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
Vvi17g936 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g937 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme12g01784 . . . . . . . . . . . . . . . . . Bhi08g01358 . . . Hepe07g2316 . . . . . . . . . . . . .
Vvi17g938 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme12g01785 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g939 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g940 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g941 . . . . . . . . . . . . . . . Cpe20g00182 . . . . . . . . . . . . . . . . . . . . . Chy12g01355 Cme12g01786 . . . . . . . . . . . Cma13g00957 . Car13g00794 . . . . . . . . . . Cla01g01457 Cam01g1524 Cec01g1565 Cco01g1610 Clacu01g1548 Cmu01g1438 Cre01g1360 . . . .
Vvi17g942 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g943 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g944 . . . . . . . Bma12g01273 Cmo13g01209 . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0309 Lsi02g00014 Csa01g00489 Chy12g01592 Cme12g02050 . Blo15g00052 . . Bpe07g01078 . . . . . . . . Car13g00981 . . . . . . . . . . . . . . . . . . . . .
Vvi17g945 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 40722638 40723484 - XM_039039275.1 Bhi08g01358 1358
15 395158 397704 + BLOR06446 Blo15g00052 52
12 45738861 45748559 + Bma008638.1 Bma12g01273 1273
7 16157699 16161102 + Bpe021918.2 Bpe07g01078 1078
1 28797148 28797765 + CaPI482276_01g015240.1 Cam01g1524 1524
13 8793957 8794568 + Carg04878-RA Car13g00794 794
13 9767710 9797111 - Carg04690-RA Car13g00981 981
1 28813459 28814076 + CcPI632755_01g016100.1 Cco01g1610 1610
1 30234986 30235603 + CePI673135_01g015650.1 Cec01g1565 1565
12 17811645 17817536 + Chy12G219550.1 Chy12g01355 1355
12 19469523 19474717 + Chy12G221920.1 Chy12g01592 1592
1 27580162 27580779 + ClG42_01g0154800.10 Clacu01g1548 1548
1 29085453 29086349 + ClCG01G014760.2 Cla01g01457 1457
13 7504337 7504948 + CmaCh13G009570.1 Cma13g00957 957
12 24404194 24404950 + MELO3C002177.2.1 Cme12g01784 1784
12 24408506 24409287 + MELO3C002176.2.1 Cme12g01785 1785
12 24412872 24413740 + MELO3C002175.2.1 Cme12g01786 1786
12 25964765 26005602 - MELO3C001926.2.1 Cme12g02050 2050
13 9486730 9497334 - CmoCh13G012090.1 Cmo13g01209 1209
1 27923148 27923765 + CmPI595203_01g014380.1 Cmu01g1438 1438
19 2359594 2377431 + Conep19aG0032000.1 Cone19ag0309 309
20 1031937 1032548 - Cp4.1LG20g01850.1 Cpe20g00182 182
1 26796480 26797097 + CrPI670011_01g013600.1 Cre01g1360 1360
1 3182830 3217402 - CsaV3_1G004890.1 Csa01g00489 489
7 67484827 67485623 + Hsped.07g23160.1 Hepe07g2316 2316
2 170913 216301 + Lsi02G000140.1 Lsi02g00014 14
17 13695713 13701570 - Vvi17g936 Vvi17g936 936
17 13764389 13764749 + Vvi17g937 Vvi17g937 937
17 13766754 13773042 + Vvi17g938 Vvi17g938 938
17 13773084 13795036 + Vvi17g939 Vvi17g939 939
17 13829242 13829482 + Vvi17g940 Vvi17g940 940
17 13836303 13837228 + Vvi17g941 Vvi17g941 941
17 13861904 13863458 - Vvi17g942 Vvi17g942 942
17 13895317 13953615 - Vvi17g943 Vvi17g943 943
17 14000593 14084302 + Vvi17g944 Vvi17g944 944
17 14084360 14084525 + Vvi17g945 Vvi17g945 945
       

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