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
Vvi4g1182 . Blo16g00104 . . . Bpe13g00392 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1700 Cone9ag1623 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi07g01062 . . .
Vvi4g1183 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi07g01061 . . .
Vvi4g1184 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0890 Cone12ag0861 . . . . . . . . . . . . . . . . . Cma16g01271 . . . . . . . . . . . . . . . . . . . Lsi07g01060 . . .
Vvi4g1185 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1186 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1187 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1188 . . . . . . . Bma15g00889 . . Cma03g00625 Cma07g00386 Car03g00580 Car07g00339 . Cpe19g00896 Cpe10g00713 . . . . . . . Cla01g02041 Cam01g2147 Cec04g1804 Cco04g1870 Clacu01g2163 Cmu01g2039 Cre04g1715 . . Cone6ag1698 Cone9ag1622 . . . Cme08g00995 Blo05g00678 . . . . Bpe06g00158 . . . Cmo03g00653 Cmo07g00379 . . . . . . . . . . . . . . . . . . . . . Csa06g03400 . .
Vvi4g1189 Blo04g00863 . . . Bpe15g00497 Bpe13g00391 . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0892 . Cone6ag1697 Cone9ag1621 . . . . . . . . . . Bma03g00931 Bma06g00077 . . . Cma16g01278 . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1190 . . . . . . . . . . Cma03g00624 . Car03g00579 . . . . . . . . . . . . . . . . . . Cone8ag0893 Cone12ag0864 . . . . . . . . . . . . . . . Cmo03g00652 . . . . . . . . . . . . . . . . . . . . . . Csa06g03401 . .
Vvi4g1191 . . Bda04g00217 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0894 Cone12ag0865 . . . . . . Blo05g00677 . . . . Bpe06g00159 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 8336474 8341729 + Bda018506.1 Bda04g00217 217
4 9504801 9506635 + BLOR13775 Blo04g00863 863
5 22260277 22265555 + BLOR15639 Blo05g00677 677
5 22266184 22282932 - BLOR15640 Blo05g00678 678
16 2438657 2447461 - BLOR07352 Blo16g00104 104
3 9723545 9725459 + Bma017258.1 Bma03g00931 931
6 1192143 1194637 + Bma022689.1 Bma06g00077 77
15 30260011 30274689 + Bma014081.1 Bma15g00889 889
6 2962317 2975496 + Bpe019610.1 Bpe06g00158 158
6 2977459 2981222 - Bpe019611.2 Bpe06g00159 159
13 11659680 11662093 + Bpe006515.1 Bpe13g00391 391
13 11674047 11680767 + Bpe006516.1 Bpe13g00392 392
15 16220469 16222002 - Bpe001430.1 Bpe15g00497 497
1 34249854 34258017 - CaPI482276_01g021470.1 Cam01g2147 2147
3 5511680 5512584 + Carg00539-RA Car03g00579 579
3 5513261 5519687 - Carg00540-RA Car03g00580 580
7 1692667 1700143 - Carg07919-RA Car07g00339 339
4 33337388 33345452 - CcPI632755_04g018700.1 Cco04g1870 1870
4 36813361 36821510 - CePI673135_04g018040.1 Cec04g1804 1804
1 33103021 33111647 - ClG42_01g0216300.10 Clacu01g2163 2163
1 34914667 34925270 - ClCG01G020915.1 Cla01g02041 2041
3 5422972 5424264 + CmaCh03G006240.1 Cma03g00624 624
3 5424336 5430678 - CmaCh03G006250.1 Cma03g00625 625
7 1654197 1661247 - CmaCh07G003860.1 Cma07g00386 386
16 9682839 9689000 + CmaCh16G012710.1 Cma16g01271 1271
16 9726797 9729889 + CmaCh16G012780.1 Cma16g01278 1278
8 6495590 6504352 - MELO3C007975.2.1 Cme08g00995 995
3 5900474 5905759 + CmoCh03G006520.1 Cmo03g00652 652
3 5905616 5912011 - CmoCh03G006530.1 Cmo03g00653 653
7 1743637 1750955 - CmoCh07G003790.1 Cmo07g00379 379
1 33440558 33449174 - CmPI595203_01g020390.1 Cmu01g2039 2039
6 12817405 12819906 + Conep06aG0176200.1 Cone6ag1697 1697
6 12819983 12827665 - Conep06aG0176300.1 Cone6ag1698 1698
6 12838920 12843714 + Conep06aG0176500.1 Cone6ag1700 1700
8 8693574 8698348 + Conep08aG0091600.1 Cone8ag0890 890
8 8700114 8702470 - Conep08aG0091800.1 Cone8ag0892 892
8 8705777 8708598 - Conep08aG0091900.1 Cone8ag0893 893
8 8708985 8713355 - Conep08aG0092000.1 Cone8ag0894 894
9 11559669 11562073 + Conep09aG0167100.1 Cone9ag1621 1621
9 11562359 11570232 - Conep09aG0167200.1 Cone9ag1622 1622
9 11574358 11579101 + Conep09aG0167300.1 Cone9ag1623 1623
12 7716464 7720990 + Conep12aG0088600.1 Cone12ag0861 861
12 7730896 7731878 - Conep12aG0088900.1 Cone12ag0864 864
12 7732220 7736588 - Conep12aG0089000.1 Cone12ag0865 865
10 4078773 4085636 + Cp4.1LG10g10590.1 Cpe10g00713 713
19 6531901 6539354 + Cp4.1LG19g08620.1 Cpe19g00896 896
4 35298384 35306561 - CrPI670011_04g017150.1 Cre04g1715 1715
6 28168645 28179125 - CsaV3_6G047860.1 Csa06g03400 3400
6 28169355 28170138 + CsaV3_6G047870.1 Csa06g03401 3401
7 15965444 15966584 - Lsi07G010600.1 Lsi07g01060 1060
7 15966748 15974092 - Lsi07G010610.1 Lsi07g01061 1061
7 15999581 16000429 + Lsi07G010620.1 Lsi07g01062 1062
4 20599724 20603686 - Vvi4g1182 Vvi4g1182 1182
4 20609430 20612222 + Vvi4g1183 Vvi4g1183 1183
4 20612271 20621048 + Vvi4g1184 Vvi4g1184 1184
4 20632566 20634565 + Vvi4g1185 Vvi4g1185 1185
4 20659902 20663897 + Vvi4g1186 Vvi4g1186 1186
4 20663902 20665892 + Vvi4g1187 Vvi4g1187 1187
4 20669031 20711919 + Vvi4g1188 Vvi4g1188 1188
4 20725982 20733193 - Vvi4g1189 Vvi4g1189 1189
4 20738355 20739576 - Vvi4g1190 Vvi4g1190 1190
4 20752322 20765631 - Vvi4g1191 Vvi4g1191 1191
       

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