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
Vvi17g156 . . Bda06g00739 . . . . Bma12g01073 . . Cma10g00074 . Car10g00064 . Sed08g0047 . . Bhi02g00547 Tan09g2351 Cmetu02g1227 . Hepe09g0066 . . Cla06g01727 Cam06g1917 Cec06g1967 Cco06g1971 Clacu06g1873 Cmu06g1815 Cre06g2630 . . . Cone19ag0195 . . . . . Blo15g00218 . . Bpe07g00880 . . . . Cmo10g00073 . . . . . . . . . . . . . . . . . . . . . Lsi06g01622 Csa01g00074 Chy02g02645 .
Vvi17g157 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g158 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g159 . . . . Bpe12g00644 . . Bma12g01285 Cmo13g01006 Cmo18g00067 . . . . . Cpe20g00169 . . . . . . . . . . . . . . . . Cone16ag0268 . . Lsi02g00257 Csa01g00739 Chy12g01597 Cme12g01807 Blo13g00122 Blo15g00028 . . . . . Bma08g00129 . . . Cma13g00972 Cma18g00089 Car13g00806 Car18g00079 Cpe09g01101 . . . . . . . . Cla04g01024 Cam04g1066 Cec01g1580 Cco01g1629 Clacu04g1093 Cmu04g1077 Cre01g1377 . Csa01g00488 . .
Vvi17g160 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0367 . . . . . . . . . . . Bma08g00113 . . . . . . . . . . . . . . . . . . . . . . . . Csa01g00483 . .
Vvi17g161 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g162 Blo04g00860 . . . . . Bma06g00071 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00250 . . . . . . . . . Bma03g00927 . . . . . . . . . . Bhi08g01330 . . . . . . . . . . . . . . . . .
Vvi17g163 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g164 Blo04g00859 . Bda06g00868 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda14g01150 Bpe07g01089 Bpe15g00501 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g165 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 10037714 10043209 - Bda033770 Bda06g00739 739
6 11935272 11937525 - Bda024202.1 Bda06g00868 868
14 10680784 10688090 - Bda027995.1 Bda14g01150 1150
2 10319810 10325859 - XM_039023510.1 Bhi02g00547 547
8 40399182 40404842 - XM_039039259.1 Bhi08g01330 1330
4 9439956 9444280 - BLOR13771 Blo04g00859 859
4 9445101 9449828 - BLOR13772 Blo04g00860 860
13 2984275 2986537 + BLOR05403 Blo13g00122 122
15 234270 234881 + BLOR06422 Blo15g00028 28
15 2239675 2244653 - BLOR06612 Blo15g00218 218
3 9612912 9616106 - Bma017252.1 Bma03g00927 927
6 1100891 1104118 - Bma022682.1 Bma06g00071 71
8 1407794 1408798 - Bma027117.1 Bma08g00113 113
8 1683055 1685300 - Bma027135.1 Bma08g00129 129
12 43018707 43025052 + Bma030533 Bma12g01073 1073
12 45827083 45829177 - Bma008649.1 Bma12g01285 1285
7 14907877 14912838 + Bpe021723.1 Bpe07g00880 880
7 16243231 16245479 - Bpe021929.1 Bpe07g01089 1089
12 12088773 12091003 + Bpe005904.1 Bpe12g00644 644
15 16258552 16262532 + Bpe001434.1 Bpe15g00501 501
4 24799697 24804046 + CaPI482276_04g010660.1 Cam04g1066 1066
6 30125974 30131335 + CaPI482276_06g019170.1 Cam06g1917 1917
10 293251 298279 - Carg10296-RA Car10g00064 64
13 8865766 8867685 + Carg04866-RA Car13g00806 806
18 417681 419508 - Carg06644-RA Car18g00079 79
1 28999151 29001309 + CcPI632755_01g016290.1 Cco01g1629 1629
6 29860525 29866026 + CcPI632755_06g019710.1 Cco06g1971 1971
1 30412475 30414643 + CePI673135_01g015800.1 Cec01g1580 1580
6 32939839 32945216 + CePI673135_06g019670.1 Cec06g1967 1967
2 29510308 29515825 + Chy2G049120.1 Chy02g02645 2645
12 19527270 19529361 - Chy12G221970.1 Chy12g01597 1597
4 25165946 25169767 + ClG42_04g0109300.10 Clacu04g1093 1093
6 29176803 29182174 + ClG42_06g0187300.10 Clacu06g1873 1873
4 25367873 25370324 + ClCG04G010400.1 Cla04g01024 1024
6 30809998 30816968 + ClCG06G017720.2 Cla06g01727 1727
10 305211 310325 - CmaCh10G000740.1 Cma10g00074 74
13 7575429 7577468 + CmaCh13G009720.1 Cma13g00972 972
18 406361 408599 - CmaCh18G000890.1 Cma18g00089 89
12 24542528 24544841 + MELO3C002155.2.1 Cme12g01807 1807
2 24808487 24814140 + PI0017466.1 Cmetu02g1227 1227
10 335475 340540 - CmoCh10G000730.1 Cmo10g00073 73
13 8563956 8565922 + CmoCh13G010060.1 Cmo13g01006 1006
18 451754 454010 - CmoCh18G000670.1 Cmo18g00067 67
4 25352290 25356103 + CmPI595203_04g010770.1 Cmu04g1077 1077
6 29079330 29084649 + CmPI595203_06g018150.1 Cmu06g1815 1815
16 2992420 2994479 + Conep16aG0261700.1 Cone16ag0268 268
19 1223324 1228632 + Conep19aG0020100.1 Cone19ag0195 195
19 3109354 3110821 + Conep19aG0038000.1 Cone19ag0367 367
9 9501073 9503247 + Cp4.1LG09g10940.1 Cpe09g01101 1101
20 959200 961335 - Cp4.1LG20g01650.1 Cpe20g00169 169
1 26983274 26985427 + CrPI670011_01g013770.1 Cre01g1377 1377
6 33905990 33911456 + CrPI670011_06g026300.1 Cre06g2630 2630
1 433361 446871 - CsaV3_1G000740.1 Csa01g00074 74
1 3144705 3146035 + CsaV3_1G004830.1 Csa01g00483 483
1 3175342 3178799 + CsaV3_1G004880.1 Csa01g00488 488
1 4678750 4681650 - CsaV3_1G007390.1 Csa01g00739 739
9 558731 564077 - Hsped.09g00660.1 Hepe09g0066 66
2 2121759 2127682 + Lsi02G002500.1 Lsi02g00250 250
2 2194024 2196861 - Lsi02G002570.1 Lsi02g00257 257
6 26554135 26566200 + Lsi06G016220.1 Lsi06g01622 1622
8 233622 239842 - Sed0022036.1 Sed08g0047 47
9 73252143 73257661 + Tan0006096.1 Tan09g2351 2351
17 1396400 1415227 - Vvi17g156 Vvi17g156 156
17 1415290 1419190 + Vvi17g157 Vvi17g157 157
17 1419220 1420253 - Vvi17g158 Vvi17g158 158
17 1436682 1438596 + Vvi17g159 Vvi17g159 159
17 1475024 1475958 + Vvi17g160 Vvi17g160 160
17 1487786 1491499 - Vvi17g161 Vvi17g161 161
17 1497930 1501792 + Vvi17g162 Vvi17g162 162
17 1501866 1502124 - Vvi17g163 Vvi17g163 163
17 1502920 1509601 + Vvi17g164 Vvi17g164 164
17 1512041 1517370 + Vvi17g165 Vvi17g165 165
       

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