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
Vvi18g190 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g191 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g192 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g193 Blo01g01561 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag0810 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g194 . . . . . . . . Cmo04g02520 . Cma01g01027 . . . . . . Bhi04g01849 . . . . . Lcy10g1283 Cla08g00643 . . . . . . . Cone7ag1496 . . . . . Cme03g00456 Blo17g00161 . . . . Bpe14g00403 . Bma02g00195 . . . . . . . . Cpe02g00871 . . . . . . . . . . . . . . Lsi08g00497 . Chy03g00554 .
Vvi18g195 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g196 . . . . . . . . Cmo04g02519 Cmo15g00654 . . Car01g00906 . . . . Bhi04g01850 . . . . . Lcy10g1281 Cla08g00641 . . . . . . . Cone7ag1498 . . . . . Cme03g00459 Blo17g00163 . . Bda13g01455 Bpe02g01680 . . Bma02g00198 . Cmo01g01069 . . . . . Cpe01g02085 . . . . . . . . . . . . . . . Lsi08g00492 . Chy03g00552 .
Vvi18g197 . . . . . Bpe04g00544 . . . . . . . . Sed01g0939 . . Bhi04g01851 Tan11g1219 Cmetu03g0027 . Hepe02g2737 . . Cla08g00640 Cam08g1059 Cec08g0644 Cco08g0755 Clacu08g0766 . Cre08g0572 . . . . . . . Cme03g00462 . . . . . . . . . . . . . . Car15g00590 . . . . . . . . . . . . . . . . Lsi08g00487 . Chy03g00549 .
Vvi18g198 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe14g00402 . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy03g00546 .
Vvi18g199 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
13 37372959 37375918 - Bda000291.1 Bda13g01455 1455
4 46101641 46104550 - XM_039028378.1 Bhi04g01849 1849
4 46165461 46168999 - XM_039028379.1 Bhi04g01850 1850
4 46305090 46308165 + XM_039029987.1 Bhi04g01851 1851
1 55375486 55383823 - BLOR01561 Blo01g01561 1561
17 1487430 1488767 + BLOR15982 Blo17g00161 161
17 1521023 1523892 + BLOR15984 Blo17g00163 163
2 1831481 1834111 + Bma014652.1 Bma02g00195 195
2 2113518 2117780 - Bma014656.1 Bma02g00198 198
2 19410197 19412510 + Bpe009516.1 Bpe02g01680 1680
4 3449381 3461061 - Bpe015222.1 Bpe04g00544 544
14 3765593 3766441 + Bpe007056.1 Bpe14g00402 402
14 3774662 3782278 + Bpe007057.1 Bpe14g00403 403
8 16943396 16946771 - CaPI482276_08g010590.1 Cam08g1059 1059
1 8559815 8562324 - Carg26871-RA Car01g00906 906
15 3261009 3262718 + Carg01565-RA Car15g00590 590
8 19334531 19337113 - CcPI632755_08g007550.1 Cco08g0755 755
8 18159741 18163180 - CePI673135_08g006440.1 Cec08g0644 644
3 7694123 7694911 + Chy3G055260.1 Chy03g00546 546
3 7787986 7789593 - Chy3G055290.1 Chy03g00549 549
3 7833214 7836072 + Chy3G055320.1 Chy03g00552 552
3 7866525 7871622 + Chy3G055340.1 Chy03g00554 554
8 17671996 17675326 - ClG42_08g0076600.10 Clacu08g0766 766
8 18515540 18518870 - ClCG08G006170.1 Cla08g00640 640
8 18530570 18536046 + ClCG08G006180.2 Cla08g00641 641
8 18583193 18592839 + ClCG08G006200.1 Cla08g00643 643
1 7547175 7547786 - CmaCh01G010270.1 Cma01g01027 1027
3 6494662 6499073 - MELO3C008452.2.1 Cme03g00456 456
3 6529735 6530986 - MELO3C027309.2.1 Cme03g00459 459
3 6613822 6615686 - MELO3C030020.2.1 Cme03g00462 462
3 10817073 10820053 + PI0020964.1 Cmetu03g0027 27
1 8592936 8594168 - CmoCh01G010690.1 Cmo01g01069 1069
4 18545050 18548475 - CmoCh04G025190.1 Cmo04g02519 2519
4 18552116 18555353 + CmoCh04G025200.1 Cmo04g02520 2520
15 3163820 3166728 + CmoCh15G006540.1 Cmo15g00654 654
7 10464340 10465665 - Conep07aG0153900.1 Cone7ag1496 1496
7 10473344 10475743 - Conep07aG0154100.1 Cone7ag1498 1498
17 6412094 6416125 + Conep17aG0082900.1 Cone17ag0810 810
1 17681591 17685014 + Cp4.1LG01g20800.1 Cpe01g02085 2085
2 5850147 5854121 - Cp4.1LG02g00020.1 Cpe02g00871 871
8 18584156 18587578 - CrPI670011_08g005720.1 Cre08g0572 572
2 75852635 75855430 - Hsped.02g27370.1 Hepe02g2737 2737
10 35593004 35596313 - Maker00008657 Lcy10g1281 1281
10 35625683 35629071 - Maker00008591 Lcy10g1283 1283
8 12741948 12746711 + Lsi08G004870.1 Lsi08g00487 487
8 12807446 12811271 + Lsi08G004920.1 Lsi08g00492 492
8 12840607 12845993 + Lsi08G004970.1 Lsi08g00497 497
1 6868309 6871242 - Sed0023917.1 Sed01g0939 939
11 10203623 10205275 + Tan0000307.1 Tan11g1219 1219
18 1824484 1825384 - Vvi18g190 Vvi18g190 190
18 1825415 1828541 + Vvi18g191 Vvi18g191 191
18 1835239 1835677 - Vvi18g192 Vvi18g192 192
18 1856438 1864097 + Vvi18g193 Vvi18g193 193
18 1877360 1894797 - Vvi18g194 Vvi18g194 194
18 1897285 1948700 - Vvi18g195 Vvi18g195 195
18 1952679 1968096 - Vvi18g196 Vvi18g196 196
18 1982672 1985445 - Vvi18g197 Vvi18g197 197
18 1996713 1997619 - Vvi18g198 Vvi18g198 198
18 2086363 2087547 + Vvi18g199 Vvi18g199 199
       

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