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
Vvi19g1034 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1035 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1036 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1037 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1038 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1039 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1040 . . . . . . . . . . . . . . . . . . . . . . . . Cla02g01813 Cam02g1918 Cec02g1939 Cco02g1983 Clacu02g1900 Cmu02g1847 Cre02g2162 . . . . . . . . Blo15g00605 . . . . . . Bma12g00598 Sed14g1679 . . . . . . . . Bhi10g00965 Tan05g0609 Cmetu11g0122 . . . . . . . . . . . . Csa06g01170 Chy11g01023 .
Vvi19g1041 . . . . . . . . Cmo16g00543 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma16g00499 . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1042 . . . . . . . . . . . . . . Sed05g1854 Cpe04g00856 . Bhi05g02025 Tan02g0063 Cmetu01g1532 Lac12g0891 Hepe02g0029 . . Cla02g01814 Cam02g1919 Cec02g1940 Cco02g1984 Clacu02g1901 Cmu02g1848 Cre02g2163 . . . . . Csa07g01185 . . Blo15g00606 . . . . . . . Sed01g0750 . . . . . . . . Bhi10g00963 Tan05g0608 Cmetu11g1961 . Hepe08g0630 . . . . . . . . . . Csa06g01169 Chy11g01024 Cme01g01534
Vvi19g1043 . . . . . . . . . . . . . . Sed01g3865 Cpe04g00857 . Bhi05g02024 Tan02g0062 Cmetu01g2034 Lac12g0892 Hepe02g0028 . . Cla02g01815 Cam02g1920 Cec02g1941 Cco02g1985 Clacu02g1902 Cmu02g1849 Cre02g2164 . . . . . Csa07g01186 . Cme11g01597 . . . . . . . . Sed01g0752 . . . . . . . . Bhi10g00962 Tan05g0607 Cmetu11g1980 . Hepe08g0631 . . . . . . . . . . Csa06g01167 Chy11g01026 Cme01g01531
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 62136196 62138503 + XM_039032957.1 Bhi05g02024 2024
5 62169715 62172180 - XM_039032455.1 Bhi05g02025 2025
10 19651503 19653593 + XM_039046688.1 Bhi10g00962 962
10 19755429 19757987 - XM_039046205.1 Bhi10g00963 963
10 19817402 19842522 + XM_039045739.1 Bhi10g00965 965
15 14640929 14655203 - BLOR06999 Blo15g00605 605
15 14709666 14718934 + BLOR07000 Blo15g00606 606
12 27002751 27031624 + Bma007774.3 Bma12g00598 598
2 32238764 32261878 - CaPI482276_02g019180.1 Cam02g1918 1918
2 32276117 32278274 + CaPI482276_02g019190.1 Cam02g1919 1919
2 32289003 32290546 - CaPI482276_02g019200.1 Cam02g1920 1920
2 32748541 32769566 - CcPI632755_02g019830.1 Cco02g1983 1983
2 32785538 32787700 + CcPI632755_02g019840.1 Cco02g1984 1984
2 32796982 32798518 - CcPI632755_02g019850.1 Cco02g1985 1985
2 37252697 37269526 - CePI673135_02g019390.1 Cec02g1939 1939
2 37289655 37291823 + CePI673135_02g019400.1 Cec02g1940 1940
2 37302410 37303929 - CePI673135_02g019410.1 Cec02g1941 1941
11 14414837 14443147 - Chy11G196030.1 Chy11g01023 1023
11 14506810 14509058 + Chy11G196040.1 Chy11g01024 1024
11 14599852 14601272 - Chy11G196060.1 Chy11g01026 1026
2 32499365 32522091 - ClG42_02g0190000.10 Clacu02g1900 1900
2 32536253 32538399 + ClG42_02g0190100.10 Clacu02g1901 1901
2 32549015 32550524 - ClG42_02g0190200.10 Clacu02g1902 1902
2 33189636 33213249 - ClCG02G018530.2 Cla02g01813 1813
2 33227293 33229852 + ClCG02G018540.1 Cla02g01814 1814
2 33240172 33241673 - ClCG02G018550.2 Cla02g01815 1815
16 2546331 2551268 + CmaCh16G004990.1 Cma16g00499 499
1 20274030 20276182 + MELO3C012623.2.1 Cme01g01531 1531
1 20301579 20304319 - MELO3C012624.2.1 Cme01g01534 1534
11 23782428 23784839 - MELO3C019654.2.1 Cme11g01597 1597
1 7472183 7474522 - PI0008166.1 Cmetu01g1532 1532
1 7452727 7454522 + PI0021180.1 Cmetu01g2034 2034
11 9006879 9054102 + PI0019291.1 Cmetu11g0122 122
11 8965122 8967535 - PI0016751.1 Cmetu11g1961 1961
11 8884466 8886089 + PI0014677.1 Cmetu11g1980 1980
16 2636864 2642110 + CmoCh16G005430.1 Cmo16g00543 543
2 32361575 32384297 - CmPI595203_02g018470.1 Cmu02g1847 1847
2 32398445 32400591 + CmPI595203_02g018480.1 Cmu02g1848 1848
2 32411308 32412818 - CmPI595203_02g018490.1 Cmu02g1849 1849
4 7887266 7888292 + Cp4.1LG04g02270.1 Cpe04g00856 856
4 7888888 7890452 - Cp4.1LG04g02210.1 Cpe04g00857 857
2 35197626 35220809 - CrPI670011_02g021620.1 Cre02g2162 2162
2 35235154 35237234 + CrPI670011_02g021630.1 Cre02g2163 2163
2 35248220 35249734 - CrPI670011_02g021640.1 Cre02g2164 2164
6 9796099 9798161 + CsaV3_6G013650.1 Csa06g01167 1167
6 9817253 9820028 - CsaV3_6G013670.1 Csa06g01169 1169
6 9843637 9878665 + CsaV3_6G013680.1 Csa06g01170 1170
7 11638640 11641537 - CsaV3_7G022740.1 Csa07g01185 1185
7 11652744 11654814 - CsaV3_7G022750.1 Csa07g01186 1186
2 436830 438102 + Hsped.02g00280.1 Hepe02g0028 28
2 441251 441857 - Hsped.02g00290.1 Hepe02g0029 29
8 5603072 5605142 + Hsped.08g06300.1 Hepe08g0630 630
8 5614028 5615289 - Hsped.08g06310.1 Hepe08g0631 631
12 9335793 9337966 + Lag0015263.1 Lac12g0891 891
12 9343975 9345006 - Lag0015264.1 Lac12g0892 892
1 5548781 5554190 + Sed0009084.1 Sed01g0750 750
1 5562448 5563872 - Sed0011603.2 Sed01g0752 752
1 67910357 67912966 + Sed0000359.1 Sed01g3865 3865
5 31967644 31971370 - Sed0027593.1 Sed05g1854 1854
14 24817719 24820360 + Sed0008992.3 Sed14g1679 1679
2 817228 819226 + Tan0011814.1 Tan02g0062 62
2 823586 827071 - Tan0014877.1 Tan02g0063 63
5 4433187 4434703 + Tan0008873.1 Tan05g0607 607
5 4443176 4445660 - Tan0008848.1 Tan05g0608 608
5 4461711 4481798 + Tan0009852.1 Tan05g0609 609
19 20534126 20535179 - Vvi19g1034 Vvi19g1034 1034
19 20535308 20537409 + Vvi19g1035 Vvi19g1035 1035
19 20583943 20587021 - Vvi19g1036 Vvi19g1036 1036
19 20593526 20595940 - Vvi19g1037 Vvi19g1037 1037
19 20595961 20596458 - Vvi19g1038 Vvi19g1038 1038
19 20596643 20609026 - Vvi19g1039 Vvi19g1039 1039
19 20683309 20804352 - Vvi19g1040 Vvi19g1040 1040
19 20810624 20819467 - Vvi19g1041 Vvi19g1041 1041
19 20862596 20865868 + Vvi19g1042 Vvi19g1042 1042
19 20911180 20912549 - Vvi19g1043 Vvi19g1043 1043
       

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