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
Vvi18g40 . . . . Bpe02g00291 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g02425 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla11g01855 Cam11g1922 Cec11g1948 Cco11g1961 Clacu11g2087 Cmu11g1890 Cre11g2299 . . . .
Vvi18g41 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g42 . . . . . . . . . . . Cma09g00018 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo09g00017 . . . . . . . . . . . . . . . . . . . . . . . Cme07g00021
Vvi18g43 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g44 . . . . . . . . Cmo05g00978 Cmo12g00631 . . . Car12g00668 . . Cpe07g00603 . . . . . . . Cla08g00924 Cam08g1369 Cec08g0952 Cco08g1071 Clacu08g1077 . Cre08g0861 . . . . . . . Cme03g01324 Blo17g00909 Blo18g00730 . Bda01g01575 Bpe02g01768 . Bma01g00691 . . . . Cma12g00695 Cma05g00958 Car05g00841 . Cpe11g00771 . . . . . . . . . . . . . . . Lsi08g00767 . . .
Vvi18g45 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1479 . . . . . . Blo18g00731 . Bda01g01574 Bpe02g01767 . Bma01g00692 . . . . . . . Car09g00017 . . . . . . . . . . . . . . . . . . . .
Vvi18g46 . . . . . . . . Cmo05g00981 . . . . . . . . Bhi04g01203 . . . . . . Cla08g00926 Cam08g1371 Cec08g0954 Cco08g1073 Clacu08g1079 . Cre08g0863 . . . . . . . Cme03g01326 . Blo18g00732 . Bda01g01573 . . . . . . . . Cma05g00960 Car05g00843 . Cpe11g00773 . . . . . . . . . . . . . . . Lsi08g00769 . . .
Vvi18g47 . . . . . . . . Cmo05g00982 Cmo12g00629 Cma01g02039 . Car01g01608 . . . Cpe07g00602 Bhi04g01204 . . . Hepe08g1523 . . Cla08g00927 Cam08g1372 Cec08g0955 Cco08g1074 Clacu08g1080 . Cre08g0864 . . Cone17ag1478 . Lsi04g02421 Csa04g02738 . Cme03g01327 Blo17g00908 . . . . . . . . Cmo01g02098 . Cma12g00694 Cma05g00961 Car05g00844 . Cpe11g00774 Cpe02g00014 Bhi09g02829 . . . . Mch11g0030 . Cla11g01851 Cam11g1917 Cec11g1942 Cco11g1956 Clacu11g2082 Cmu11g1886 Cre11g2294 Lsi08g00770 . Chy07g00425 Cme07g00024
Vvi18g48 Blo01g01648 Blo12g00845 . Bda03g00328 Bpe02g00295 Bpe04g00291 . Bma01g02421 . . Cma01g02038 . Car01g01607 . . Cpe06g00003 . . . . . . . . . . . . . . . Cone4ag2038 Cone7ag1949 . . Lsi04g02420 Csa04g02737 . . . . . . . . . . . Cmo01g02097 Cmo09g00027 . . . Car09g00023 . Cpe02g00015 Bhi09g02831 . . . . Mch11g0031 . Cla11g01850 Cam11g1916 Cec11g1941 Cco11g1955 Clacu11g2081 Cmu11g1885 Cre11g2293 . . Chy07g00424 Cme07g00025
Vvi18g49 Blo01g01647 . . . . . . Bma01g02420 . . Cma01g02036 . Car01g01606 . . Cpe06g00004 . . . . . . . . . . . . . . . Cone4ag2037 . . . Lsi04g02419 Csa04g02736 . . . . Bda11g00987 . . . . . Sed05g1024 Cmo01g02095 Cmo09g00028 . . . Car09g00024 . Cpe02g00016 Bhi09g02832 Tan01g5153 Cmetu07g0142 . Hepe01g2366 Mch11g0032 . Cla11g01849 Cam11g1915 Cec11g1940 Cco11g1954 Clacu11g2080 Cmu11g1884 Cre11g2292 . . Chy07g00423 Cme07g00026
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 51576035 51577073 + Bda003841.1 Bda01g01573 1573
1 51577440 51580044 - Bda003842.1 Bda01g01574 1574
1 51584906 51588016 - Bda003843.1 Bda01g01575 1575
3 2782881 2785388 - Bda016288.1 Bda03g00328 328
11 9610088 9610528 + Bda005750.1 Bda11g00987 987
4 29238009 29241678 - XM_039029648.1 Bhi04g01203 1203
4 29285074 29289344 + XM_039028212.1 Bhi04g01204 1204
9 75017586 75020914 + XM_039042165.1 Bhi09g02829 2829
9 75020905 75023574 - XM_039042162.1 Bhi09g02831 2831
9 75086794 75087564 - XM_039040910.1 Bhi09g02832 2832
1 56278178 56279889 + BLOR01647 Blo01g01647 1647
1 56280352 56284136 + BLOR01648 Blo01g01648 1648
12 26723094 26725534 - BLOR04864 Blo12g00845 845
17 29889996 29891897 - BLOR08454 Blo17g00908 908
17 29897934 29900285 - BLOR08455 Blo17g00909 909
18 19540387 19545804 + BLOR09218 Blo18g00730 730
18 19605658 19608589 + BLOR09219 Blo18g00731 731
18 19608929 19610032 - BLOR09220 Blo18g00732 732
1 6340650 6343754 + Bma000900.4 Bma01g00691 691
1 6348451 6351068 + Bma000901.1 Bma01g00692 692
1 81847899 81848343 + Bma003292.1 Bma01g02420 2420
1 81848707 81851099 + Bma003293.1 Bma01g02421 2421
2 1920389 1921785 - Bpe008135.1 Bpe02g00291 291
2 1941329 1944350 - Bpe008138.1 Bpe02g00295 295
2 19971999 19974605 - Bpe009598.3 Bpe02g01767 1767
2 19979848 19982766 - Bpe009599.1 Bpe02g01768 1768
4 1860974 1863511 + Bpe014995.1 Bpe04g00291 291
8 20019565 20022793 + CaPI482276_08g013690.1 Cam08g1369 1369
8 20033375 20036235 - CaPI482276_08g013710.1 Cam08g1371 1371
8 20042464 20051368 + CaPI482276_08g013720.1 Cam08g1372 1372
11 31601278 31601742 + CaPI482276_11g019150.1 Cam11g1915 1915
11 31603494 31605726 + CaPI482276_11g019160.1 Cam11g1916 1916
11 31605971 31608802 - CaPI482276_11g019170.1 Cam11g1917 1917
11 31634104 31636994 + CaPI482276_11g019220.1 Cam11g1922 1922
1 13211236 13211959 + Carg21349-RA Car01g01606 1606
1 13212374 13214475 + Carg21348-RA Car01g01607 1607
1 13213409 13218046 - Carg21347-RA Car01g01608 1608
5 8313438 8317502 + Carg21898-RA Car05g00841 841
5 8325923 8328641 - Carg21896-RA Car05g00843 843
5 8331160 8335085 + Carg21895-RA Car05g00844 844
9 104899 106732 - Carg08600-RA Car09g00017 17
9 127346 129734 - Carg08606-RA Car09g00023 23
9 130985 131246 - Carg08607-RA Car09g00024 24
12 4531145 4532440 - Carg17634-RA Car12g00668 668
8 22519645 22522898 + CcPI632755_08g010710.1 Cco08g1071 1071
8 22529730 22536147 - CcPI632755_08g010730.1 Cco08g1073 1073
8 22542348 22551498 + CcPI632755_08g010740.1 Cco08g1074 1074
11 32075138 32075599 + CcPI632755_11g019540.1 Cco11g1954 1954
11 32077387 32079625 + CcPI632755_11g019550.1 Cco11g1955 1955
11 32080088 32082716 - CcPI632755_11g019560.1 Cco11g1956 1956
11 32108373 32111214 + CcPI632755_11g019610.1 Cco11g1961 1961
8 21372661 21375898 + CePI673135_08g009520.1 Cec08g0952 952
8 21386431 21389395 - CePI673135_08g009540.1 Cec08g0954 954
8 21395096 21404086 + CePI673135_08g009550.1 Cec08g0955 955
11 33523410 33523879 + CePI673135_11g019400.1 Cec11g1940 1940
11 33525548 33527767 + CePI673135_11g019410.1 Cec11g1941 1941
11 33528232 33530860 - CePI673135_11g019420.1 Cec11g1942 1942
11 33559380 33559776 + CePI673135_11g019480.1 Cec11g1948 1948
7 3283969 3284473 + Chy7G132530.1 Chy07g00423 423
7 3285410 3287691 + Chy7G132540.1 Chy07g00424 424
7 3288150 3290694 - Chy7G132550.1 Chy07g00425 425
8 20791936 20796592 + ClG42_08g0107700.10 Clacu08g1077 1077
8 20805462 20808414 - ClG42_08g0107900.10 Clacu08g1079 1079
8 20814560 20823387 + ClG42_08g0108000.10 Clacu08g1080 1080
11 31638936 31639428 + ClG42_11g0208000.10 Clacu11g2080 2080
11 31641237 31643447 + ClG42_11g0208100.10 Clacu11g2081 2081
11 31643692 31646543 - ClG42_11g0208200.10 Clacu11g2082 2082
11 31671316 31674483 + ClG42_11g0208700.10 Clacu11g2087 2087
8 21785447 21789375 + ClCG08G009160.2 Cla08g00924 924
8 21802203 21805338 - ClCG08G009180.2 Cla08g00926 926
8 21810985 21815086 + ClCG08G009190.1 Cla08g00927 927
11 32045587 32048339 + ClCG11G019020.2 Cla11g01849 1849
11 32049816 32052024 + ClCG11G019030.1 Cla11g01850 1850
11 32052269 32055673 - ClCG11G019040.2 Cla11g01851 1851
11 32080129 32083318 + ClCG11G019080.2 Cla11g01855 1855
1 12979552 12983585 + CmaCh01G020360.1 Cma01g02036 2036
1 12983922 12986272 + CmaCh01G020380.1 Cma01g02038 2038
1 12986204 12989715 - CmaCh01G020390.1 Cma01g02039 2039
5 7751193 7756811 + CmaCh05G009580.1 Cma05g00958 958
5 7763791 7766773 - CmaCh05G009600.1 Cma05g00960 960
5 7769242 7772938 + CmaCh05G009610.1 Cma05g00961 961
9 110002 117295 - CmaCh09G000180.1 Cma09g00018 18
12 3753696 3757377 - CmaCh12G006940.1 Cma12g00694 694
12 3766593 3773947 - CmaCh12G006950.1 Cma12g00695 695
3 22795501 22804229 + MELO3C026514.2.1 Cme03g01324 1324
3 22813834 22817923 - MELO3C026518.2.1 Cme03g01326 1326
3 22821262 22825179 + MELO3C026519.2.1 Cme03g01327 1327
7 183156 185930 - MELO3C017061.2.1 Cme07g00021 21
7 197832 201647 + MELO3C017058.2.1 Cme07g00024 24
7 201257 203614 - MELO3C017057.2.1 Cme07g00025 25
7 204533 205419 - MELO3C017056.2.1 Cme07g00026 26
7 24605820 24606447 + PI0021436.1 Cmetu07g0142 142
1 14530799 14531815 + CmoCh01G020950.1 Cmo01g02095 2095
1 14532599 14534932 + CmoCh01G020970.1 Cmo01g02097 2097
1 14534772 14537474 - CmoCh01G020980.1 Cmo01g02098 2098
5 7887989 7892219 + CmoCh05G009780.1 Cmo05g00978 978
5 7901478 7904567 - CmoCh05G009810.1 Cmo05g00981 981
5 7907590 7911010 + CmoCh05G009820.1 Cmo05g00982 982
9 114350 117236 - CmoCh09G000170.1 Cmo09g00017 17
9 135014 137611 - CmoCh09G000270.1 Cmo09g00027 27
9 138480 139361 - CmoCh09G000280.1 Cmo09g00028 28
12 3929478 3936746 - CmoCh12G006290.1 Cmo12g00629 629
12 3949107 3953065 - CmoCh12G006310.1 Cmo12g00631 631
11 30888515 30888977 + CmPI595203_11g018840.1 Cmu11g1884 1884
11 30890739 30892947 + CmPI595203_11g018850.1 Cmu11g1885 1885
11 30893192 30896043 - CmPI595203_11g018860.1 Cmu11g1886 1886
11 30921141 30924016 + CmPI595203_11g018900.1 Cmu11g1890 1890
4 14126568 14127293 + Conep04aG0210200.1 Cone4ag2037 2037
4 14128382 14130737 + Conep04aG0210300.1 Cone4ag2038 2038
7 12435722 12438088 + Conep07aG0200700.1 Cone7ag1949 1949
17 9974559 9977472 - Conep17aG0151900.1 Cone17ag1478 1478
17 9978302 9981391 - Conep17aG0152000.1 Cone17ag1479 1479
2 94801 98732 + Cp4.1LG02g08710.1 Cpe02g00014 14
2 97873 100532 - Cp4.1LG02g08620.1 Cpe02g00015 15
2 100693 101844 - Cp4.1LG02g08640.1 Cpe02g00016 16
6 10080 12935 - Cp4.1LG06g00120.1 Cpe06g00003 3
6 14086 14405 - Cp4.1LG06g00110.1 Cpe06g00004 4
7 4043733 4047478 - Cp4.1LG07g05730.1 Cpe07g00602 602
7 4056858 4064008 - Cp4.1LG07g05700.1 Cpe07g00603 603
11 6242929 6248047 + Cp4.1LG11g07750.1 Cpe11g00771 771
11 6259178 6262125 - Cp4.1LG11g07810.1 Cpe11g00773 773
11 6264454 6268561 + Cp4.1LG11g07770.1 Cpe11g00774 774
8 21759592 21763347 + CrPI670011_08g008610.1 Cre08g0861 861
8 21772271 21776724 - CrPI670011_08g008630.1 Cre08g0863 863
8 21782933 21792077 + CrPI670011_08g008640.1 Cre08g0864 864
11 34573176 34573628 + CrPI670011_11g022920.1 Cre11g2292 2292
11 34575432 34577625 + CrPI670011_11g022930.1 Cre11g2293 2293
11 34578089 34580718 - CrPI670011_11g022940.1 Cre11g2294 2294
11 34606621 34609509 + CrPI670011_11g022990.1 Cre11g2299 2299
4 26291655 26292689 + CsaV3_4G037620.1 Csa04g02736 2736
4 26293322 26295606 + CsaV3_4G037630.1 Csa04g02737 2737
4 26296064 26298610 - CsaV3_4G037640.1 Csa04g02738 2738
1 88098629 88099293 + Hsped.01g23660.1 Hepe01g2366 2366
8 19506738 19510318 - Hsped.08g15230.1 Hepe08g1523 1523
4 31314050 31314613 + Lsi04G024190.1 Lsi04g02419 2419
4 31316394 31319028 + Lsi04G024200.1 Lsi04g02420 2420
4 31318792 31322400 - Lsi04G024210.1 Lsi04g02421 2421
4 31351954 31356529 + Lsi04G024250.1 Lsi04g02425 2425
8 16065831 16072326 + Lsi08G007670.1 Lsi08g00767 767
8 16084359 16085658 - Lsi08G007690.1 Lsi08g00769 769
8 16089755 16093959 + Lsi08G007700.1 Lsi08g00770 770
11 223655 228107 + MC11g0026 Mch11g0030 30
11 224333 230275 - MC11g0027 Mch11g0031 31
11 231034 232523 - MC11g0028 Mch11g0032 32
5 8906373 8907365 + Sed0010344.1 Sed05g1024 1024
1 116699948 116700449 + Tan0021851.1 Tan01g5153 5153
18 505113 509609 + Vvi18g40 Vvi18g40 40
18 509644 513093 + Vvi18g41 Vvi18g41 41
18 514834 520024 + Vvi18g42 Vvi18g42 42
18 520377 522292 + Vvi18g43 Vvi18g43 43
18 524836 530439 + Vvi18g44 Vvi18g44 44
18 531975 535425 + Vvi18g45 Vvi18g45 45
18 535474 538079 - Vvi18g46 Vvi18g46 46
18 539605 545129 + Vvi18g47 Vvi18g47 47
18 545162 551309 - Vvi18g48 Vvi18g48 48
18 553738 554202 - Vvi18g49 Vvi18g49 49
       

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