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
Vvi3g946 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g947 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g948 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g949 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g950 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g951 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g952 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g953 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g954 . . . . . . . . . . . . . . . . . . . . . . . . Cla10g00920 Cam10g0940 Cec10g0979 Cco10g0938 Clacu10g0965 Cmu10g1748 Cre10g1124 . . . . . . . . . . . . . . . . . . Cmo16g00295 . . . . Cpe14g00229 Cpe01g00595 . . . . . . . . . . . . . . . . . Cme07g02244
Vvi3g955 . . . . . . . Bma12g00378 Cmo19g00493 Cmo11g01464 . . . . . Cpe04g00370 Cpe15g00374 Bhi05g00935 . . . . . . . . . . . . . . . . . . . . Cme01g00203 . . Bda15g00491 . . . . . . . . Cma11g01667 Cma19g00476 Car11g01178 Car19g00351 . . . . . . . . . Cla09g01575 Cam09g1578 Cec09g1732 Cco09g1794 . . Cre09g1623 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
15 8051920 8053485 + Bda012319.1 Bda15g00491 491
5 32782524 32786533 - XM_039031996.1 Bhi05g00935 935
12 7224813 7235341 - Bma007320.1 Bma12g00378 378
9 26651842 26654550 - CaPI482276_09g015780.1 Cam09g1578 1578
10 21314130 21319064 - CaPI482276_10g009400.1 Cam10g0940 940
11 9448501 9450174 - Carg23072-RA Car11g01178 1178
19 5421820 5423538 + Carg22813-RA Car19g00351 351
9 30711100 30713835 + CcPI632755_09g017940.1 Cco09g1794 1794
10 20509999 20515024 - CcPI632755_10g009380.1 Cco10g0938 938
9 32510666 32515187 + CePI673135_09g017320.1 Cec09g1732 1732
10 22200985 22205736 - CePI673135_10g009790.1 Cec10g0979 979
10 20935956 20940915 - ClG42_10g0096500.10 Clacu10g0965 965
9 31401189 31403300 + ClCG09G016050.1 Cla09g01575 1575
10 21884129 21889149 - ClCG10G009610.1 Cla10g00920 920
11 10962449 10964128 + CmaCh11G016670.1 Cma11g01667 1667
19 5716594 5718456 + CmaCh19G004760.1 Cma19g00476 476
1 1451743 1453670 + MELO3C018602.2.1 Cme01g00203 203
7 26559927 26563354 + MELO3C018056.2.1 Cme07g02244 2244
11 10297302 10301867 - CmoCh11G014640.1 Cmo11g01464 1464
16 1336227 1339517 - CmoCh16G002950.1 Cmo16g00295 295
19 5895110 5896828 + CmoCh19G004930.1 Cmo19g00493 493
10 21544839 21549798 - CmPI595203_10g017480.1 Cmu10g1748 1748
1 3434320 3438059 + Cp4.1LG01g00700.1 Cpe01g00595 595
4 4327331 4329010 - Cp4.1LG04g07200.1 Cpe04g00370 370
14 1317342 1320721 - Cp4.1LG14g04880.1 Cpe14g00229 229
15 4988108 4989826 + Cp4.1LG15g03710.1 Cpe15g00374 374
9 33315759 33317943 + CrPI670011_09g016230.1 Cre09g1623 1623
10 23259411 23262488 - CrPI670011_10g011240.1 Cre10g1124 1124
3 14121436 14132378 + Vvi3g946 Vvi3g946 946
3 14136487 14155287 + Vvi3g947 Vvi3g947 947
3 14204862 14212245 + Vvi3g948 Vvi3g948 948
3 14222857 14227556 + Vvi3g949 Vvi3g949 949
3 14249407 14249473 + Vvi3g950 Vvi3g950 950
3 14310743 14311619 - Vvi3g951 Vvi3g951 951
3 14356253 14357174 + Vvi3g952 Vvi3g952 952
3 14403149 14403506 + Vvi3g953 Vvi3g953 953
3 14489674 14495034 + Vvi3g954 Vvi3g954 954
3 14578245 14585659 - Vvi3g955 Vvi3g955 955
       

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