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
Vvi1g11 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone2ag0792 Cone16ag0222 Cone13ag0026 Cone19ag0035 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g12 . Blo16g01078 . . . . . . Cmo04g01795 Cmo18g01120 . Cma18g01098 . Car18g01013 Sed07g2037 Cpe09g00228 Cpe01g01514 Bhi07g01472 Tan04g0975 Cmetu10g1095 . . . . . . . . . . . Cone13ag0895 Cone19ag0892 . . Lsi04g00355 Csa05g02521 . Cme10g00349 . . . . . . . . . . . Cma04g01709 . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g13 . . . . . . Bma14g01678 . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0896 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g14 Blo01g00460 . . Bda11g01166 Bpe13g01365 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01166 . Bpe02g02309 Bma01g00129 . . . . . . . . . Cpe07g00091 . . . . . . . . . . . . . . . . . .
Vvi1g15 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g16 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g17 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g18 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g19 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0897 . . Cone9ag0531 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g20 . . . . . Bpe10g00904 . Bma15g00128 . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0898 Cone19ag0895 . . . . . . Blo06g00930 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 11989802 11992425 + Bda007659.1 Bda11g01166 1166
7 43206383 43209683 - XM_039037416.1 Bhi07g01472 1472
1 5081350 5083767 + BLOR00460 Blo01g00460 460
6 32532101 32534511 + BLOR17513 Blo06g00930 930
16 39331050 39332573 + BLOR21865 Blo16g01078 1078
1 1260216 1262805 + Bma000294.2 Bma01g00129 129
14 35712974 35721876 + Bma012420.1 Bma14g01678 1678
15 1399255 1400592 - Bma013106.2 Bma15g00128 128
2 23769864 23772483 - Bpe010125.1 Bpe02g02309 2309
10 14702301 14703749 + Bpe024722 Bpe10g00904 904
13 18884890 18887443 + Bpe011026.1 Bpe13g01365 1365
18 10558350 10561534 - Carg17317-RA Car18g01013 1013
4 8594676 8596684 + CmaCh04G017090.1 Cma04g01709 1709
18 8991641 8995269 - CmaCh18G010980.1 Cma18g01098 1098
10 2260905 2262649 - MELO3C034075.2.1 Cme10g00349 349
10 19750794 19752973 + PI0000741.1 Cmetu10g1095 1095
4 9028899 9030980 + CmoCh04G017950.1 Cmo04g01795 1795
18 11567244 11572287 - CmoCh18G011200.1 Cmo18g01120 1120
2 33927478 33931980 + Conep02aG0181900.1 Cone2ag0792 792
9 2544585 2545803 + Conep09aG0054100.1 Cone9ag0531 531
13 172955 175342 + Conep13aG0002800.1 Cone13ag0026 26
13 7927670 7928678 - Conep13aG0092300.1 Cone13ag0895 895
13 7935681 7942182 + Conep13aG0092400.1 Cone13ag0896 896
13 7942550 7943343 + Conep13aG0092500.1 Cone13ag0897 897
13 7943604 7946136 - Conep13aG0092600.1 Cone13ag0898 898
16 1572811 1576916 - Conep16aG0022600.1 Cone16ag0222 222
19 246608 249074 + Conep19aG0003800.1 Cone19ag0035 35
19 6993345 6994205 - Conep19aG0091700.1 Cone19ag0892 892
19 7001557 7002509 - Conep19aG0092000.1 Cone19ag0895 895
1 9051093 9053781 + Cp4.1LG01g15160.1 Cpe01g01514 1514
7 440421 443265 - Cp4.1LG07g00880.1 Cpe07g00091 91
9 1313947 1316378 + Cp4.1LG09g02290.1 Cpe09g00228 228
5 26755968 26758348 + CsaV3_5G033400.1 Csa05g02521 2521
4 3547540 3550695 - Lsi04G003550.1 Lsi04g00355 355
7 35501300 35503495 + Sed0007972.1 Sed07g2037 2037
4 8848483 8850406 - Tan0016725.1 Tan04g0975 975
1 230333 235218 + Vvi1g11 Vvi1g11 11
1 237201 239435 - Vvi1g12 Vvi1g12 12
1 246095 257603 + Vvi1g13 Vvi1g13 13
1 258816 261979 - Vvi1g14 Vvi1g14 14
1 263081 269275 - Vvi1g15 Vvi1g15 15
1 279358 279820 - Vvi1g16 Vvi1g16 16
1 279893 281109 + Vvi1g17 Vvi1g17 17
1 284311 287530 - Vvi1g18 Vvi1g18 18
1 297104 301979 + Vvi1g19 Vvi1g19 19
1 302205 305739 - Vvi1g20 Vvi1g20 20
       

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