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
Vvi16g1014 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1015 Blo06g01058 Blo15g00081 . . . Bpe07g01022 . . . . Cma02g01129 . Car02g00934 . . Cpe05g00592 . . . . . . . . Cla01g00033 Cam01g0030 . . Clacu01g0032 Cmu01g0031 . . . . Cone15ag0004 . . . . . . . . . Bpe12g00346 . Bma12g01217 . Cmo02g01159 . . . . . . . Bhi12g00661 . . . . . . . . . . . . . Lsi09g00013 . . .
Vvi16g1016 . Blo15g00082 . . . Bpe07g01021 . . . . . Cma15g01020 . . . . . . . . . . . . Cla01g00034 Cam01g0031 Cec01g0030 Cco01g0032 Clacu01g0034 Cmu01g0032 Cre09g2475 Cone1ag0998 Cone5ag0702 . . . Csa05g00039 Chy09g01445 . . . Bda06g00791 . . . . . . . Cmo15g01083 . . . . . Cpe13g00319 Bhi12g00659 . . . . . . . . . . . . . Lsi09g00015 . . Cme09g01992
Vvi16g1017 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1018 . Blo15g00083 . . . Bpe07g01020 . . . . . . . . Sed07g2373 . . Bhi01g01509 Tan01g0073 Cmetu06g2632 . Hepe07g0046 Mch10g0046 . . . . . . . . Cone1ag0997 . . . . . . Cme06g01158 . . . . . . . Bma12g01216 . . . . . . Car18g01232 . . . . . . . . . Cla05g00982 Cam05g1073 Cec05g1080 Cco05g1072 Clacu05g1067 Cmu05g1018 Cre05g1092 . Csa03g01971 Chy06g01184 .
Vvi16g1019 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1020 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1021 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1022 . Blo15g00084 . . . Bpe07g01019 . . . . Cma02g01125 Cma15g01022 Car02g00933 Car15g00954 . . . . . . . . . . Cla01g00035 Cam01g0032 Cec01g0031 Cco01g0033 Clacu01g0035 Cmu01g0033 Cre09g2473 Cone1ag0996 Cone5ag0701 . . . Csa05g00040 Chy09g01444 . . . Bda06g00790 Bda15g00788 . Bpe12g00347 Bma08g00391 Bma12g01215 . Cmo02g01157 Cmo15g01084 . . . . . . Bhi12g00657 . . . . . . . . . . . . . Lsi09g00016 . . Cme09g01991
Vvi16g1023 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 10966767 10969478 - Bda024113.1 Bda06g00790 790
6 10981795 10987454 - Bda024114.1 Bda06g00791 791
15 11786270 11788971 - Bda012649.1 Bda15g00788 788
1 30841747 30846798 - XM_039024423.1 Bhi01g01509 1509
12 19688094 19692598 - XM_039050595.1 Bhi12g00657 657
12 19708071 19716213 - XM_039019343.1 Bhi12g00659 659
12 19785835 19788283 - XM_039050943.1 Bhi12g00661 661
6 33948009 33961266 + BLOR17641 Blo06g01058 1058
15 690277 691365 + BLOR06475 Blo15g00081 81
15 692093 695929 + BLOR06476 Blo15g00082 82
15 697019 698458 + BLOR06477 Blo15g00083 83
15 701227 715351 + BLOR06478 Blo15g00084 84
8 9563532 9566232 - Bma027464.1 Bma08g00391 391
12 45068631 45071345 - Bma008576.1 Bma12g01215 1215
12 45072969 45081155 - Bma008577.1 Bma12g01216 1216
12 45087006 45088094 - Bma008579.1 Bma12g01217 1217
7 15797874 15800587 - Bpe021863.1 Bpe07g01019 1019
7 15802380 15803807 - Bpe021864.1 Bpe07g01020 1020
7 15804644 15810294 - Bpe021865.1 Bpe07g01021 1021
7 15810961 15812088 - Bpe021866.1 Bpe07g01022 1022
12 8528283 8529814 + Bpe005601.1 Bpe12g00346 346
12 8531472 8534162 + Bpe005602.1 Bpe12g00347 347
1 699209 720275 + CaPI482276_01g000300.1 Cam01g0030 30
1 722264 730918 + CaPI482276_01g000310.1 Cam01g0031 31
1 734752 737514 + CaPI482276_01g000320.1 Cam01g0032 32
5 9797621 9801283 - CaPI482276_05g010730.1 Cam05g1073 1073
2 6607215 6617981 - Carg14008-RA Car02g00933 933
2 6618242 6621951 - Carg14007-RA Car02g00934 934
15 6954573 6957675 + Carg26609-RA Car15g00954 954
18 11827859 11829377 + Carg20338-RA Car18g01232 1232
1 231619 240239 + CcPI632755_01g000320.1 Cco01g0032 32
1 246897 249637 + CcPI632755_01g000330.1 Cco01g0033 33
5 9555923 9559945 - CcPI632755_05g010720.1 Cco05g1072 1072
1 263159 271758 + CePI673135_01g000300.1 Cec01g0030 30
1 275911 278627 + CePI673135_01g000310.1 Cec01g0031 31
5 9538809 9542788 - CePI673135_05g010800.1 Cec05g1080 1080
6 10588337 10591753 + Chy6G117120.1 Chy06g01184 1184
9 15992738 15995449 - Chy9G171600.1 Chy09g01444 1444
9 15998482 16005065 - Chy9G171610.1 Chy09g01445 1445
1 313529 321549 + ClG42_01g0003200.10 Clacu01g0032 32
1 326443 335084 + ClG42_01g0003400.10 Clacu01g0034 34
1 339235 342001 + ClG42_01g0003500.10 Clacu01g0035 35
5 9529832 9533488 - ClG42_05g0106700.10 Clacu05g1067 1067
1 242469 244271 + ClCG01G000310.1 Cla01g00033 33
1 249131 266244 + ClCG01G000320.2 Cla01g00034 34
1 266306 272861 + ClCG01G000340.2 Cla01g00035 35
5 9881672 9885328 - ClCG05G009070.2 Cla05g00982 982
2 6677795 6680847 - CmaCh02G011250.1 Cma02g01125 1125
2 6688009 6694711 - CmaCh02G011290.1 Cma02g01129 1129
15 6305934 6315043 + CmaCh15G010200.1 Cma15g01020 1020
15 6317514 6320549 + CmaCh15G010220.1 Cma15g01022 1022
6 8922972 8926954 - MELO3C019374.2.1 Cme06g01158 1158
9 23736668 23739776 - MELO3C005893.2.1 Cme09g01991 1991
9 23744040 23751104 - MELO3C005894.2.1 Cme09g01992 1992
6 8343464 8348104 - PI0024385.1 Cmetu06g2632 2632
2 6989508 6992204 - CmoCh02G011570.1 Cmo02g01157 1157
2 6994535 6996191 - CmoCh02G011590.1 Cmo02g01159 1159
15 7180695 7189154 + CmoCh15G010830.1 Cmo15g01083 1083
15 7191335 7195811 + CmoCh15G010840.1 Cmo15g01084 1084
1 258434 266460 + CmPI595203_01g000310.1 Cmu01g0031 31
1 266644 269363 + CmPI595203_01g000320.1 Cmu01g0032 32
1 271356 286879 + CmPI595203_01g000330.1 Cmu01g0033 33
5 9369880 9373536 - CmPI595203_05g010180.1 Cmu05g1018 1018
1 54992393 54996816 - Conep01aG0104100.1 Cone1ag0996 996
1 55000758 55002375 - Conep01aG0104200.1 Cone1ag0997 997
1 55002643 55005912 - Conep01aG0104300.1 Cone1ag0998 998
5 3005872 3010971 - Conep05aG0072500.1 Cone5ag0701 701
5 3012722 3018324 - Conep05aG0072600.1 Cone5ag0702 702
15 42480 44336 + Conep15aG0000500.1 Cone15ag0004 4
5 3587007 3599048 + Cp4.1LG05g05930.1 Cpe05g00592 592
13 2767335 2775908 - Cp4.1LG13g03200.1 Cpe13g00319 319
5 10245492 10249360 - CrPI670011_05g010920.1 Cre05g1092 1092
9 44038202 44040942 - CrPI670011_09g024730.1 Cre09g2473 2473
9 44055706 44058411 - CrPI670011_09g024750.1 Cre09g2475 2475
3 15556021 15559926 + CsaV3_3G019710.1 Csa03g01971 1971
5 180422 187525 + CsaV3_5G000390.1 Csa05g00039 39
5 189412 192755 + CsaV3_5G000400.1 Csa05g00040 40
7 491122 493648 + Hsped.07g00460.1 Hepe07g0046 46
9 111623 113809 + Lsi09G000130.1 Lsi09g00013 13
9 125579 134616 + Lsi09G000150.1 Lsi09g00015 15
9 136983 140561 + Lsi09G000160.1 Lsi09g00016 16
10 257062 261831 + MC10g0042 Mch10g0046 46
7 39594504 39598638 - Sed0008995.1 Sed07g2373 2373
1 828178 830324 + Tan0013272.1 Tan01g0073 73
16 21712143 21712399 + Vvi16g1014 Vvi16g1014 1014
16 21731309 21733916 + Vvi16g1015 Vvi16g1015 1015
16 21733932 21737609 + Vvi16g1016 Vvi16g1016 1016
16 21738677 21742840 - Vvi16g1017 Vvi16g1017 1017
16 21743484 21744182 + Vvi16g1018 Vvi16g1018 1018
16 21746014 21749300 + Vvi16g1019 Vvi16g1019 1019
16 21749318 21751201 + Vvi16g1020 Vvi16g1020 1020
16 21751204 21756610 + Vvi16g1021 Vvi16g1021 1021
16 21758098 21763009 + Vvi16g1022 Vvi16g1022 1022
16 21768760 21771164 + Vvi16g1023 Vvi16g1023 1023
       

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