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
Vvi1g821 Blo01g00413 . . . Bpe13g00470 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone20ag1384 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g822 . . . . . Bpe10g00814 . Bma15g00210 Cmo04g01691 . . . . . Sed06g1583 . Cpe01g01428 Bhi07g01640 Tan04g1144 Cmetu10g1056 . . . . . . . . . . . Cone2ag0873 Cone16ag0137 Cone13ag0098 Cone19ag0101 Lsi04g00490 Csa05g02393 Chy10g00955 Cme10g00470 Blo06g00856 . . . . . . . . . . Cma04g01614 . Car04g01655 . . . . . . . . . . . . . . . . . . . . .
Vvi1g823 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0628 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g824 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g825 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g826 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g827 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda07g01447 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g828 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g829 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g830 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 26892464 26895421 + Bda028274.1 Bda07g01447 1447
7 46199297 46203090 - XM_039037377.1 Bhi07g01640 1640
1 4671433 4674435 - BLOR00413 Blo01g00413 413
6 31810596 31816852 - BLOR17439 Blo06g00856 856
15 2109900 2112938 + Bma013194.1 Bma15g00210 210
10 14207382 14210640 - Bpe003117.1 Bpe10g00814 814
13 12194178 12197188 + Bpe010182.1 Bpe13g00470 470
4 9546593 9549631 + Carg01745-RA Car04g01655 1655
10 15109618 15112701 + Chy10G181490.1 Chy10g00955 955
4 8156954 8160434 + CmaCh04G016140.1 Cma04g01614 1614
10 2967927 2971862 - MELO3C012047.2.1 Cme10g00470 470
10 19030035 19033826 + PI0002255.1 Cmetu10g1056 1056
4 8582297 8591760 + CmoCh04G016910.1 Cmo04g01691 1691
2 34665051 34668640 - Conep02aG0190300.1 Cone2ag0873 873
8 6202061 6203390 + Conep08aG0064900.1 Cone8ag0628 628
13 600046 603634 - Conep13aG0010300.1 Cone13ag0098 98
16 780228 783889 + Conep16aG0013900.1 Cone16ag0137 137
19 575228 578674 - Conep19aG0010700.1 Cone19ag0101 101
20 8826703 8831209 - Conep20aG0143100.1 Cone20ag1384 1384
1 8576602 8580143 + Cp4.1LG01g12900.1 Cpe01g01428 1428
5 26087624 26091759 + CsaV3_5G032120.1 Csa05g02393 2393
4 4523640 4528028 - Lsi04G004900.1 Lsi04g00490 490
6 40621164 40625631 - Sed0019201.1 Sed06g1583 1583
4 10640244 10644008 - Tan0010018.1 Tan04g1144 1144
1 10246454 10250255 - Vvi1g821 Vvi1g821 821
1 10253869 10258080 + Vvi1g822 Vvi1g822 822
1 10259337 10260965 - Vvi1g823 Vvi1g823 823
1 10268686 10268818 - Vvi1g824 Vvi1g824 824
1 10275244 10279439 + Vvi1g825 Vvi1g825 825
1 10280340 10281165 + Vvi1g826 Vvi1g826 826
1 10281463 10283659 - Vvi1g827 Vvi1g827 827
1 10284071 10289573 - Vvi1g828 Vvi1g828 828
1 10289970 10290132 - Vvi1g829 Vvi1g829 829
1 10300522 10305820 + Vvi1g830 Vvi1g830 830
       

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