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
Vvi1g1311 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1312 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00173 Cam06g0039 Cec06g0193 Cco06g0186 Clacu06g0188 Cmu06g0183 Cre06g0955 . . . . . . Chy11g01815 Cme11g02349 . . . . . . . . Sed09g0793 . . . . . . Cpe17g00928 . Bhi12g02414 Tan06g1469 Cmetu11g2431 . Hepe03g1151 . . . . . . . . . Lsi09g01751 . . .
Vvi1g1313 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1314 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1315 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00172 . . . . . . . . . . . . Chy11g01816 Cme11g02350 . Blo12g00288 . . . . . . . . . . . . . . . Bhi12g02413 . . . . . . . . . . . . . Lsi09g01752 . . .
Vvi1g1316 . Blo16g00704 . . . . . . . . . . . . . . . . . . . . . . Cla06g00171 Cam06g0041 Cec06g0191 Cco06g0184 Clacu06g0186 Cmu06g0181 Cre06g0953 . . . . . . Chy11g01817 Cme11g02351 . . . . . . . . Sed07g0121 . . . . . . Cpe17g00930 . Bhi12g02412 Tan06g1467 Cmetu11g1130 . Hepe03g1153 . . . . . . . . . Lsi09g01753 . . .
Vvi1g1317 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00291 . . Blo02g00200 . . . Bpe14g00805 . . . . . . . . . . . Cpe03g01214 . . . . . . . . . . . . . . . . Chy07g01489 Cme07g01927
Vvi1g1318 . . . Bda11g00381 Bpe13g00821 . . . . . . . . . . . . . . . . . . . Cla06g00170 . . . . . . . . . . . Csa04g00289 . Cme11g02352 Blo02g00201 Blo12g00289 . Bda11g00381 Bpe14g00806 . . Bma06g01336 . . . . . . . Cpe17g00931 Cpe03g01213 Bhi12g02411 . . . . . . . . . . . . . Lsi09g01754 . Chy07g01492 Cme07g01929
Vvi1g1319 . . . Bda11g00380 Bpe13g00822 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g00380 . . . Bma06g01335 Sed07g0123 . . . . . . . . Bhi12g02410 Tan06g1465 Cmetu11g1851 . . . . . . . . . . . . . . .
Vvi1g1320 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 4173526 4175068 + Bda005119.1 Bda11g00380 380
11 4178297 4179413 - Bda005120.1 Bda11g00381 381
12 75983581 75991349 + XM_039019096.1 Bhi12g02410 2410
12 75995919 75997673 - XM_039019095.1 Bhi12g02411 2411
12 76091579 76095413 + XM_039019870.1 Bhi12g02412 2412
12 76096598 76102753 - XM_039018452.1 Bhi12g02413 2413
12 76139551 76140111 + XM_039020069.1 Bhi12g02414 2414
2 1816515 1818245 + BLOR09930 Blo02g00200 200
2 1826040 1827101 + BLOR09931 Blo02g00201 201
12 17085939 17088765 + BLOR04307 Blo12g00288 288
12 17091990 17093000 + BLOR04308 Blo12g00289 289
16 27022139 27025546 - BLOR21491 Blo16g00704 704
6 50301505 50303016 + Bma024446.1 Bma06g01335 1335
6 50306730 50307834 - Bma024447.1 Bma06g01336 1336
13 14499833 14500948 + Bpe010512.1 Bpe13g00821 821
13 14504069 14505590 - Bpe010513.1 Bpe13g00822 822
14 6065318 6067086 + Bpe014182.1 Bpe14g00805 805
14 6073793 6074916 + Bpe014183.1 Bpe14g00806 806
6 2205472 2205861 - CaPI482276_06g000390.1 Cam06g0039 39
6 2231361 2234156 - CaPI482276_06g000410.1 Cam06g0041 41
6 1942592 1945307 + CcPI632755_06g001840.1 Cco06g0184 184
6 1970836 1971225 + CcPI632755_06g001860.1 Cco06g0186 186
6 1971453 1974227 + CePI673135_06g001910.1 Cec06g0191 191
6 1999823 2000212 + CePI673135_06g001930.1 Cec06g0193 193
7 19188915 19189928 + Chy7G143190.1 Chy07g01489 1489
7 19206972 19207922 + Chy7G143220.1 Chy07g01492 1492
11 24507400 24507928 - Chy11G203950.1 Chy11g01815 1815
11 24519828 24524229 + Chy11G203960.1 Chy11g01816 1816
11 24525755 24528413 - Chy11G203970.1 Chy11g01817 1817
6 2125003 2127758 + ClG42_06g0018600.10 Clacu06g0186 186
6 2153486 2153875 + ClG42_06g0018800.10 Clacu06g0188 188
6 1952493 1954295 - ClCG06G001870.1 Cla06g00170 170
6 2005437 2008235 + ClCG06G001880.2 Cla06g00171 171
6 2009391 2015210 - ClCG06G001890.1 Cla06g00172 172
6 2037147 2037536 + ClCG06G001900.1 Cla06g00173 173
7 24481544 24482823 + MELO3C017752.2.1 Cme07g01927 1927
7 24500988 24502518 + MELO3C017754.2.1 Cme07g01929 1929
11 30494799 30495239 - MELO3C022339.2.1 Cme11g02349 2349
11 30503519 30509090 + MELO3C022340.2.1 Cme11g02350 2350
11 30509871 30512205 - MELO3C022341.2.1 Cme11g02351 2351
11 30536828 30538881 + MELO3C022342.2.1 Cme11g02352 2352
11 1549963 1552944 + PI0016205.1 Cmetu11g1130 1130
11 1513915 1518407 + PI0025186.1 Cmetu11g1851 1851
11 1571326 1571931 + PI0025585.1 Cmetu11g2431 2431
6 1920433 1923195 + CmPI595203_06g001810.1 Cmu06g0181 181
6 1948923 1949312 + CmPI595203_06g001830.1 Cmu06g0183 183
3 9905080 9906604 - Cp4.1LG03g12850.1 Cpe03g01213 1213
3 9911818 9913225 - Cp4.1LG03g12880.1 Cpe03g01214 1214
17 7164865 7165245 - Cp4.1LG17g09310.1 Cpe17g00928 928
17 7172058 7174764 - Cp4.1LG17g09330.1 Cpe17g00930 930
17 7175803 7178080 + Cp4.1LG17g09240.1 Cpe17g00931 931
6 3009918 3012675 + CrPI670011_06g009530.1 Cre06g0953 953
6 3038617 3039006 + CrPI670011_06g009550.1 Cre06g0955 955
4 1800450 1802736 - CsaV3_4G002890.1 Csa04g00289 289
4 1816715 1817725 - CsaV3_4G002910.1 Csa04g00291 291
3 64933921 64934439 - Hsped.03g11510.1 Hepe03g1151 1151
3 65001573 65006862 - Hsped.03g11530.1 Hepe03g1153 1153
9 26176902 26177294 - Lsi09G017510.1 Lsi09g01751 1751
9 26197883 26204462 + Lsi09G017520.1 Lsi09g01752 1752
9 26204995 26209945 - Lsi09G017530.1 Lsi09g01753 1753
9 26264656 26267018 + Lsi09G017540.1 Lsi09g01754 1754
7 1096194 1099444 - Sed0004482.2 Sed07g0121 121
7 1131198 1134990 - Sed0025765.1 Sed07g0123 123
9 23229695 23230188 + Sed0003426.1 Sed09g0793 793
6 19638454 19652382 + Tan0001690.3 Tan06g1465 1465
6 19777429 19781046 + Tan0019765.1 Tan06g1467 1467
6 19861867 19862250 + Tan0000284.1 Tan06g1469 1469
1 22030978 22031840 + Vvi1g1311 Vvi1g1311 1311
1 22035761 22036085 - Vvi1g1312 Vvi1g1312 1312
1 22044690 22044819 + Vvi1g1313 Vvi1g1313 1313
1 22058281 22060336 + Vvi1g1314 Vvi1g1314 1314
1 22067038 22072113 + Vvi1g1315 Vvi1g1315 1315
1 22072444 22074122 - Vvi1g1316 Vvi1g1316 1316
1 22080241 22083611 + Vvi1g1317 Vvi1g1317 1317
1 22097587 22099439 + Vvi1g1318 Vvi1g1318 1318
1 22102564 22108124 - Vvi1g1319 Vvi1g1319 1319
1 22115840 22118070 + Vvi1g1320 Vvi1g1320 1320
       

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