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
Vvi17g896 . . . . . . . . . . . . . Car11g00044 Sed08g0048 . . Bhi02g00562 Tan09g2348 Cmetu02g1737 . Hepe09g0068 . . . . . . . . . . . . . . . . . . Blo15g00233 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme02g02052
Vvi17g897 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g898 . Blo16g00249 . . . Bpe13g00216 Bma06g00244 . Cmo13g00809 Cmo18g00187 Cma10g00076 . . . . . . . . . . . . . . . . . . . . Cone2ag0951 Cone16ag0049 . . Lsi02g00468 Csa01g00924 Chy12g01202 . . . Bda11g01624 . . Bpe15g00667 . . Sed01g1585 . . . Cma18g00210 Car13g00626 . . Cpe18g00886 Bhi08g01698 Tan05g2901 Cmetu12g1074 Lac10g0539 . . . Cla03g00324 Cam03g0341 Cec03g0333 Cco03g0346 Clacu03g0343 Cmu03g0948 Cre03g0641 . Csa01g00077 . Cme02g02055
Vvi17g899 . . . . . . . . Cmo13g00810 Cmo18g00188 . . . . . Cpe20g00332 . . . . . . . . . . . . . . . Cone2ag0952 Cone16ag0048 . . . Csa01g00925 . Cme12g01625 . . . . . . . . Sed08g2463 . . Cma13g00778 Cma18g00212 . Car18g00204 Cpe09g00986 . Bhi08g01699 Tan05g2902 Cmetu12g0903 Lac10g0540 Hepe07g2160 . . . . . . . . . . . . .
Vvi17g900 . . . . . Bpe13g00215 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone16ag0047 . . Lsi02g00469 Csa01g00926 Chy12g01201 . . . Bda11g01623 . . . . . . . . . . . . . . . . . . . . . Cla03g00325 Cam03g0342 Cec03g0334 Cco03g0347 Clacu03g0344 Cmu03g0949 Cre03g0642 . . . .
Vvi17g901 . . . . . . . . Cmo13g00811 Cmo18g00189 . . . . . Cpe20g00331 . . . . . . . . . . . . . . . . Cone16ag0046 . . Lsi02g00470 Csa01g00928 Chy12g01199 Cme12g01623 . . . . . . . . . . . Cma13g00779 . Car13g00627 Car18g00205 Cpe09g00985 . Bhi08g01703 Tan05g2910 . . . . . Cla03g00327 Cam03g0344 Cec03g0335 Cco03g0348 Clacu03g0345 Cmu03g0951 Cre03g0643 . . . .
Vvi17g902 . . . Bda15g00525 Bpe12g00684 . . . . . . . Car10g00067 . . . . . . . . . . . . . . . . . . . . . . . . . . Blo13g00160 . . . . . . . . Cmo10g00076 . . . . . . . . . . . . . . . . . . . . . . . . Cme02g02056
Vvi17g903 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g904 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g905 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 49978317 49980353 + Bda008512.1 Bda11g01623 1623
11 49981866 49984961 - Bda008513.1 Bda11g01624 1624
15 8299439 8301064 - Bda012355.1 Bda15g00525 525
2 10331285 10406524 - XM_039022921.1 Bhi02g00562 562
8 47861697 47863720 + XM_039037822.1 Bhi08g01698 1698
8 47864702 47866429 + XM_039037664.1 Bhi08g01699 1699
8 47900667 47905705 + XM_039038960.1 Bhi08g01703 1703
13 5480773 5482580 + BLOR05441 Blo13g00160 160
15 2430545 2444595 - BLOR06627 Blo15g00233 233
16 5710953 5712060 + BLOR07497 Blo16g00249 249
6 3248410 3249529 + Bma022872.1 Bma06g00244 244
12 12440166 12441958 + Bpe005943.1 Bpe12g00684 684
13 10209291 10211419 + Bpe006337.2 Bpe13g00215 215
13 10212913 10214029 - Bpe006338.1 Bpe13g00216 216
15 17359209 17362632 + Bpe001600.1 Bpe15g00667 667
3 4595968 4597291 + CaPI482276_03g003410.1 Cam03g0341 341
3 4598492 4600726 - CaPI482276_03g003420.1 Cam03g0342 342
3 4604348 4609614 + CaPI482276_03g003440.1 Cam03g0344 344
10 307107 308726 - Carg10299-RA Car10g00067 67
11 227521 259105 - Carg20182-RA Car11g00044 44
13 7937469 7941803 + Carg07574-RA Car13g00626 626
13 7942984 7946797 + Carg07575-RA Car13g00627 627
18 1166391 1170246 + Carg06771-RA Car18g00204 204
18 1172510 1173363 + Carg06772-RA Car18g00205 205
3 3807818 3811858 + CcPI632755_03g003460.1 Cco03g0346 346
3 3813062 3815866 - CcPI632755_03g003470.1 Cco03g0347 347
3 3819169 3825181 + CcPI632755_03g003480.1 Cco03g0348 348
3 3757497 3758820 + CePI673135_03g003330.1 Cec03g0333 333
3 3760003 3762813 - CePI673135_03g003340.1 Cec03g0334 334
3 3765859 3771198 + CePI673135_03g003350.1 Cec03g0335 335
12 16767473 16770257 - Chy12G217990.1 Chy12g01199 1199
12 16775861 16777793 + Chy12G218010.1 Chy12g01201 1201
12 16778923 16783228 - Chy12G218020.1 Chy12g01202 1202
3 3912244 3913567 + ClG42_03g0034300.10 Clacu03g0343 343
3 3914766 3916980 - ClG42_03g0034400.10 Clacu03g0344 344
3 3920093 3926884 + ClG42_03g0034500.10 Clacu03g0345 345
3 3845706 3850344 + ClCG03G003440.2 Cla03g00324 324
3 3851220 3853801 - ClCG03G003460.2 Cla03g00325 325
3 3857168 3862479 + ClCG03G003480.1 Cla03g00327 327
10 316764 318136 + CmaCh10G000760.1 Cma10g00076 76
13 6703237 6704948 + CmaCh13G007780.1 Cma13g00778 778
13 6705777 6709635 + CmaCh13G007790.1 Cma13g00779 779
18 1145484 1147282 + CmaCh18G002100.1 Cma18g00210 210
18 1149020 1150251 + CmaCh18G002120.1 Cma18g00212 212
2 26529912 26563083 - MELO3C026219.2.1 Cme02g02052 2052
2 26565203 26566365 + MELO3C026216.2.1 Cme02g02055 2055
2 26567404 26569182 - MELO3C026215.2.1 Cme02g02056 2056
12 23403160 23408345 - MELO3C002331.2.1 Cme12g01623 1623
12 23414293 23419242 - MELO3C002329.2.1 Cme12g01625 1625
2 24773974 24803917 + PI0014036.1 Cmetu02g1737 1737
12 2916960 2918755 + PI0013701.1 Cmetu12g0903 903
12 2913787 2916041 + PI0000921.3 Cmetu12g1074 1074
10 349474 351087 - CmoCh10G000760.1 Cmo10g00076 76
13 7621064 7623044 + CmoCh13G008090.1 Cmo13g00809 809
13 7624044 7625446 + CmoCh13G008100.1 Cmo13g00810 810
13 7626643 7630536 + CmoCh13G008110.1 Cmo13g00811 811
18 1276568 1278197 + CmoCh18G001870.1 Cmo18g00187 187
18 1279305 1282868 + CmoCh18G001880.1 Cmo18g00188 188
18 1282878 1286158 + CmoCh18G001890.1 Cmo18g00189 189
3 4126340 4127663 + CmPI595203_03g009480.1 Cmu03g0948 948
3 4128863 4131079 - CmPI595203_03g009490.1 Cmu03g0949 949
3 4134688 4140988 + CmPI595203_03g009510.1 Cmu03g0951 951
2 35154631 35157237 + Conep02aG0198500.1 Cone2ag0951 951
2 35158003 35159275 + Conep02aG0198600.1 Cone2ag0952 952
16 251249 254766 - Conep16aG0004600.1 Cone16ag0046 46
16 256358 259098 + Conep16aG0004700.1 Cone16ag0047 47
16 259437 261011 - Conep16aG0004800.1 Cone16ag0048 48
16 261794 264390 - Conep16aG0004900.1 Cone16ag0049 49
9 8727528 8730957 - Cp4.1LG09g09770.1 Cpe09g00985 985
9 8732661 8737382 - Cp4.1LG09g09790.1 Cpe09g00986 986
18 8026054 8029045 - Cp4.1LG18g08890.1 Cpe18g00886 886
20 1858703 1862982 - Cp4.1LG20g03320.1 Cpe20g00331 331
20 1864285 1868715 - Cp4.1LG20g03220.1 Cpe20g00332 332
3 5329351 5330674 + CrPI670011_03g006410.1 Cre03g0641 641
3 5331863 5334663 - CrPI670011_03g006420.1 Cre03g0642 642
3 5337729 5344067 + CrPI670011_03g006430.1 Cre03g0643 643
1 485025 487141 + CsaV3_1G000770.1 Csa01g00077 77
1 5763243 5764703 + CsaV3_1G009240.1 Csa01g00924 924
1 5765689 5767748 + CsaV3_1G009250.1 Csa01g00925 925
1 5768389 5771097 - CsaV3_1G009260.1 Csa01g00926 926
1 5775346 5778670 + CsaV3_1G009280.1 Csa01g00928 928
7 65854491 65856251 - Hsped.07g21600.1 Hepe07g2160 2160
9 578070 623598 - Hsped.09g00680.1 Hepe09g0068 68
10 4188777 4190241 + Lag0024584.1 Lac10g0539 539
10 4191795 4193119 + Lag0024585.1 Lac10g0540 540
2 3907289 3912254 + Lsi02G004680.1 Lsi02g00468 468
2 3912797 3915745 - Lsi02G004690.1 Lsi02g00469 469
2 3918338 3922749 + Lsi02G004700.1 Lsi02g00470 470
1 11517385 11519671 + Sed0003126.3 Sed01g1585 1585
8 240593 296111 - Sed0027476.1 Sed08g0048 48
8 37573080 37575147 - Sed0010331.1 Sed08g2463 2463
5 81344632 81346885 + Tan0003075.2 Tan05g2901 2901
5 81346911 81348929 + Tan0015980.1 Tan05g2902 2902
5 81356707 81360663 + Tan0013060.5 Tan05g2910 2910
9 73160972 73246117 + Tan0006424.1 Tan09g2348 2348
17 12121983 12149054 - Vvi17g896 Vvi17g896 896
17 12198711 12199283 + Vvi17g897 Vvi17g897 897
17 12203722 12206685 + Vvi17g898 Vvi17g898 898
17 12208440 12210355 + Vvi17g899 Vvi17g899 899
17 12212621 12215044 - Vvi17g900 Vvi17g900 900
17 12251717 12257309 + Vvi17g901 Vvi17g901 901
17 12257608 12259195 - Vvi17g902 Vvi17g902 902
17 12269628 12274239 + Vvi17g903 Vvi17g903 903
17 12284469 12313319 + Vvi17g904 Vvi17g904 904
17 12313633 12324023 - Vvi17g905 Vvi17g905 905
       

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