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
Vvi5g949 . Blo12g00108 . . . . Bma04g01167 . . . . . Car06g01061 . . . . . . . . . . . . . . . . . . . . . . . . . Cme06g00374 . . . . . . . . . Cmo06g01245 . . . . . . . . . . . . . . . . . . . . . . . Chy06g00355 .
Vvi5g950 . . Bda03g01134 . Bpe04g01077 . . . . . . . . . Sed02g1516 Cpe08g00405 . Bhi01g00216 Tan10g0506 Cmetu06g0645 Lac12g2024 Hepe05g1769 . Lcy11g1784 . . . . . . . . Cone15ag0259 . . Lsi05g01851 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g951 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g952 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g953 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g954 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g955 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g956 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g957 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g958 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 11965742 11975477 + Bda033519 Bda03g01134 1134
1 4114381 4122373 - XM_039046877.1 Bhi01g00216 216
12 7800131 7807034 + BLOR04127 Blo12g00108 108
4 30111432 30119609 - Bma019902.1 Bma04g01167 1167
4 8293116 8300532 + Bpe015749.1 Bpe04g01077 1077
6 7965190 7977243 - Carg06298-RA Car06g01061 1061
6 2365904 2372223 - Chy6G108830.1 Chy06g00355 355
6 2323226 2332307 - MELO3C006304.2.1 Cme06g00374 374
6 2537488 2544193 - PI0007684.1 Cmetu06g0645 645
6 9407983 9418677 - CmoCh06G012450.1 Cmo06g01245 1245
15 1215693 1222426 + Conep15aG0026500.1 Cone15ag0259 259
8 2585603 2596677 + Cp4.1LG08g02820.1 Cpe08g00405 405
5 67993731 68002461 + Hsped.05g17690.1 Hepe05g1769 1769
12 37234918 37238320 + Lag0016396.1 Lac12g2024 2024
11 41630880 41640300 + Maker00031623 Lcy11g1784 1784
5 25748942 25757288 + Lsi05G018510.1 Lsi05g01851 1851
2 50947643 50956620 + Sed0015957.2 Sed02g1516 1516
10 4075720 4083619 - Tan0014836.1 Tan10g0506 506
5 15889271 15890243 - Vvi5g949 Vvi5g949 949
5 15891381 15916025 - Vvi5g950 Vvi5g950 950
5 15921762 15922767 + Vvi5g951 Vvi5g951 951
5 15932660 15935511 + Vvi5g952 Vvi5g952 952
5 15946854 15952125 - Vvi5g953 Vvi5g953 953
5 15959510 15959702 - Vvi5g954 Vvi5g954 954
5 15961075 15961633 - Vvi5g955 Vvi5g955 955
5 15967369 15971395 - Vvi5g956 Vvi5g956 956
5 16036557 16036890 - Vvi5g957 Vvi5g957 957
5 16042061 16042274 - Vvi5g958 Vvi5g958 958
       

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