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
Vvi19g874 Blo03g00728 . . . . . . . . . . . . . . . . Bhi09g03594 . . . Hepe01g1487 . . . . . . . . . Cone6ag0227 Cone9ag0260 . . Lsi04g01952 . . . . Blo10g00713 . Bda12g00801 . . Bma07g01119 . . . Cmo09g00683 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g875 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g876 Blo03g00727 . . . . . . . . . . . . . Sed05g2484 . . Bhi09g03592 Tan01g4230 Cmetu07g1493 . Hepe01g1486 Mch11g0961 . . . . . . . . Cone6ag0228 Cone9ag0261 . . Lsi04g01953 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g877 Blo03g00725 . . . Bpe09g00276 . . . . . . . . . Sed05g2485 . . Bhi09g03590 Tan01g4232 Cmetu07g0229 . Hepe01g1484 Mch11g0963 . . . . . . . . Cone6ag0230 Cone9ag0263 . . Lsi04g01956 . . . . . . Bda12g00800 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g878 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g879 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo09g00723 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g880 Blo03g00724 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0231 Cone9ag0264 . . Lsi04g01957 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g881 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g882 Blo03g00723 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g01958 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g883 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g01960 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
12 36991788 36998411 - Bda009303.1 Bda12g00800 800
12 37016085 37016521 + Bda009305.1 Bda12g00801 801
9 89816995 89819829 - XM_039040826.1 Bhi09g03590 3590
9 89824723 89828622 - XM_039044249.1 Bhi09g03592 3592
9 89849577 89853984 + XM_039041577.1 Bhi09g03594 3594
3 30465133 30467698 - BLOR11904 Blo03g00723 723
3 30482203 30484699 - BLOR11905 Blo03g00724 724
3 30544314 30546530 - BLOR11906 Blo03g00725 725
3 30551441 30555112 - BLOR11908 Blo03g00727 727
3 30579878 30586787 + BLOR11909 Blo03g00728 728
10 22726028 22730210 - BLOR02503 Blo10g00713 713
7 44688414 44692273 - Bma026340.1 Bma07g01119 1119
9 2050203 2052847 - Bpe023946.1 Bpe09g00276 276
7 21032315 21036750 + PI0010172.1 Cmetu07g0229 229
7 21025270 21029201 + PI0007004.1 Cmetu07g1493 1493
9 3387638 3392756 + CmoCh09G006830.1 Cmo09g00683 683
9 3606315 3611918 + CmoCh09G007230.1 Cmo09g00723 723
6 1061636 1065528 - Conep06aG0022900.1 Cone6ag0227 227
6 1065869 1068821 + Conep06aG0023000.1 Cone6ag0228 228
6 1069146 1070094 + Conep06aG0023200.1 Cone6ag0230 230
6 1071493 1073654 + Conep06aG0023300.1 Cone6ag0231 231
9 1095015 1099301 - Conep09aG0026300.1 Cone9ag0260 260
9 1099842 1100931 + Conep09aG0026400.1 Cone9ag0261 261
9 1103081 1104557 + Conep09aG0026600.1 Cone9ag0263 263
9 1105061 1107072 + Conep09aG0026700.1 Cone9ag0264 264
1 80125405 80128819 - Hsped.01g14840.1 Hepe01g1484 1484
1 80133447 80137596 - Hsped.01g14860.1 Hepe01g1486 1486
1 80144088 80149604 + Hsped.01g14870.1 Hepe01g1487 1487
4 26628252 26634686 - Lsi04G019520.1 Lsi04g01952 1952
4 26645535 26649544 + Lsi04G019530.1 Lsi04g01953 1953
4 26653564 26656892 + Lsi04G019560.1 Lsi04g01956 1956
4 26673143 26678367 + Lsi04G019570.1 Lsi04g01957 1957
4 26681173 26685126 + Lsi04G019580.1 Lsi04g01958 1958
4 26698375 26704601 + Lsi04G019600.1 Lsi04g01960 1960
11 6567722 6571433 + MC11g_new0166 Mch11g0961 961
11 6575455 6578415 + MC11g_new0167 Mch11g0963 963
5 36901610 36905820 + Sed0008182.1 Sed05g2484 2484
5 36906270 36908935 + Sed0007673.1 Sed05g2485 2485
1 107061816 107065722 + Tan0016793.1 Tan01g4230 4230
1 107070130 107072575 + Tan0002174.1 Tan01g4232 4232
19 14064458 14074173 - Vvi19g874 Vvi19g874 874
19 14523825 14525599 + Vvi19g875 Vvi19g875 875
19 14613169 14618041 + Vvi19g876 Vvi19g876 876
19 14642628 14652553 + Vvi19g877 Vvi19g877 877
19 14661829 14666329 + Vvi19g878 Vvi19g878 878
19 14717385 14720889 + Vvi19g879 Vvi19g879 879
19 14894754 14897484 + Vvi19g880 Vvi19g880 880
19 14902432 14920509 + Vvi19g881 Vvi19g881 881
19 14920740 14923863 + Vvi19g882 Vvi19g882 882
19 14954548 14957701 + Vvi19g883 Vvi19g883 883
       

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