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
Vvi19g1144 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1145 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1146 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1147 Blo04g00463 Blo13g00601 . . . . . . . . . . . . Sed05g1836 Cpe04g00865 Cpe16g00709 Bhi05g01995 Tan02g0029 . Lac12g0041 Hepe02g0014 . . . . . . . . . . . . . . Csa07g01207 . Cme11g01634 . . . . Bpe15g00918 . . . Sed05g3308 . . . . . . Cpe15g00903 Cpe05g01033 Bhi10g00938 Tan05g0584 Cmetu11g0258 . Hepe08g0647 . . . . . . . . . . Csa06g01151 Chy11g01041 Cme01g01504
Vvi19g1148 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1149 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1150 Blo04g00462 Blo13g00602 . . . . Bma08g00821 . . . . . . . Sed05g1833 Cpe04g00866 . Bhi05g01993 Tan02g0025 . . . . . . . . . . . . . . . . . Csa07g01210 . . . . . . Bpe15g00919 . Bma03g00495 . . . . . . . . Cpe15g00904 . . . . . . . . . . . . . . . . . . Cme01g01501
Vvi19g1151 Blo04g00461 . . . . . . . . . . . . . . . Cpe16g00708 . . . . . . . Cla02g01828 Cam02g1937 Cec02g1964 Cco02g2003 Clacu02g1917 Cmu02g1866 Cre02g2179 . . . . . . . Cme11g01635 . . . . Bpe15g00920 . Bma03g00494 . . . . . . . . . Cpe05g01032 Bhi10g00937 . . . . . . . . . . . . . . Csa06g01150 Chy11g01042 .
Vvi19g1152 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1153 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 61370294 61374744 + XM_039032780.1 Bhi05g01993 1993
5 61479378 61483973 - XM_039031080.1 Bhi05g01995 1995
10 19189933 19192014 - XM_039045700.1 Bhi10g00937 937
10 19193420 19198077 - XM_039044641.1 Bhi10g00938 938
4 3837993 3839625 - BLOR13373 Blo04g00461 461
4 3840798 3846213 + BLOR13374 Blo04g00462 462
4 3846877 3852750 - BLOR13375 Blo04g00463 463
13 28426206 28430011 + BLOR19653 Blo13g00601 601
13 28431058 28437535 - BLOR19654 Blo13g00602 602
3 3879568 3890693 - Bma016776.1 Bma03g00494 494
3 3884439 3886993 + Bma030976 Bma03g00495 495
8 45907827 45911260 - Bma028214.1 Bma08g00821 821
15 18982348 18986214 + Bpe001840.1 Bpe15g00918 918
15 18986931 18989995 - Bpe001841.1 Bpe15g00919 919
15 18994390 18996058 + Bpe001842.1 Bpe15g00920 920
2 32476223 32478090 + CaPI482276_02g019370.1 Cam02g1937 1937
2 32986294 32995039 + CcPI632755_02g020030.1 Cco02g2003 2003
2 37492571 37494438 + CePI673135_02g019640.1 Cec02g1964 1964
11 14883645 14888004 + Chy11G196210.1 Chy11g01041 1041
11 14890452 14892447 + Chy11G196220.1 Chy11g01042 1042
2 32727894 32736566 + ClG42_02g0191700.10 Clacu02g1917 1917
2 33432399 33441192 + ClCG02G018680.2 Cla02g01828 1828
1 19782767 19796310 + MELO3C012597.2.1 Cme01g01501 1501
1 19812082 19815890 - MELO3C012599.2.1 Cme01g01504 1504
11 24221845 24226640 + MELO3C019633.2.1 Cme11g01634 1634
11 24228610 24230852 + MELO3C019632.2.1 Cme11g01635 1635
11 8567114 8572093 - PI0026640.1 Cmetu11g0258 258
2 32596987 32598832 + CmPI595203_02g018660.1 Cmu02g1866 1866
4 7943557 7947361 + Cp4.1LG04g02290.1 Cpe04g00865 865
4 7949711 7954254 - Cp4.1LG04g02200.1 Cpe04g00866 866
5 6770540 6772390 - Cp4.1LG05g10300.1 Cpe05g01032 1032
5 6773286 6777713 - Cp4.1LG05g10310.1 Cpe05g01033 1033
15 8679143 8683278 + Cp4.1LG15g09080.1 Cpe15g00903 903
15 8683531 8689056 - Cp4.1LG15g09120.1 Cpe15g00904 904
16 7252016 7254612 - Cp4.1LG16g07110.1 Cpe16g00708 708
16 7255572 7259737 - Cp4.1LG16g07140.1 Cpe16g00709 709
2 35433191 35447827 + CrPI670011_02g021790.1 Cre02g2179 2179
6 9591178 9594649 - CsaV3_6G013480.1 Csa06g01150 1150
6 9595907 9601280 - CsaV3_6G013490.1 Csa06g01151 1151
7 11880570 11885604 + CsaV3_7G022960.1 Csa07g01207 1207
7 11904846 11909645 - CsaV3_7G022990.1 Csa07g01210 1210
2 289718 294044 - Hsped.02g00140.1 Hepe02g0014 14
8 5772166 5776538 + Hsped.08g06470.1 Hepe08g0647 647
12 531669 535517 - Lag0014413.1 Lac12g0041 41
5 31866608 31872443 + Sed0027108.8 Sed05g1833 1833
5 31873346 31877875 - Sed0017423.3 Sed05g1836 1836
5 42442831 42447893 + Sed0009028.1 Sed05g3308 3308
2 613298 621578 + Tan0008758.2 Tan02g0025 25
2 628867 633094 - Tan0010272.2 Tan02g0029 29
5 4247181 4251810 - Tan0019387.1 Tan05g0584 584
19 22939140 22943152 + Vvi19g1144 Vvi19g1144 1144
19 22972847 22973241 - Vvi19g1145 Vvi19g1145 1145
19 22999083 22999621 - Vvi19g1146 Vvi19g1146 1146
19 23001164 23010177 + Vvi19g1147 Vvi19g1147 1147
19 23010942 23012091 + Vvi19g1148 Vvi19g1148 1148
19 23036857 23037511 - Vvi19g1149 Vvi19g1149 1149
19 23045180 23055363 - Vvi19g1150 Vvi19g1150 1150
19 23086958 23090029 + Vvi19g1151 Vvi19g1151 1151
19 23090086 23092179 + Vvi19g1152 Vvi19g1152 1152
19 23111232 23122962 - Vvi19g1153 Vvi19g1153 1153
       

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