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
Vvi4g1282 . . . . . . . . . Cmo20g01073 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma20g01065 . . . . Bhi10g01667 . . . Hepe08g1246 . . Cla02g00059 . . . . . . Lsi10g00721 . . Cme11g00063
Vvi4g1283 . . . . . . . . . . Cma03g01090 . Car03g00981 . Sed10g0499 . Cpe10g00342 Bhi03g01357 Tan03g1314 Cmetu08g0769 . Hepe04g1117 . . Cla01g01520 . . . . . . . . Cone6ag1289 . Lsi01g01145 . . Cme08g01079 . Blo06g00198 . . . . . . . Cmo03g01076 . . . . . . . . . . . . . . . . . . . . . . Csa06g02786 Chy02g01049 .
Vvi4g1284 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1285 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1286 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone20ag0846 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1287 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1288 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1289 . . . Bda10g00393 . . . Bma15g00795 . . . Cma07g00799 . Car07g00786 Sed14g0225 . . Bhi03g01355 Tan03g1312 Cmetu08g1351 . Hepe04g1115 . . . . . . . . . . . . . . . . . . . . . Bpe10g00255 . . . . . Cmo07g00821 . . . . . . . . . . . . . . . . . . . . . . Chy02g01051 .
Vvi4g1290 . . . . . . . Bma15g00794 . . Cma03g01091 . Car03g00983 . . Cpe19g00531 Cpe10g00339 . . . . . . . Cla01g01518 Cam01g1588 Cec04g1231 Cco04g1302 Clacu01g1613 Cmu01g1499 Cre04g1177 . . . . Lsi01g01147 . . Cme08g01081 . Blo06g00197 . . . . . . . Cmo03g01077 . . . . . . . . . . . . . . . . . . . . . . Csa06g02784 . .
Vvi4g1291 . . . Bda10g00395 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe10g00258 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
10 35921391 35924002 - Bda007219.1 Bda10g00393 393
10 36008515 36011513 + Bda007222.1 Bda10g00395 395
3 28133377 28141814 - XM_039025945.1 Bhi03g01355 1355
3 28220069 28229257 - XM_039025301.1 Bhi03g01357 1357
10 42191500 42193589 - XM_039045404.1 Bhi10g01667 1667
6 8173483 8175391 - BLOR16780 Blo06g00197 197
6 8196813 8202870 - BLOR16781 Blo06g00198 198
15 17076248 17078892 + Bma013876.1 Bma15g00794 794
15 17294126 17296681 + Bma013880.1 Bma15g00795 795
10 9624595 9626964 - Bpe002589.1 Bpe10g00255 255
10 9720393 9723243 + Bpe002593.1 Bpe10g00258 258
1 29356562 29359707 - CaPI482276_01g015880.1 Cam01g1588 1588
3 7569732 7574753 + Carg10540-RA Car03g00981 981
3 7579221 7581502 + Carg10538-RA Car03g00983 983
7 4113022 4115719 + Carg05308-RA Car07g00786 786
4 28286554 28293548 - CcPI632755_04g013020.1 Cco04g1302 1302
4 31848494 31855483 - CePI673135_04g012310.1 Cec04g1231 1231
2 7191495 7196396 + Chy2G033160.1 Chy02g01049 1049
2 7212086 7215233 + Chy2G033180.1 Chy02g01051 1051
1 28147767 28150900 - ClG42_01g0161300.10 Clacu01g1613 1613
1 29670031 29678383 - ClCG01G015460.2 Cla01g01518 1518
1 29702681 29709422 - ClCG01G015480.1 Cla01g01520 1520
2 609747 611225 + ClCG02G000570.1 Cla02g00059 59
3 7468367 7472770 + CmaCh03G010900.1 Cma03g01090 1090
3 7477736 7480176 + CmaCh03G010910.1 Cma03g01091 1091
7 3639736 3642244 + CmaCh07G007990.1 Cma07g00799 799
20 8020915 8032168 + CmaCh20G010650.1 Cma20g01065 1065
8 7092056 7097152 + MELO3C008048.2.1 Cme08g01079 1079
8 7114046 7117536 + MELO3C008050.2.1 Cme08g01081 1081
11 537357 539937 + MELO3C034573.2.1 Cme11g00063 63
8 18416212 18421200 - PI0021380.1 Cmetu08g0769 769
8 18395309 18402660 - PI0022440.1 Cmetu08g1351 1351
3 8048733 8053335 + CmoCh03G010760.1 Cmo03g01076 1076
3 8058099 8060361 + CmoCh03G010770.1 Cmo03g01077 1077
7 3832096 3838560 + CmoCh07G008210.1 Cmo07g00821 821
20 9924630 9928761 + CmoCh20G010730.1 Cmo20g01073 1073
1 28496185 28503254 - CmPI595203_01g014990.1 Cmu01g1499 1499
6 10322146 10325922 + Conep06aG0133700.1 Cone6ag1289 1289
20 6163140 6168186 + Conep20aG0087200.1 Cone20ag0846 846
10 1985903 1987732 - Cp4.1LG10g03460.1 Cpe10g00339 339
10 1993033 1997462 - Cp4.1LG10g03450.1 Cpe10g00342 342
19 4510969 4513043 - Cp4.1LG19g11980.1 Cpe19g00531 531
4 30359798 30366489 - CrPI670011_04g011770.1 Cre04g1177 1177
6 24278625 24281606 - CsaV3_6G041700.1 Csa06g02784 2784
6 24296507 24301833 - CsaV3_6G041720.1 Csa06g02786 2786
4 66065518 66068607 - Hsped.04g11150.1 Hepe04g1115 1115
4 66081787 66087688 - Hsped.04g11170.1 Hepe04g1117 1117
8 13274600 13276840 + Hsped.08g12460.1 Hepe08g1246 1246
1 9625359 9632625 + Lsi01G011450.1 Lsi01g01145 1145
1 9652055 9655569 + Lsi01G011470.1 Lsi01g01147 1147
10 10074054 10078203 - Lsi10G007210.1 Lsi10g00721 721
10 3271368 3277026 + Sed0020894.2 Sed10g0499 499
14 2490734 2499896 + Sed0009181.1 Sed14g0225 225
3 69602248 69612373 - Tan0006402.1 Tan03g1312 1312
3 69633787 69641327 - Tan0000981.1 Tan03g1314 1314
4 22409269 22410748 - Vvi4g1282 Vvi4g1282 1282
4 22411377 22436792 - Vvi4g1283 Vvi4g1283 1283
4 22455729 22458751 + Vvi4g1284 Vvi4g1284 1284
4 22463211 22468132 + Vvi4g1285 Vvi4g1285 1285
4 22468202 22470668 + Vvi4g1286 Vvi4g1286 1286
4 22475451 22477877 + Vvi4g1287 Vvi4g1287 1287
4 22479190 22485297 + Vvi4g1288 Vvi4g1288 1288
4 22516461 22518881 + Vvi4g1289 Vvi4g1289 1289
4 22531683 22533280 - Vvi4g1290 Vvi4g1290 1290
4 22535020 22554070 + Vvi4g1291 Vvi4g1291 1291
       

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