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
Vvi19g794 . . . . Bpe09g00095 . Bma10g00638 Bma13g01146 . Cmo06g00665 . . . . . . . . . . . . . . Cla10g00374 . . . . . . . . Cone14ag1277 Cone15ag1303 . . . . . Blo10g00892 . Bda12g00992 . Bpe03g00733 . . . . . . Cma16g00995 . Car16g00952 . . . . . . . . . . . . . . . . . . . .
Vvi19g795 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1278 Cone15ag1304 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g796 . . . . Bpe09g00094 . . Bma13g01147 . . . . . . . . . . . . . . . . Cla10g00363 Cam10g0375 Cec10g0394 Cco10g0388 Clacu10g0379 Cmu10g1216 Cre10g0630 . . . . . . . . . Blo10g00893 . Bda12g00993 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g797 . . . . . . . . . . . Cma09g01048 . Car09g00956 Sed01g2636 Cpe06g00856 . Bhi09g01852 Tan01g3265 Cmetu01g2709 . . Mch11g1340 . . . . . . . . . . . . Lsi02g01779 Csa07g01034 . . . . . . . . . . . . Cmo09g01054 . . . . . . . . . . . . . Cla09g02121 Cam09g2208 Cec09g2281 . . . . . . . .
Vvi19g798 . . . . . . . . Cmo16g01053 . . . . . . . . . . . . . . . Cla10g00340 Cam10g0353 Cec10g0367 Cco10g0361 Clacu10g0354 Cmu10g1190 Cre10g0602 . . . . . Csa03g00360 . Cme06g02677 . . . Bda12g00810 . . . . Sed08g2852 . . . . . . Cpe14g00830 . Bhi11g00377 Tan01g1928 Cmetu06g1879 . . Mch10g1456 . . . . . . . . . . Chy06g01963 .
Vvi19g799 . . . . . . . . Cmo16g01054 . . . . . . . . . . . . . . . Cla10g00339 Cam10g0352 Cec10g0366 Cco10g0360 Clacu10g0353 Cmu10g1189 Cre10g0600 . . . . . Csa03g00359 . Cme06g02676 . Blo10g00896 . . . . . . Sed08g2851 . . . . . . Cpe14g00831 . Bhi11g00376 Tan01g1930 Cmetu06g2650 . Hepe06g1220 Mch10g1457 . . . . . . . . . . Chy06g01964 .
Vvi19g800 . . . . Bpe09g00092 . . Bma13g01149 Cmo16g01055 . . . . . . . . . . . . . . . Cla10g00338 Cam10g0351 Cec10g0364 Cco10g0359 Clacu10g0352 Cmu10g1188 Cre10g0599 . . Cone14ag1279 Cone15ag1306 . Csa03g00358 . Cme06g02675 Blo07g00850 . Bda05g00656 Bda12g00995 . Bpe03g00732 . . Sed08g2850 . . . . . . Cpe14g00832 . Bhi11g00375 Tan01g1931 Cmetu06g1763 . Hepe06g1219 Mch10g1459 . . . . . . . . . . Chy06g01965 .
Vvi19g801 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g802 . . . Bda09g00455 . Bpe08g01071 . . . . Cma01g01037 . Car01g00912 . . . Cpe02g00854 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma07g01230 . . Cmo01g01076 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g803 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 54765224 54773094 - Bda021782.1 Bda05g00656 656
9 5956307 5960306 - Bda031044.1 Bda09g00455 455
12 37323613 37325718 + Bda009319.1 Bda12g00810 810
12 41247437 41249157 - Bda009543.1 Bda12g00992 992
12 41255424 41255936 + Bda009544.1 Bda12g00993 993
12 41262084 41270792 + Bda009546.1 Bda12g00995 995
9 50896839 50899248 - XM_039044164.1 Bhi09g01852 1852
11 8848659 8860603 + XM_039048246.1 Bhi11g00375 375
11 8873960 8875767 - XM_039047101.1 Bhi11g00376 376
11 8989949 9001391 - XM_039049212.1 Bhi11g00377 377
7 26854556 26869283 - BLOR18782 Blo07g00850 850
10 27901421 27904222 - BLOR02682 Blo10g00892 892
10 27921502 27921999 + BLOR02683 Blo10g00893 893
10 27940535 27941851 - BLOR02686 Blo10g00896 896
7 47200718 47204818 + Bma026482.1 Bma07g01230 1230
10 8786790 8789437 + Bma004358.1 Bma10g00638 638
13 44637853 44640528 - Bma010278.1 Bma13g01146 1146
13 44646193 44646711 + Bma010279.1 Bma13g01147 1147
13 44652639 44660364 + Bma010281.1 Bma13g01149 1149
3 27411169 27419013 - Bpe012640.1 Bpe03g00732 732
3 27429969 27432392 + Bpe012641.1 Bpe03g00733 733
8 12866872 12870961 + Bpe023196.1 Bpe08g01071 1071
9 630927 638415 - Bpe023770.1 Bpe09g00092 92
9 650445 650945 - Bpe023773.1 Bpe09g00094 94
9 657603 660275 + Bpe023774.1 Bpe09g00095 95
9 36627549 36635878 - CaPI482276_09g022080.1 Cam09g2208 2208
10 5675253 5687498 + CaPI482276_10g003510.1 Cam10g0351 351
10 5701014 5702667 - CaPI482276_10g003520.1 Cam10g0352 352
10 5720285 5729158 - CaPI482276_10g003530.1 Cam10g0353 353
10 6031200 6033560 - CaPI482276_10g003750.1 Cam10g0375 375
1 8840783 8851342 - Carg23370-RA Car01g00912 912
9 5948377 5950788 - Carg26620-RA Car09g00956 956
16 7891861 7896439 + Carg25231-RA Car16g00952 952
10 4178051 4190283 + CcPI632755_10g003590.1 Cco10g0359 359
10 4204461 4206109 - CcPI632755_10g003600.1 Cco10g0360 360
10 4223389 4232239 - CcPI632755_10g003610.1 Cco10g0361 361
10 4548974 4551372 - CcPI632755_10g003880.1 Cco10g0388 388
9 39666772 39669058 - CePI673135_09g022810.1 Cec09g2281 2281
10 4363456 4377328 + CePI673135_10g003640.1 Cec10g0364 364
10 4390631 4392285 - CePI673135_10g003660.1 Cec10g0366 366
10 4408085 4417001 - CePI673135_10g003670.1 Cec10g0367 367
10 4749332 4751725 - CePI673135_10g003940.1 Cec10g0394 394
6 23624897 23633383 + Chy6G124910.1 Chy06g01963 1963
6 23644163 23645616 + Chy6G124920.1 Chy06g01964 1964
6 23657128 23668958 - Chy6G124930.1 Chy06g01965 1965
10 4452097 4464277 + ClG42_10g0035200.10 Clacu10g0352 352
10 4477546 4479203 - ClG42_10g0035300.10 Clacu10g0353 353
10 4496676 4505543 - ClG42_10g0035400.10 Clacu10g0354 354
10 4818502 4819002 - ClG42_10g0037900.10 Clacu10g0379 379
9 38814028 38816547 - ClCG09G021800.2 Cla09g02121 2121
10 4423368 4437178 + ClCG10G003580.1 Cla10g00338 338
10 4449962 4451615 - ClCG10G003590.2 Cla10g00339 339
10 4469979 4482457 - ClCG10G003600.1 Cla10g00340 340
10 4850370 4853065 - ClCG10G003870.2 Cla10g00363 363
10 5003276 5007536 - ClCG10G003980.1 Cla10g00374 374
1 7668170 7678448 - CmaCh01G010370.1 Cma01g01037 1037
9 5462167 5464640 - CmaCh09G010480.1 Cma09g01048 1048
16 7656778 7660177 + CmaCh16G009950.1 Cma16g00995 995
6 33856658 33869815 + MELO3C014028.2.1 Cme06g02675 2675
6 33880211 33882954 - MELO3C014029.2.1 Cme06g02676 2676
6 33897738 33906050 - MELO3C014031.2.1 Cme06g02677 2677
1 9271694 9273958 + PI0015018.1 Cmetu01g2709 2709
6 27808115 27819918 - PI0028966.1 Cmetu06g1763 1763
6 27770049 27778375 + PI0021787.1 Cmetu06g1879 1879
6 27794010 27795857 + PI0005238.1 Cmetu06g2650 2650
1 8961934 8972298 - CmoCh01G010760.1 Cmo01g01076 1076
6 3368431 3373038 + CmoCh06G006650.1 Cmo06g00665 665
9 5698149 5701277 - CmoCh09G010540.1 Cmo09g01054 1054
16 7378460 7385155 + CmoCh16G010530.1 Cmo16g01053 1053
16 7391292 7394265 + CmoCh16G010540.1 Cmo16g01054 1054
16 7401671 7411567 - CmoCh16G010550.1 Cmo16g01055 1055
10 4593025 4605258 + CmPI595203_10g011880.1 Cmu10g1188 1188
10 4618540 4620197 - CmPI595203_10g011890.1 Cmu10g1189 1189
10 4637610 4646486 - CmPI595203_10g011900.1 Cmu10g1190 1190
10 4959428 4962650 - CmPI595203_10g012160.1 Cmu10g1216 1216
14 10214634 10218435 - Conep14aG0130900.1 Cone14ag1277 1277
14 10219443 10222952 - Conep14aG0131000.1 Cone14ag1278 1278
14 10240195 10242919 + Conep14aG0131100.1 Cone14ag1279 1279
15 10178582 10182177 - Conep15aG0133200.1 Cone15ag1303 1303
15 10182636 10186718 - Conep15aG0133300.1 Cone15ag1304 1304
15 10197942 10206451 + Conep15aG0133500.1 Cone15ag1306 1306
2 5558019 5569612 + Cp4.1LG02g00210.1 Cpe02g00854 854
6 5556087 5559026 - Cp4.1LG06g07990.1 Cpe06g00856 856
14 6723905 6730497 + Cp4.1LG14g08290.1 Cpe14g00830 830
14 6736174 6737912 + Cp4.1LG14g08270.1 Cpe14g00831 831
14 6745583 6755948 - Cp4.1LG14g08380.1 Cpe14g00832 832
10 5510807 5522984 + CrPI670011_10g005990.1 Cre10g0599 599
10 5536234 5537888 - CrPI670011_10g006000.1 Cre10g0600 600
10 5556265 5565115 - CrPI670011_10g006020.1 Cre10g0602 602
10 5872784 5875145 - CrPI670011_10g006300.1 Cre10g0630 630
3 2971193 2983973 + CsaV3_3G003580.1 Csa03g00358 358
3 2994784 2997024 - CsaV3_3G003590.1 Csa03g00359 359
3 3006430 3014515 - CsaV3_3G003600.1 Csa03g00360 360
7 9698476 9701064 + CsaV3_7G021230.1 Csa07g01034 1034
6 61774647 61792700 + Hsped.06g12190.1 Hepe06g1219 1219
6 61818709 61825056 - Hsped.06g12200.1 Hepe06g1220 1220
2 23560043 23562483 + Lsi02G017790.1 Lsi02g01779 1779
10 14397752 14404866 + MC10g1148 Mch10g1456 1456
10 14420047 14421776 + MC10g1149 Mch10g1457 1457
10 14440637 14459016 - MC10g1150 Mch10g1459 1459
11 9513156 9516955 - MC11g1110 Mch11g1340 1340
1 20974054 20977837 - Sed0016468.1 Sed01g2636 2636
8 39684067 39699327 + Sed0000599.1 Sed08g2850 2850
8 39714130 39716068 - Sed0010842.1 Sed08g2851 2851
8 39723223 39728995 - Sed0013362.1 Sed08g2852 2852
1 20952623 20961454 + Tan0016748.2 Tan01g1928 1928
1 20994328 20996252 + Tan0017551.1 Tan01g1930 1930
1 21023853 21054030 - Tan0022370.1 Tan01g1931 1931
1 87981610 87983940 - Tan0000194.1 Tan01g3265 3265
19 10665035 10669055 - Vvi19g794 Vvi19g794 794
19 10675526 10680100 - Vvi19g795 Vvi19g795 795
19 10691449 10694026 + Vvi19g796 Vvi19g796 796
19 10694907 10702975 + Vvi19g797 Vvi19g797 797
19 10712858 10726195 + Vvi19g798 Vvi19g798 798
19 10747970 10749212 + Vvi19g799 Vvi19g799 799
19 10785517 10830108 - Vvi19g800 Vvi19g800 800
19 10840647 10841808 + Vvi19g801 Vvi19g801 801
19 10934466 10947175 - Vvi19g802 Vvi19g802 802
19 10992612 10993131 + Vvi19g803 Vvi19g803 803
       

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