cpe04g00346 Cpe15g00404 Bhi05g00978 Tan02g1096 Cmetu01g2563 Lac12g0119 Hepe02g0683 . . . . . . . . . . . Cone3ag1063 Cone10ag1078 Lsi03g00651 . . . . . . . . Bpe05g00451 . . . . . Cma11g01683 Cma19g00509 Car11g01159 Car19g00382 . . . . . . . . . . . . . . . . . . . .
Vvi3g831 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g832 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g833 . . . . Bpe07g00307 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi10g00271 . . . . . . . . . . . . . . . . . . . . Bhi10g01654 . . . . . . Cla09g01668 . . . . . . . . . .
Vvi3g834 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g835 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi10g00270 . . . . . . . . . . . . . . . . . . . . Bhi10g01653 . . . . . . Cla09g01633 . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 40372271 40376513 - Bda022939.1 Bda06g01142 1142
5 34484170 34487506 - XM_039031351.1 Bhi05g00978 978
5 34544124 34577381 - XM_039033041.1 Bhi05g00980 980
5 34647596 34648951 + XM_039032503.1 Bhi05g00984 984
5 34822664 34825334 + XM_039032151.1 Bhi05g00987 987
10 41689108 41691165 - XM_039046290.1 Bhi10g01653 1653
10 41726020 41728044 + XM_039046686.1 Bhi10g01654 1654
3 1781940 1784226 - BLOR11227 Blo03g00046 46
5 37185417 37187746 - Bma021655.1 Bma05g00627 627
12 4767714 4770075 + Bma007232.1 Bma12g00318 318
5 18886764 18889088 - Bpe017870.1 Bpe05g00451 451
7 2192547 2194821 + Bpe026051 Bpe07g00302 302
7 2237303 2239411 + Bpe021116.1 Bpe07g00307 307
2 9551971 9553605 + CaPI482276_02g007750.1 Cam02g0775 775
2 9573802 9578253 + CaPI482276_02g007760.1 Cam02g0776 776
2 9589482 9599106 - CaPI482276_02g007770.1 Cam02g0777 777
11 9287297 9290997 - Carg23051-RA Car11g01157 1157
11 9297448 9302155 + Carg23053-RA Car11g01159 1159
19 5668379 5671935 - Carg16303-RA Car19g00382 382
19 5676239 5681889 + Carg16305-RA Car19g00384 384
19 5688042 5692376 - Carg16307-RA Car19g00386 386
19 5695566 5698114 + Carg16309-RA Car19g00388 388
2 8853929 8855561 - CcPI632755_02g008020.1 Cco02g0802 802
2 8911675 8916133 + CcPI632755_02g008030.1 Cco02g0803 803
2 8927442 8937124 - CcPI632755_02g008050.1 Cco02g0805 805
2 8743432 8745066 - CePI673135_02g007730.1 Cec02g0773 773
2 8809334 8815331 + CePI673135_02g007740.1 Cec02g0774 774
2 8826624 8836283 - CePI673135_02g007760.1 Cec02g0776 776
1 1134875 1136528 - Chy1G001640.1 Chy01g00164 164
2 8480081 8481715 + ClG42_02g0077000.10 Clacu02g0770 770
2 8506252 8510700 + ClG42_02g0077100.10 Clacu02g0771 771
2 8521669 8531308 - ClG42_02g0077200.10 Clacu02g0772 772
2 8874435 8876309 + ClCG02G007480.1 Cla02g00729 729
2 8903494 8907942 + ClCG02G007540.2 Cla02g00730 730
2 8918489 8928547 - ClCG02G007560.2 Cla02g00732 732
9 32526836 32528965 + ClCG09G016650.1 Cla09g01633 1633
9 33440685 33443623 + ClCG09G017000.2 Cla09g01668 1668
11 11096559 11100687 - CmaCh11G016830.1 Cma11g01683 1683
19 5995884 5999209 - CmaCh19G005090.1 Cma19g00509 509
19 6000727 6009126 + CmaCh19G005100.1 Cma19g00510 510
19 6015039 6018660 - CmaCh19G005120.1 Cma19g00512 512
19 6022892 6025550 + CmaCh19G005130.1 Cma19g00513 513
1 1112296 1115047 - MELO3C018555.2.1 Cme01g00155 155
1 1268679 1271370 - PI0014884.1 Cmetu01g1268 1268
1 1371135 1374910 - PI0002562.1 Cmetu01g2563 2563
11 10127297 10135082 - CmoCh11G014410.1 Cmo11g01441 1441
11 10138997 10143255 + CmoCh11G014430.1 Cmo11g01443 1443
19 6124525 6128414 - CmoCh19G005220.1 Cmo19g00522 522
19 6129654 6138538 + CmoCh19G005230.1 Cmo19g00523 523
19 6144439 6148693 - CmoCh19G005250.1 Cmo19g00525 525
19 6152064 6155387 + CmoCh19G005260.1 Cmo19g00526 526
2 8419685 8421319 + CmPI595203_02g007630.1 Cmu02g0763 763
2 8445844 8450290 + CmPI595203_02g007640.1 Cmu02g0764 764
2 8461263 8470899 - CmPI595203_02g007650.1 Cmu02g0765 765
3 29330045 29332287 - Conep03aG0156400.1 Cone3ag1063 1063
8 9602508 9604598 + Conep08aG0107300.1 Cone8ag1045 1045
8 9604459 9606791 - Conep08aG0107400.1 Cone8ag1046 1046
8 9609525 9610669 + Conep08aG0107500.1 Cone8ag1047 1047
10 7482605 7484898 - Conep10aG0110500.1 Cone10ag1078 1078
12 8562913 8566971 + Conep12aG0104400.1 Cone12ag1016 1016
12 8567203 8568954 - Conep12aG0104500.1 Cone12ag1017 1017
4 4145872 4149654 - Cp4.1LG04g07400.1 Cpe04g00344 344
4 4155497 4160536 + Cp4.1LG04g07510.1 Cpe04g00346 346
15 5214054 5218453 - Cp4.1LG15g04170.1 Cpe15g00404 404
15 5220505 5228586 + Cp4.1LG15g04110.1 Cpe15g00405 405
15 5234138 5238146 - Cp4.1LG15g04160.1 Cpe15g00407 407
15 5241709 5244982 + Cp4.1LG15g04040.1 Cpe15g00409 409
2 8979916 8981545 - CrPI670011_02g010770.1 Cre02g1077 1077
2 9012535 9017016 + CrPI670011_02g010780.1 Cre02g1078 1078
2 9028248 9037902 - CrPI670011_02g010790.1 Cre02g1079 1079
7 4647975 4650800 + CsaV3_7G007460.1 Csa07g00647 647
2 7449077 7452158 - Hsped.02g06760.1 Hepe02g0676 676
2 7498005 7501908 + Hsped.02g06830.1 Hepe02g0683 683
12 1328857 1333311 - Lag0014491.1 Lac12g0119 119
12 1338596 1342257 + Lag0014493.1 Lac12g0121 121
12 1380366 1382054 + Lag0014498.1 Lac12g0126 126
3 8103519 8106253 - Lsi03G006440.1 Lsi03g00644 644
3 8145486 8149042 + Lsi03G006450.1 Lsi03g00645 645
3 8165978 8175162 - Lsi03G006470.1 Lsi03g00647 647
3 8230448 8234631 + Lsi03G006510.1 Lsi03g00651 651
10 4327645 4329561 + Lsi10G002700.1 Lsi10g00270 270
10 4339587 4344208 - Lsi10G002710.1 Lsi10g00271 271
6 8708031 8711800 - Sed0004910.1 Sed06g0813 813
10 35950574 35953850 + Sed0024556.2 Sed10g1926 1926
2 18735197 18737919 - Tan0003575.1 Tan02g1087 1087
2 18853418 18888669 - Tan0017853.2 Tan02g1093 1093
2 19181413 19185134 + Tan0012125.1 Tan02g1096 1096
3 9524909 9527107 + Vvi3g826 Vvi3g826 826
3 9538946 9552380 + Vvi3g827 Vvi3g827 827
3 9553244 9614269 - Vvi3g828 Vvi3g828 828
3 9675334 9678621 - Vvi3g829 Vvi3g829 829
3 9698360 9706951 + Vvi3g830 Vvi3g830 830
3 9707223 9708876 - Vvi3g831 Vvi3g831 831
3 9711239 9711365 + Vvi3g832 Vvi3g832 832
3 9739485 9744665 - Vvi3g833 Vvi3g833 833
3 9745730 9750978 + Vvi3g834 Vvi3g834 834
3 9751599 9771387 - Vvi3g835 Vvi3g835 835
       

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