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
Vvi19g784 . . . . . . . Bma13g01142 . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1271 Cone15ag1297 . . . . . Blo10g00889 . Bda12g00989 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g785 . . . . . . . Bma13g01143 . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1272 Cone15ag1298 . . . . . . . Bda12g00990 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g786 . . . . Bpe09g00097 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo07g00855 Blo10g00890 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g787 Blo03g00479 Blo03g01494 Bda07g00438 Bda09g00453 . Bpe08g01074 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1273 Cone15ag1299 . Csa03g00380 . . . . . . Bpe11g00614 . Bma07g01232 Bma14g00656 . . . . Cma16g00998 . Car16g00955 Cpe14g00821 . . . . . . . . . . . . . . . . . Chy06g01934 .
Vvi19g788 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1274 Cone15ag1300 . . . Cme06g02708 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g789 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g790 . Blo03g01495 . . . Bpe08g01073 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1275 Cone15ag1301 . . . . . . . . . . . . . . . . Cma16g00997 . Car16g00954 . . . . . . . . . . . . . . . . . . . .
Vvi19g791 . Blo03g01496 . Bda09g00454 . Bpe08g01072 . . . . Cma01g01040 Cma09g01046 Car01g00914 Car09g00953 Sed07g2784 Cpe06g00853 Cpe02g00852 Bhi09g01848 Tan01g3262 Cmetu01g0448 . . Mch11g1337 . . . . . . . . . . . . Lsi02g01782 Csa07g01040 . . . . . . . . Bma07g01231 . . Cmo01g01079 Cmo09g01052 . . . . . . . . . . . . . Cla09g02118 Cam09g2205 Cec09g2278 . . . . . . . .
Vvi19g792 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g793 . . . . Bpe09g00096 . Bma10g00617 Bma13g01145 . . . . . . . . . . . . . . . . Cla10g00375 . . . . . . . . Cone14ag1276 Cone15ag1302 . . . . Blo07g00854 Blo10g00891 . Bda12g00991 . Bpe03g00734 . . Sed08g2869 . . . Cma16g00996 . Car16g00953 . . Bhi11g00403 Tan01g1903 Cmetu06g1959 . Hepe06g1241 . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 5588642 5592164 - Bda025534.1 Bda07g00438 438
9 5940053 5942512 - Bda031041.1 Bda09g00453 453
9 5950908 5953947 - Bda031043.1 Bda09g00454 454
12 41209416 41214737 + Bda009540.1 Bda12g00989 989
12 41215928 41219575 + Bda009541.1 Bda12g00990 990
12 41237344 41243470 + Bda009542.1 Bda12g00991 991
9 50636673 50640691 + XM_039041882.1 Bhi09g01848 1848
11 9666994 9687664 + XM_039049053.1 Bhi11g00403 403
3 16580906 16584755 + BLOR11660 Blo03g00479 479
3 41781624 41784494 - BLOR12675 Blo03g01494 1494
3 41786515 41791072 - BLOR12676 Blo03g01495 1495
3 41793970 41802658 - BLOR12677 Blo03g01496 1496
7 26930143 26936835 - BLOR18786 Blo07g00854 854
7 26938815 26940068 - BLOR18787 Blo07g00855 855
10 27873038 27873520 + BLOR02679 Blo10g00889 889
10 27877630 27886880 + BLOR02680 Blo10g00890 890
10 27891718 27899889 + BLOR02681 Blo10g00891 891
7 47219814 47222849 + Bma026483.1 Bma07g01231 1231
7 47232095 47237271 + Bma026484.1 Bma07g01232 1232
10 8468312 8473095 + Bma004335.1 Bma10g00617 617
13 44618263 44618757 + Bma010274.1 Bma13g01142 1142
13 44620708 44624163 + Bma010275.2 Bma13g01143 1143
13 44630504 44636297 + Bma010277.1 Bma13g01145 1145
14 7091062 7094556 + Bma011102.1 Bma14g00656 656
3 27433462 27438433 - Bpe012642.1 Bpe03g00734 734
8 12872759 12875786 + Bpe023197.1 Bpe08g01072 1072
8 12878637 12882351 + Bpe023198.1 Bpe08g01073 1073
8 12884240 12886627 + Bpe023199.1 Bpe08g01074 1074
9 661404 668705 - Bpe023775.1 Bpe09g00096 96
9 671520 672737 - Bpe023776.1 Bpe09g00097 97
11 4675216 4678711 - Bpe003979.1 Bpe11g00614 614
9 36594489 36597140 - CaPI482276_09g022050.1 Cam09g2205 2205
1 8866443 8869043 + Carg23368-RA Car01g00914 914
9 5919608 5921961 - Carg26617-RA Car09g00953 953
16 7894467 7901386 - Carg25230-RA Car16g00953 953
16 7907891 7912347 + Carg25229-RA Car16g00954 954
16 7920406 7923593 + Carg25228-RA Car16g00955 955
9 39624375 39627462 - CePI673135_09g022780.1 Cec09g2278 2278
6 23273710 23276912 + Chy6G124620.1 Chy06g01934 1934
9 38775448 38779082 - ClCG09G021770.1 Cla09g02118 2118
10 5023664 5036827 + ClCG10G003990.1 Cla10g00375 375
1 7691606 7700303 + CmaCh01G010400.1 Cma01g01040 1040
9 5433544 5437290 - CmaCh09G010460.1 Cma09g01046 1046
16 7660170 7666538 - CmaCh16G009960.1 Cma16g00996 996
16 7670971 7676712 + CmaCh16G009970.1 Cma16g00997 997
16 7684952 7688802 + CmaCh16G009980.1 Cma16g00998 998
6 34278657 34281827 + MELO3C014062.2.1 Cme06g02708 2708
1 9464233 9466897 + PI0022622.1 Cmetu01g0448 448
6 27419830 27427983 - PI0009564.1 Cmetu06g1959 1959
1 8993682 8997142 + CmoCh01G010790.1 Cmo01g01079 1079
9 5668601 5671920 - CmoCh09G010520.1 Cmo09g01052 1052
14 10171705 10172513 + Conep14aG0130300.1 Cone14ag1271 1271
14 10172910 10175425 + Conep14aG0130400.1 Cone14ag1272 1272
14 10181416 10184290 - Conep14aG0130500.1 Cone14ag1273 1273
14 10185514 10189291 + Conep14aG0130600.1 Cone14ag1274 1274
14 10191155 10197623 - Conep14aG0130700.1 Cone14ag1275 1275
14 10209468 10214619 + Conep14aG0130800.1 Cone14ag1276 1276
15 10147573 10148067 + Conep15aG0132600.1 Cone15ag1297 1297
15 10148603 10150516 + Conep15aG0132700.1 Cone15ag1298 1298
15 10155693 10157709 - Conep15aG0132800.1 Cone15ag1299 1299
15 10159878 10162877 + Conep15aG0132900.1 Cone15ag1300 1300
15 10165370 10172454 - Conep15aG0133000.1 Cone15ag1301 1301
15 10173264 10178377 + Conep15aG0133100.1 Cone15ag1302 1302
2 5536996 5540519 - Cp4.1LG02g00160.1 Cpe02g00852 852
6 5528037 5531536 - Cp4.1LG06g07970.1 Cpe06g00853 853
14 6588579 6592492 + Cp4.1LG14g08210.1 Cpe14g00821 821
3 3186334 3191107 - CsaV3_3G003800.1 Csa03g00380 380
7 9773439 9778127 + CsaV3_7G021290.1 Csa07g01040 1040
6 62172464 62187489 + Hsped.06g12410.1 Hepe06g1241 1241
2 23590700 23594324 + Lsi02G017820.1 Lsi02g01782 1782
11 9484952 9488427 - MC11g1107 Mch11g1337 1337
7 42825618 42829696 - Sed0014853.3 Sed07g2784 2784
8 39867720 39875163 + Sed0027047.3 Sed08g2869 2869
1 20374091 20395878 - Tan0020579.1 Tan01g1903 1903
1 87835634 87839805 - Tan0021536.2 Tan01g3262 3262
19 10465710 10466295 + Vvi19g784 Vvi19g784 784
19 10490144 10498164 + Vvi19g785 Vvi19g785 785
19 10503114 10505322 + Vvi19g786 Vvi19g786 786
19 10511018 10515821 - Vvi19g787 Vvi19g787 787
19 10527534 10529868 + Vvi19g788 Vvi19g788 788
19 10530105 10530525 + Vvi19g789 Vvi19g789 789
19 10531059 10542440 - Vvi19g790 Vvi19g790 790
19 10550625 10562773 - Vvi19g791 Vvi19g791 791
19 10569069 10570617 + Vvi19g792 Vvi19g792 792
19 10605054 10620089 + Vvi19g793 Vvi19g793 793
       

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