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
Vvi16g834 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g835 . . . . . . . . . . . . . . . Cpe05g00623 . . . . . . . . . . . . . . . . . . . . . Chy09g01406 . . . . . . . . . . Cmo02g01116 . . . . . . . . . . . . . . . . . . . . . . . . Cme09g01951
Vvi16g836 . . . Bda07g01913 Bpe03g00165 . . . Cmo16g00089 Cmo18g01319 . . Car02g00961 . Sed05g0275 . Cpe14g00069 Bhi01g01431 Tan01g0170 Cmetu04g2585 . Hepe07g0104 Mch10g0106 . . . . . . . . Cone1ag0946 Cone5ag0665 . . Lsi05g01173 . . Cme06g01059 . Blo09g00048 . . . . . . . . . Cma16g00086 Cma18g01290 Car16g00075 Car18g01207 Cpe09g00052 . . . . . . . . Cla05g00935 Cam05g1022 Cec05g1026 Cco05g1022 Clacu05g1011 Cmu05g0964 Cre05g1045 . Csa03g02178 Chy06g01277 .
Vvi16g837 . . . . . . . . . . . . . . . . . . . . . . . . Cla01g00210 Cam01g0215 Cec01g0209 Cco01g0213 Clacu01g0210 Cmu01g0204 Cre09g2303 . . . . . Csa05g00227 Chy09g01273 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme09g01816
Vvi16g838 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g839 . . . . . . . . . . Cma02g01094 . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00083 Chy09g01408 . . . . . . . . . . . . . . . . . . Bhi12g00591 . . Lac11g0118 Hepe06g0757 . Lcy12g0093 . . . . . . . Lsi09g00054 . Chy06g01276 .
Vvi16g840 . . . . . . . . Cmo16g00088 . . . . . Sed02g1729 . Cpe14g00068 Bhi01g01432 Tan01g0168 Cmetu06g2105 Lac11g0131 Hepe07g0103 Mch10g0105 . Cla01g00072 Cam01g0072 Cec01g0073 Cco01g0073 Clacu01g0073 Cmu01g0074 Cre09g2436 . Cone5ag0662 . Cone15ag0046 Lsi05g01172 Csa05g00082 Chy09g01409 Cme06g01060 . . . . . . . . . Cmo02g01118 . Cma16g00085 . Car16g00074 . . . . . . . . . . Cla05g00936 Cam05g1024 Cec05g1028 Cco05g1024 Clacu05g1013 Cmu05g0966 Cre05g1047 Lsi09g00052 . . Cme09g01953
Vvi16g841 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag0950 . Cone14ag0042 Cone15ag0044 . Csa05g00081 Chy09g01410 Cme06g01062 . . . . . . . . . Cmo02g01119 . . . . . . . Bhi12g00606 . . Lac11g0127 . . Lcy12g0107 . . . . . . . Lsi09g00044 . Chy06g01275 Cme09g01954
Vvi16g842 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g843 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda15g00769 . Bpe12g00362 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 36586383 36590204 + Bda028889.1 Bda07g01913 1913
15 11510783 11511766 - Bda012628.1 Bda15g00769 769
1 29117009 29122667 + XM_039019063.1 Bhi01g01431 1431
1 29129486 29130391 - XM_039019068.1 Bhi01g01432 1432
12 18591437 18592329 + XM_039019853.1 Bhi12g00591 591
12 18795340 18797044 + XM_039018995.1 Bhi12g00606 606
9 751049 755645 - BLOR20963 Blo09g00048 48
3 2101916 2106525 + Bpe012011.1 Bpe03g00165 165
12 8864577 8866382 - Bpe005618.1 Bpe12g00362 362
1 1027272 1028147 - CaPI482276_01g000720.1 Cam01g0072 72
1 2489053 2491071 + CaPI482276_01g002150.1 Cam01g0215 215
5 9225835 9231177 + CaPI482276_05g010220.1 Cam05g1022 1022
5 9238184 9239448 - CaPI482276_05g010240.1 Cam05g1024 1024
2 6765991 6769606 - Carg13980-RA Car02g00961 961
16 475929 476828 + Carg15093-RA Car16g00074 74
16 477191 482656 - Carg15094-RA Car16g00075 75
18 11646840 11651835 + Carg20363-RA Car18g01207 1207
1 544289 545164 - CcPI632755_01g000730.1 Cco01g0073 73
1 2092341 2094359 + CcPI632755_01g002130.1 Cco01g0213 213
5 8985770 8991169 + CcPI632755_05g010220.1 Cco05g1022 1022
5 8997676 8998921 - CcPI632755_05g010240.1 Cco05g1024 1024
1 570854 571729 - CePI673135_01g000730.1 Cec01g0073 73
1 2086669 2088687 + CePI673135_01g002090.1 Cec01g0209 209
5 8966327 8971288 + CePI673135_05g010260.1 Cec05g1026 1026
5 8978687 8979982 - CePI673135_05g010280.1 Cec05g1028 1028
6 11724543 11725900 + Chy6G118030.1 Chy06g01275 1275
6 11728912 11729814 + Chy6G118040.1 Chy06g01276 1276
6 11731178 11736443 - Chy6G118050.1 Chy06g01277 1277
9 14737279 14739291 - Chy9G169890.1 Chy09g01273 1273
9 15752036 15760659 - Chy9G171220.1 Chy09g01406 1406
9 15767727 15768695 + Chy9G171240.1 Chy09g01408 1408
9 15771827 15772705 + Chy9G171250.1 Chy09g01409 1409
9 15773888 15774775 - Chy9G171260.1 Chy09g01410 1410
1 636103 636978 - ClG42_01g0007300.10 Clacu01g0073 73
1 2106006 2108024 + ClG42_01g0021000.10 Clacu01g0210 210
5 8942266 8947667 + ClG42_05g0101100.10 Clacu05g1011 1011
5 8954679 8955964 - ClG42_05g0101300.10 Clacu05g1013 1013
1 595520 603142 + ClCG01G000710.1 Cla01g00072 72
1 2129348 2131366 + ClCG01G002150.1 Cla01g00210 210
5 9250829 9257805 + ClCG05G008570.2 Cla05g00935 935
5 9261180 9268746 - ClCG05G008580.1 Cla05g00936 936
2 6510262 6519507 - CmaCh02G010940.1 Cma02g01094 1094
16 368199 369098 + CmaCh16G000850.1 Cma16g00085 85
16 369796 382084 - CmaCh16G000860.1 Cma16g00086 86
18 9940941 9945794 + CmaCh18G012900.1 Cma18g01290 1290
6 7701305 7707333 + MELO3C006964.2.1 Cme06g01059 1059
6 7708160 7709352 - MELO3C006965.2.1 Cme06g01060 1060
6 7735865 7737758 - MELO3C006967.2.1 Cme06g01062 1062
9 22475524 22480493 - MELO3C005727.2.1 Cme09g01816 1816
9 23496885 23506404 - MELO3C005855.2.1 Cme09g01951 1951
9 23515271 23516403 + MELO3C005858.2.1 Cme09g01953 1953
9 23517536 23518651 - MELO3C005859.2.1 Cme09g01954 1954
4 32861516 32869354 - PI0009459.1 Cmetu04g2585 2585
6 972925 974118 + PI0022023.1 Cmetu06g2105 2105
2 6782599 6792220 - CmoCh02G011160.1 Cmo02g01116 1116
2 6798911 6799774 - CmoCh02G011180.1 Cmo02g01118 1118
2 6801705 6802568 - CmoCh02G011190.1 Cmo02g01119 1119
16 407404 408303 + CmoCh16G000880.1 Cmo16g00088 88
16 408675 414091 - CmoCh16G000890.1 Cmo16g00089 89
18 12557293 12563402 + CmoCh18G013190.1 Cmo18g01319 1319
1 580889 581764 - CmPI595203_01g000740.1 Cmu01g0074 74
1 2059160 2061178 + CmPI595203_01g002040.1 Cmu01g0204 204
5 8787452 8792820 + CmPI595203_05g009640.1 Cmu05g0964 964
5 8799829 8801114 - CmPI595203_05g009660.1 Cmu05g0966 966
1 54748288 54752881 + Conep01aG0098900.1 Cone1ag0946 946
1 54761095 54761997 - Conep01aG0099300.1 Cone1ag0950 950
5 2832170 2833217 + Conep05aG0068600.1 Cone5ag0662 662
5 2844580 2849267 - Conep05aG0068900.1 Cone5ag0665 665
14 280119 281227 + Conep14aG0004400.1 Cone14ag0042 42
15 277058 277951 + Conep15aG0004600.1 Cone15ag0044 44
15 287196 292428 + Conep15aG0004800.1 Cone15ag0046 46
5 3792450 3802003 + Cp4.1LG05g06120.1 Cpe05g00623 623
9 316510 321550 - Cp4.1LG09g00630.1 Cpe09g00052 52
14 378606 379505 + Cp4.1LG14g06410.1 Cpe14g00068 68
14 379996 385414 - Cp4.1LG14g06370.1 Cpe14g00069 69
5 9668869 9674405 + CrPI670011_05g010450.1 Cre05g1045 1045
5 9681179 9682471 - CrPI670011_05g010470.1 Cre05g1047 1047
9 42227991 42230009 - CrPI670011_09g023030.1 Cre09g2303 2303
9 43740515 43741393 - CrPI670011_09g024360.1 Cre09g2436 2436
3 18911019 18917120 + CsaV3_3G021780.1 Csa03g02178 2178
5 403296 404823 + CsaV3_5G000810.1 Csa05g00081 81
5 406145 407041 - CsaV3_5G000820.1 Csa05g00082 82
5 409523 410792 - CsaV3_5G000830.1 Csa05g00083 83
5 1385520 1390734 + CsaV3_5G002270.1 Csa05g00227 227
6 54088532 54089528 - Hsped.06g07570.1 Hepe06g0757 757
7 978543 979738 + Hsped.07g01030.1 Hepe07g0103 103
7 980918 987105 - Hsped.07g01040.1 Hepe07g0104 104
11 1091773 1092651 - Lag0030756.1 Lac11g0118 118
11 1152574 1154721 - Lag0030765.1 Lac11g0127 127
11 1203111 1204926 + Lag0030769.1 Lac11g0131 131
12 1228241 1229137 - Maker00038639 Lcy12g0093 93
12 1379253 1381533 + Maker00038434 Lcy12g0107 107
5 19652754 19653656 + Lsi05G011720.1 Lsi05g01172 1172
5 19656033 19661420 - Lsi05G011730.1 Lsi05g01173 1173
9 393979 395364 - Lsi09G000440.1 Lsi09g00044 44
9 442347 443225 + Lsi09G000520.1 Lsi09g00052 52
9 446418 446990 - Lsi09G000540.1 Lsi09g00054 54
10 619509 620616 + MC10g_new0013 Mch10g0105 105
10 621280 627094 - MC10g_new0014 Mch10g0106 106
2 52182659 52183921 + Sed0025449.1 Sed02g1729 1729
5 1693141 1701053 + Sed0015755.1 Sed05g0275 275
1 1563320 1564219 + Tan0001851.1 Tan01g0168 168
1 1571450 1577327 - Tan0001359.2 Tan01g0170 170
16 19120409 19123943 - Vvi16g834 Vvi16g834 834
16 19135126 19149867 - Vvi16g835 Vvi16g835 835
16 19150697 19157465 + Vvi16g836 Vvi16g836 836
16 19158251 19164166 - Vvi16g837 Vvi16g837 837
16 19171397 19171505 + Vvi16g838 Vvi16g838 838
16 19171527 19172421 - Vvi16g839 Vvi16g839 839
16 19180520 19191510 - Vvi16g840 Vvi16g840 840
16 19193724 19196236 - Vvi16g841 Vvi16g841 841
16 19197890 19201020 - Vvi16g842 Vvi16g842 842
16 19205044 19206556 - Vvi16g843 Vvi16g843 843
       

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