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
Vvi19g974 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g975 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g976 . . . . . . . Bma13g00896 Cmo16g00506 Cmo04g00682 Cma01g01298 Cma09g00746 Car01g01106 Car09g00654 . . Cpe02g00632 . . . . . . . Cla11g01590 Cam11g1657 Cec11g1685 Cco11g1682 Clacu11g1814 Cmu11g1628 Cre11g2044 . . . . Lsi04g01869 . . . . Blo10g00684 . Bda12g00778 . Bpe03g00880 . . . Cmo01g01351 Cmo09g00738 Cma04g00633 . Car04g00592 Car16g00422 Cpe14g00394 Cpe01g00570 . . . . . . . Cla07g01012 Cam07g1089 Cec07g1161 Cco07g1139 Clacu07g1063 Cmu07g1054 Cre07g1430 . . Chy07g01048 .
Vvi19g977 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g978 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g979 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone15ag0979 . . . . Blo07g01001 . . . . . . . . . . . . . . . . . . . . . . . Cla07g01016 Cam07g1094 Cec07g1166 Cco07g1145 Clacu07g1067 Cmu07g1058 Cre07g1435 . . Chy07g01052 .
Vvi19g980 . . . . Bpe09g00294 . . Bma13g00895 Cmo16g00508 Cmo04g00679 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo07g01002 Blo10g00682 . Bda12g00776 . Bpe03g00881 . . . . . . Cma16g00467 Car04g00590 Car16g00424 . . . . . . . . . . . . . . . . . . . .
Vvi19g981 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g982 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g983 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
12 36466749 36469876 - Bda009271.1 Bda12g00776 776
12 36494919 36496226 + Bda009273.1 Bda12g00778 778
7 29591070 29601744 - BLOR18933 Blo07g01001 1001
7 29603550 29610396 + BLOR18934 Blo07g01002 1002
10 21892713 21895872 - BLOR02472 Blo10g00682 682
10 21917886 21919166 + BLOR02474 Blo10g00684 684
13 38913506 38918248 - Bma009969.1 Bma13g00895 895
13 38945491 38946798 + Bma009970.1 Bma13g00896 896
3 28567823 28569097 - Bpe012785.1 Bpe03g00880 880
3 28580832 28583144 + Bpe012786.1 Bpe03g00881 881
9 2347478 2350715 + Bpe023963.1 Bpe09g00294 294
7 25387780 25389165 - CaPI482276_07g010890.1 Cam07g1089 1089
7 25427089 25431413 + CaPI482276_07g010940.1 Cam07g1094 1094
11 29277576 29278790 - CaPI482276_11g016570.1 Cam11g1657 1657
1 10336046 10337275 - Carg14771-RA Car01g01106 1106
4 3365743 3368526 + Carg13115-RA Car04g00590 590
4 3383978 3385303 + Carg13113-RA Car04g00592 592
9 3832384 3833607 + Carg20061-RA Car09g00654 654
16 2638051 2639421 - Carg11389-RA Car16g00422 422
16 2649297 2652626 - Carg11391-RA Car16g00424 424
7 25119734 25121119 - CcPI632755_07g011390.1 Cco07g1139 1139
7 25160965 25165371 + CcPI632755_07g011450.1 Cco07g1145 1145
11 29657280 29658494 - CcPI632755_11g016820.1 Cco11g1682 1682
7 27021102 27022493 - CePI673135_07g011610.1 Cec07g1161 1161
7 27063296 27067706 + CePI673135_07g011660.1 Cec07g1166 1166
11 31113339 31114553 - CePI673135_11g016850.1 Cec11g1685 1685
7 15426679 15428055 - Chy7G138780.1 Chy07g01048 1048
7 15459291 15463438 + Chy7G138820.1 Chy07g01052 1052
7 25201475 25202860 - ClG42_07g0106300.10 Clacu07g1063 1063
7 25240575 25244985 + ClG42_07g0106700.10 Clacu07g1067 1067
11 29298202 29299416 - ClG42_11g0181400.10 Clacu11g1814 1814
7 26537239 26538624 - ClCG07G010650.2 Cla07g01012 1012
7 26579226 26583980 + ClCG07G010690.1 Cla07g01016 1016
11 29599215 29600429 - ClCG11G016320.1 Cla11g01590 1590
1 9300313 9301542 - CmaCh01G012980.1 Cma01g01298 1298
4 3249517 3250839 + CmaCh04G006330.1 Cma04g00633 633
9 3562027 3563250 + CmaCh09G007460.1 Cma09g00746 746
16 2360646 2372210 - CmaCh16G004670.1 Cma16g00467 467
1 10695397 10696626 - CmoCh01G013510.1 Cmo01g01351 1351
4 3370962 3374423 + CmoCh04G006790.1 Cmo04g00679 679
4 3387448 3388773 + CmoCh04G006820.1 Cmo04g00682 682
9 3690192 3691415 + CmoCh09G007380.1 Cmo09g00738 738
16 2439400 2440770 - CmoCh16G005060.1 Cmo16g00506 506
16 2450461 2454667 - CmoCh16G005080.1 Cmo16g00508 508
7 25446074 25447459 - CmPI595203_07g010540.1 Cmu07g1054 1054
7 25485203 25489614 + CmPI595203_07g010580.1 Cmu07g1058 1058
11 28551046 28552260 - CmPI595203_11g016280.1 Cmu11g1628 1628
15 7816919 7820255 + Conep15aG0100000.1 Cone15ag0979 979
1 3312736 3314375 + Cp4.1LG01g00920.1 Cpe01g00570 570
2 3846354 3847583 + Cp4.1LG02g02400.1 Cpe02g00632 632
14 2435430 2436800 - Cp4.1LG14g03220.1 Cpe14g00394 394
7 29372139 29373524 - CrPI670011_07g014300.1 Cre07g1430 1430
7 29415260 29419682 + CrPI670011_07g014350.1 Cre07g1435 1435
11 32218357 32219571 - CrPI670011_11g020440.1 Cre11g2044 2044
4 25837982 25839193 - Lsi04G018690.1 Lsi04g01869 1869
19 19011211 19012009 - Vvi19g974 Vvi19g974 974
19 19016465 19020315 - Vvi19g975 Vvi19g975 975
19 19037308 19039116 - Vvi19g976 Vvi19g976 976
19 19051525 19078587 + Vvi19g977 Vvi19g977 977
19 19093050 19093640 + Vvi19g978 Vvi19g978 978
19 19094250 19106285 - Vvi19g979 Vvi19g979 979
19 19137066 19142116 + Vvi19g980 Vvi19g980 980
19 19171697 19179184 - Vvi19g981 Vvi19g981 981
19 19180147 19180384 - Vvi19g982 Vvi19g982 982
19 19190006 19191200 - Vvi19g983 Vvi19g983 983
       

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