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
Vvi16g854 . . . . . . . Bma14g01992 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car16g00067 . . . . . . . . . . . . . . . . . . Csa03g02186 Chy06g01267 .
Vvi16g855 . . . . . . . . Cmo16g00079 . . . . . . . Cpe14g00061 . . . . . . . . . . . . . . . . . . . . . . . Blo09g00042 . . . . . . . . . Cma16g00076 . . . . . . . . . . . . . . . . . . . . Csa03g02187 . .
Vvi16g856 . . . . . . . Bma14g01991 . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag0657 . . . . . . Blo07g00352 . . . . . . . . . . . . . Car18g01211 Cpe09g00047 . . . . . . . . . . . . . . . . . . .
Vvi16g857 Blo06g01071 Blo15g00101 Bda05g00107 . Bpe03g00169 . Bma10g01274 Bma14g01988 . Cmo18g01322 . . . . Sed01g3831 . . Bhi01g01436 Tan01g0162 Cmetu06g1241 . . Mch10g0101 . Cla01g00205 . . . . . . . . . . Lsi05g01167 Csa05g00072 . . . . . Bda15g00771 . Bpe12g00368 . . . . . . Cma18g01293 . . . . Bhi12g00607 . . . Hepe06g0766 . . Cla05g00940 Cam05g1029 Cec05g1032 Cco05g1028 Clacu05g1018 Cmu05g0971 Cre05g1050 . . . Cme09g01822
Vvi16g858 . . . . . Bpe07g01003 . . . . Cma02g01095 . . . . Cpe05g00621 . . . . . . . . Cla01g00066 Cam01g0064 Cec01g0065 Cco01g0065 Clacu01g0065 Cmu01g0065 Cre09g2443 . . . . . . . . . . Bda06g00772 . . Bpe12g00366 . Bma12g01188 . Cmo02g01121 . . . . . . . Bhi12g00605 . . Lac11g0125 Hepe06g0765 . Lcy12g0103 . . . . . . . . . . .
Vvi16g859 . . . . . . . . . . Cma02g01096 . . . . Cpe05g00620 . . . . . . . . . . . . . . . . Cone5ag0660 . . . . Chy09g01416 Cme06g01065 . . . . . Bpe12g00365 . . . Cmo02g01122 . . . . . . . Bhi12g00601 . . . . . Lcy12g0102 . . . . . . . . . . Cme09g01959
Vvi16g860 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe12g00364 . . . . . . . . . . Cpe13g00301 Bhi12g00598 . . Lac11g0122 . . Lcy12g0101 . . . . . . . . . . .
Vvi16g861 . . . . . . . . . . Cma02g01097 . . . . Cpe05g00619 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe12g00363 . . . . . . . . . . . Bhi12g00596 . . Lac11g0121 Hepe06g0760 . Lcy12g0100 . . . . . . . . . . .
Vvi16g862 . . . Bda07g01916 . . . Bma14g01987 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi12g00595 . . Lac11g0120 Hepe06g0759 . Lcy12g0099 . . . . . . . . . . .
Vvi16g863 . . . . . . . Bma14g01983 . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag0661 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 5269163 5276140 + Bda020717.1 Bda05g00107 107
6 10718738 10725259 - Bda024093.1 Bda06g00772 772
7 36613706 36615488 + Bda028892.1 Bda07g01916 1916
15 11541146 11543326 + Bda033317 Bda15g00771 771
1 29248920 29252068 + XM_039050499.1 Bhi01g01436 1436
12 18704629 18709396 + XM_039018941.1 Bhi12g00595 595
12 18710554 18713237 - XM_039018942.1 Bhi12g00596 596
12 18715858 18720742 - XM_039018599.1 Bhi12g00598 598
12 18729187 18733805 + XM_039018481.1 Bhi12g00601 601
12 18734445 18737083 - XM_039018484.1 Bhi12g00605 605
12 18814218 18816920 + XM_039020121.1 Bhi12g00607 607
6 34065200 34070177 + BLOR17654 Blo06g01071 1071
7 5609626 5611115 + BLOR18284 Blo07g00352 352
9 624651 626659 + BLOR20957 Blo09g00042 42
15 853914 855984 - BLOR06495 Blo15g00101 101
10 45296710 45302120 + Bma005376.2 Bma10g01274 1274
12 44718787 44720546 - Bma008547.1 Bma12g01188 1188
14 43164818 43170615 + Bma012791.1 Bma14g01983 1983
14 43203384 43206857 + Bma012795.1 Bma14g01987 1987
14 43209204 43211730 + Bma012796.1 Bma14g01988 1988
14 43231013 43232664 - Bma012799.1 Bma14g01991 1991
14 43233459 43235254 - Bma012800.1 Bma14g01992 1992
3 2142145 2144868 + Bpe012015.1 Bpe03g00169 169
7 15715812 15716942 - Bpe021847.1 Bpe07g01003 1003
12 8867283 8869878 - Bpe005619.1 Bpe12g00363 363
12 8911446 8913332 - Bpe005620.2 Bpe12g00364 364
12 8935676 8938119 + Bpe005621.1 Bpe12g00365 365
12 8939306 8940525 - Bpe005622.1 Bpe12g00366 366
12 8943900 8946101 + Bpe005624.1 Bpe12g00368 368
1 982108 984095 + CaPI482276_01g000640.1 Cam01g0064 64
5 9285598 9288440 + CaPI482276_05g010290.1 Cam05g1029 1029
16 438023 439808 + Carg15086-RA Car16g00067 67
18 11693528 11696289 - Carg20359-RA Car18g01211 1211
1 498568 500550 + CcPI632755_01g000650.1 Cco01g0065 65
5 9041861 9044732 + CcPI632755_05g010280.1 Cco05g1028 1028
1 525294 527275 + CePI673135_01g000650.1 Cec01g0065 65
5 9014177 9021445 + CePI673135_05g010320.1 Cec05g1032 1032
6 11633708 11636289 + Chy6G117950.1 Chy06g01267 1267
9 15799984 15802213 + Chy9G171320.1 Chy09g01416 1416
1 590407 592390 + ClG42_01g0006500.10 Clacu01g0065 65
5 8999712 9002584 + ClG42_05g0101800.10 Clacu05g1018 1018
1 551186 553587 + ClCG01G000640.2 Cla01g00066 66
1 2033852 2047038 - ClCG01G002090.2 Cla01g00205 205
5 9316029 9319673 + ClCG05G008640.2 Cla05g00940 940
2 6519847 6522219 + CmaCh02G010950.1 Cma02g01095 1095
2 6522935 6527224 - CmaCh02G010960.1 Cma02g01096 1096
2 6529041 6531776 + CmaCh02G010970.1 Cma02g01097 1097
16 329719 331519 + CmaCh16G000760.1 Cma16g00076 76
18 9962609 9966211 + CmaCh18G012930.1 Cma18g01293 1293
6 7781833 7785195 + MELO3C006971.2.1 Cme06g01065 1065
9 22536861 22542327 + MELO3C005733.2.1 Cme09g01822 1822
9 23541961 23546170 + MELO3C005864.2.1 Cme09g01959 1959
6 7742132 7745530 + PI0025003.1 Cmetu06g1241 1241
2 6809404 6811698 + CmoCh02G011210.1 Cmo02g01121 1121
2 6813662 6817655 - CmoCh02G011220.1 Cmo02g01122 1122
16 368539 370311 + CmoCh16G000790.1 Cmo16g00079 79
18 12578033 12584583 + CmoCh18G013220.1 Cmo18g01322 1322
1 535261 537244 + CmPI595203_01g000650.1 Cmu01g0065 65
5 8844842 8847714 + CmPI595203_05g009710.1 Cmu05g0971 971
5 2798151 2800352 + Conep05aG0067900.1 Cone5ag0657 657
5 2816135 2818515 - Conep05aG0068200.1 Cone5ag0660 660
5 2821233 2826863 + Conep05aG0068500.1 Cone5ag0661 661
5 3760983 3763365 - Cp4.1LG05g06160.1 Cpe05g00619 619
5 3765216 3769481 + Cp4.1LG05g06100.1 Cpe05g00620 620
5 3770043 3772588 - Cp4.1LG05g06180.1 Cpe05g00621 621
9 273136 275776 + Cp4.1LG09g00410.1 Cpe09g00047 47
13 2515528 2519808 - Cp4.1LG13g03050.1 Cpe13g00301 301
14 339794 341582 + Cp4.1LG14g06630.1 Cpe14g00061 61
5 9722473 9730577 + CrPI670011_05g010500.1 Cre05g1050 1050
9 43782595 43784582 - CrPI670011_09g024430.1 Cre09g2443 2443
3 19003078 19009390 - CsaV3_3G021860.1 Csa03g02186 2186
3 19010288 19010905 - CsaV3_3G021870.1 Csa03g02187 2187
5 368803 372357 - CsaV3_5G000720.1 Csa05g00072 72
6 54123327 54128228 + Hsped.06g07590.1 Hepe06g0759 759
6 54129545 54134802 - Hsped.06g07600.1 Hepe06g0760 760
6 54199868 54203079 - Hsped.06g07650.1 Hepe06g0765 765
6 54207472 54209593 + Hsped.06g07660.1 Hepe06g0766 766
11 1116064 1120120 + Lag0030758.1 Lac11g0120 120
11 1121059 1123244 - Lag0030759.1 Lac11g0121 121
11 1124900 1128351 - Lag0030760.1 Lac11g0122 122
11 1140202 1142422 - Lag0030763.1 Lac11g0125 125
12 1316298 1322013 + Maker00039072 Lcy12g0099 99
12 1323009 1325651 - Maker00038442 Lcy12g0100 100
12 1327104 1330760 - Maker00038993 Lcy12g0101 101
12 1336120 1340810 + Maker00038677 Lcy12g0102 102
12 1341825 1344554 - Maker00038658 Lcy12g0103 103
5 19606720 19610290 - Lsi05G011670.1 Lsi05g01167 1167
10 587354 590746 - MC10g0090 Mch10g0101 101
1 67496609 67502755 - Sed0006515.1 Sed01g3831 3831
1 1488954 1492717 - Tan0016835.2 Tan01g0162 162
16 19301910 19308719 + Vvi16g854 Vvi16g854 854
16 19309224 19310778 + Vvi16g855 Vvi16g855 855
16 19314107 19317425 + Vvi16g856 Vvi16g856 856
16 19346926 19354509 - Vvi16g857 Vvi16g857 857
16 19358630 19365024 + Vvi16g858 Vvi16g858 858
16 19365746 19368456 - Vvi16g859 Vvi16g859 859
16 19380322 19386092 + Vvi16g860 Vvi16g860 860
16 19388138 19394697 + Vvi16g861 Vvi16g861 861
16 19395692 19401729 - Vvi16g862 Vvi16g862 862
16 19447212 19454986 + Vvi16g863 Vvi16g863 863
       

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