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
Vvi1g1051 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01329 . .
Vvi1g1052 . . . . . . Bma14g01743 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1053 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1054 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1055 . . Bda01g01784 . . . . . . . . . . . . . Cpe01g01884 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe02g01961 . . . Cmo04g02273 . Cma04g02174 . Car04g02103 . . . Bhi12g01020 . . . Hepe02g2561 . Lcy10g1558 Cla01g00696 Cam01g0724 Cec01g0719 Cco01g0746 Clacu01g0714 Cmu01g0684 Cre09g1819 Lsi09g00753 . Chy09g00442 Cme09g01235
Vvi1g1056 . . . . . . . . . Cmo18g00280 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1057 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1058 . . . . . . . . Cmo04g01063 . . . Car04g00926 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01197 . .
Vvi1g1059 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1060 Blo01g00491 . Bda01g02088 . . . . . Cmo04g01594 Cmo18g01054 . Cma18g01037 Car04g01572 Car18g00963 . Cpe09g00623 Cpe01g01353 Bhi07g01361 . . . Hepe01g1216 . . Cla05g02324 Cam05g2497 Cec05g2521 Cco05g2563 Clacu05g2491 Cmu05g2354 Cre05g2470 . . . . Lsi04g00282 Csa05g02587 Chy10g01122 Cme10g00284 . . . . . Bpe02g02279 Bma01g00160 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 54050076 54055603 + Bda004073.1 Bda01g01784 1784
1 57039180 57041479 - Bda004416.1 Bda01g02088 2088
7 41120773 41127753 - XM_039036945.1 Bhi07g01361 1361
12 31129578 31134443 + XM_039020100.1 Bhi12g01020 1020
1 5401654 5414169 + BLOR00491 Blo01g00491 491
1 1513674 1515970 + Bma000327.2 Bma01g00160 160
14 37503194 37534875 - Bma012511.1 Bma14g01743 1743
2 21496550 21502138 + Bpe009785.2 Bpe02g01961 1961
2 23597645 23599967 - Bpe010096.3 Bpe02g02279 2279
1 8105975 8110086 + CaPI482276_01g007240.1 Cam01g0724 724
5 32788829 32800904 - CaPI482276_05g024970.1 Cam05g2497 2497
4 5292417 5313684 + Carg00101-RA Car04g00926 926
4 9117284 9120137 + Carg01828-RA Car04g01572 1572
4 17160228 17164585 + Carg17710-RA Car04g02103 2103
18 10192506 10196546 - Carg21567-RA Car18g00963 963
1 7906645 7910753 + CcPI632755_01g007460.1 Cco01g0746 746
5 33882028 33894129 - CcPI632755_05g025630.1 Cco05g2563 2563
1 7983828 7986781 + CePI673135_01g007190.1 Cec01g0719 719
5 36214607 36226734 - CePI673135_05g025210.1 Cec05g2521 2521
9 3921125 3925193 - Chy9G161580.1 Chy09g00442 442
10 16244881 16249197 + Chy10G183160.1 Chy10g01122 1122
1 7773843 7777942 + ClG42_01g0071400.10 Clacu01g0714 714
5 33002339 33014211 - ClG42_05g0249100.10 Clacu05g2491 2491
1 8182564 8189598 + ClCG01G007110.2 Cla01g00696 696
5 34802529 34821954 - ClCG05G022960.2 Cla05g02324 2324
4 15206108 15213296 + CmaCh04G021740.1 Cma04g02174 2174
18 8624980 8633834 - CmaCh18G010370.1 Cma18g01037 1037
9 17274906 17279581 - MELO3C005202.2.1 Cme09g01235 1235
10 1837320 1841721 - MELO3C012222.2.1 Cme10g00284 284
4 5319477 5329883 + CmoCh04G010630.1 Cmo04g01063 1063
4 8132916 8136861 + CmoCh04G015940.1 Cmo04g01594 1594
4 16952596 16956936 + CmoCh04G022730.1 Cmo04g02273 2273
18 1841308 1842525 + CmoCh18G002800.1 Cmo18g00280 280
18 11192245 11196203 - CmoCh18G010540.1 Cmo18g01054 1054
1 7747201 7751312 + CmPI595203_01g006840.1 Cmu01g0684 684
5 32740528 32752429 - CmPI595203_05g023540.1 Cmu05g2354 2354
1 8143332 8146430 + Cp4.1LG01g13780.1 Cpe01g01353 1353
1 16138411 16143010 + Cp4.1LG01g18770.1 Cpe01g01884 1884
9 4553663 4558145 - Cp4.1LG09g05580.1 Cpe09g00623 623
5 36076258 36088743 - CrPI670011_05g024700.1 Cre05g2470 2470
9 36583979 36588102 - CrPI670011_09g018190.1 Cre09g1819 1819
5 12434134 12479444 + CsaV3_5G015210.1 Csa05g01197 1197
5 14064908 14066935 + CsaV3_5G017520.1 Csa05g01329 1329
5 27170333 27175248 + CsaV3_5G034060.1 Csa05g02587 2587
1 77318939 77342713 - Hsped.01g12160.1 Hepe01g1216 1216
2 72546251 72550441 - Hsped.02g25610.1 Hepe02g2561 2561
10 39931633 39936848 - Maker00006919 Lcy10g1558 1558
4 2821833 2828096 - Lsi04G002820.1 Lsi04g00282 282
9 8641635 8647764 + Lsi09G007530.1 Lsi09g00753 753
1 17376949 17379343 - Vvi1g1051 Vvi1g1051 1051
1 17391224 17403345 - Vvi1g1052 Vvi1g1052 1052
1 17455711 17470659 - Vvi1g1053 Vvi1g1053 1053
1 17503355 17552700 + Vvi1g1054 Vvi1g1054 1054
1 17554521 17575405 - Vvi1g1055 Vvi1g1055 1055
1 17594006 17595167 + Vvi1g1056 Vvi1g1056 1056
1 17603864 17604970 - Vvi1g1057 Vvi1g1057 1057
1 17604977 17705405 - Vvi1g1058 Vvi1g1058 1058
1 17750965 17753365 - Vvi1g1059 Vvi1g1059 1059
1 17753385 17754738 - Vvi1g1060 Vvi1g1060 1060
       

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