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
Vvi18g1640 . . . . . . . . . . Cma01g00838 . Car01g00777 . . . . . . . . . . . Cla08g00043 Cam08g0042 Cec08g0210 Cco08g0097 Clacu08g0059 Cmu08g0057 Cre08g0047 . . . . . . . Cme09g00027 . . . . . . . . Sed07g1831 . . . . . . . Cpe02g01020 Bhi06g00232 Tan10g2027 Cmetu09g1669 . . . . . . . . . . . Lsi08g00035 . . .
Vvi18g1641 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1642 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1643 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1644 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1645 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1646 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo17g00250 . . . . . . Bma02g00315 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1647 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1177 . . . . . . . Blo17g00249 . . . . . . Bma02g00314 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1648 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1649 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo17g00248 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 5532131 5533473 + XM_039034738.1 Bhi06g00232 232
17 2467328 2469394 - BLOR16069 Blo17g00248 248
17 2482256 2483810 - BLOR16070 Blo17g00249 249
17 2494375 2498144 + BLOR16071 Blo17g00250 250
2 3773066 3774577 - Bma014769.1 Bma02g00314 314
2 3807160 3809472 - Bma014771.1 Bma02g00315 315
8 973093 973946 - CaPI482276_08g000420.1 Cam08g0042 42
1 4777023 4778869 - Carg21724-RA Car01g00777 777
8 1608816 1609684 - CcPI632755_08g000970.1 Cco08g0097 97
8 3841593 3842454 + CePI673135_08g002100.1 Cec08g0210 210
8 1373535 1374391 - ClG42_08g0005900.10 Clacu08g0059 59
8 1206412 1207793 - ClCG08G000420.1 Cla08g00043 43
1 4590681 4591763 - CmaCh01G008380.1 Cma01g00838 838
9 250139 251955 - MELO3C022208.2.1 Cme09g00027 27
9 21621332 21623241 + PI0022359.2 Cmetu09g1669 1669
8 1292049 1292905 - CmPI595203_08g000570.1 Cmu08g0057 57
4 9993287 9994940 - Conep04aG0122300.1 Cone4ag1177 1177
2 9372758 9374151 + Cp4.1LG02g10670.1 Cpe02g01020 1020
8 1188052 1188905 - CrPI670011_08g000470.1 Cre08g0047 47
8 889851 891969 - Lsi08G000350.1 Lsi08g00035 35
7 22108449 22119350 - Sed0020386.2 Sed07g1831 1831
10 64474738 64476154 + Tan0013204.1 Tan10g2027 2027
18 26908702 26916821 - Vvi18g1640 Vvi18g1640 1640
18 26935653 26938124 - Vvi18g1641 Vvi18g1641 1641
18 27006643 27007560 - Vvi18g1642 Vvi18g1642 1642
18 27008803 27013993 + Vvi18g1643 Vvi18g1643 1643
18 27016035 27023669 - Vvi18g1644 Vvi18g1644 1644
18 27102062 27102260 - Vvi18g1645 Vvi18g1645 1645
18 27122026 27124079 - Vvi18g1646 Vvi18g1646 1646
18 27135200 27138565 + Vvi18g1647 Vvi18g1647 1647
18 27159125 27159396 - Vvi18g1648 Vvi18g1648 1648
18 27159396 27180532 - Vvi18g1649 Vvi18g1649 1649
       

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