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
Vvi17g86 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g87 . . . . . . . Bma12g01084 . . . . . . . . . . . . . . . . . . . . . . . . Cone16ag0013 . . . . . . . Blo15g00093 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g88 . . . Bda15g00676 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma08g00259 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g89 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone2ag0984 Cone16ag0014 . . . Csa01g00973 . . . . . . . . Bma03g01250 . . . . . . . . . . . . . . . . . Cla03g00360 Cam03g0380 Cec03g0366 Cco03g0381 Clacu03g0379 Cmu03g0984 Cre03g0676 . . . .
Vvi17g90 . . Bda06g00723 . . . . . . . . . . . . . . . . . . . . . Cla06g01748 Cam06g1939 Cec06g1988 Cco06g1992 Clacu06g1895 Cmu06g1836 Cre06g2650 . . Cone13ag0229 . . . . . . Blo15g00203 . . Bpe07g00894 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g91 . . . . . . . . . . . . Car10g00043 . . . Cpe04g01619 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma08g00257 . . Cmo11g00030 . . . . . Cpe18g00911 . . . . . . . . . . . . . . Lsi06g01648 . Chy02g02670 Cme02g02072
Vvi17g92 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g93 . Blo16g00274 . . Bpe12g00476 . Bma06g00263 . . . Cma10g00055 Cma11g00028 . Car11g00028 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda14g01355 . Bpe15g00223 . . . Cmo10g00049 . . . . . . . . . . . . . . . . . . . . . . Csa01g00048 . .
Vvi17g94 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g95 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme12g01580 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 9923501 9925107 - Bda024025.1 Bda06g00723 723
14 15839487 15843280 + Bda011053.1 Bda14g01355 1355
15 10207709 10210166 - Bda012527.1 Bda15g00676 676
15 784984 787212 + BLOR06487 Blo15g00093 93
15 2104041 2105548 - BLOR06597 Blo15g00203 203
16 6448049 6453344 - BLOR07522 Blo16g00274 274
3 20825567 20826856 + Bma017712.1 Bma03g01250 1250
6 3632133 3636398 - Bma022895.1 Bma06g00263 263
8 3350692 3353785 - Bma027274.1 Bma08g00257 257
8 3422234 3424648 - Bma027276.1 Bma08g00259 259
12 43127933 43130215 - Bma008430.1 Bma12g01084 1084
7 14979814 14981472 + Bpe021735.1 Bpe07g00894 894
12 10516739 10524821 + Bpe005737.2 Bpe12g00476 476
15 13351646 13361360 - Bpe001159.1 Bpe15g00223 223
3 4894796 4897176 - CaPI482276_03g003800.1 Cam03g0380 380
6 30322531 30324155 + CaPI482276_06g019390.1 Cam06g1939 1939
10 184851 193441 + Carg10275-RA Car10g00043 43
11 125848 132002 + Carg24540-RA Car11g00028 28
3 4119799 4122183 - CcPI632755_03g003810.1 Cco03g0381 381
6 30065645 30067136 + CcPI632755_06g019920.1 Cco06g1992 1992
3 4061640 4064023 - CePI673135_03g003660.1 Cec03g0366 366
6 33142248 33144053 + CePI673135_06g019880.1 Cec06g1988 1988
2 29673777 29675572 - Chy2G049370.1 Chy02g02670 2670
3 4209585 4212385 - ClG42_03g0037900.10 Clacu03g0379 379
6 29373303 29374927 + ClG42_06g0189500.10 Clacu06g1895 1895
3 4154258 4157224 - ClCG03G003830.1 Cla03g00360 360
6 31028503 31030238 + ClCG06G017970.2 Cla06g01748 1748
10 199480 208402 + CmaCh10G000550.1 Cma10g00055 55
11 131766 137911 + CmaCh11G000280.1 Cma11g00028 28
2 26668137 26671212 - MELO3C026201.2.1 Cme02g02072 2072
12 23153682 23158190 - MELO3C002369.2.1 Cme12g01580 1580
10 230950 240094 + CmoCh10G000490.1 Cmo10g00049 49
11 133292 135817 + CmoCh11G000300.1 Cmo11g00030 30
3 4423612 4426412 - CmPI595203_03g009840.1 Cmu03g0984 984
6 29276304 29277907 + CmPI595203_06g018360.1 Cmu06g1836 1836
2 35275791 35276628 - Conep02aG0201800.1 Cone2ag0984 984
13 1492640 1494850 + Conep13aG0023600.1 Cone13ag0229 229
16 111720 114993 - Conep16aG0001300.1 Cone16ag0013 13
16 119860 121428 - Conep16aG0001400.1 Cone16ag0014 14
4 12561083 12563282 - Cp4.1LG04g16190.1 Cpe04g01619 1619
18 8133975 8143229 - Cp4.1LG18g09220.1 Cpe18g00911 911
3 5634260 5636675 - CrPI670011_03g006760.1 Cre03g0676 676
6 34107442 34109062 + CrPI670011_06g026500.1 Cre06g2650 2650
1 276299 282471 + CsaV3_1G000480.1 Csa01g00048 48
1 6016414 6018992 - CsaV3_1G009730.1 Csa01g00973 973
6 26762749 26773421 - Lsi06G016480.1 Lsi06g01648 1648
17 812768 813758 - Vvi17g86 Vvi17g86 86
17 818276 823191 - Vvi17g87 Vvi17g87 87
17 823667 827024 - Vvi17g88 Vvi17g88 88
17 839244 840576 - Vvi17g89 Vvi17g89 89
17 842042 844361 + Vvi17g90 Vvi17g90 90
17 845713 847010 - Vvi17g91 Vvi17g91 91
17 847009 847712 - Vvi17g92 Vvi17g92 92
17 851142 859908 - Vvi17g93 Vvi17g93 93
17 867654 868764 + Vvi17g94 Vvi17g94 94
17 878130 881091 + Vvi17g95 Vvi17g95 95
       

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