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
Vvi18g70 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag1945 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g71 Blo01g01642 . . . Bpe02g00302 . . Bma01g02415 . . Cma01g02028 Cma09g00038 Car01g01595 . . Cpe06g00011 . . . . . . . . . . . . . . . Cone4ag2030 . . . Lsi04g01826 Csa04g02721 . . . . Bda11g00980 . . . . . Sed01g2417 Cmo01g02083 Cmo09g00038 . . . Car09g00032 . Cpe02g00025 Bhi09g02845 Tan01g5130 Cmetu07g0277 . Hepe01g2354 Mch11g0043 . Cla11g01836 Cam11g1903 Cec11g1930 Cco11g1939 Clacu11g2067 Cmu11g1873 Cre11g2281 . . Chy07g00408 Cme07g00040
Vvi18g72 Blo01g01641 Blo12g00848 . Bda03g00327 Bpe02g00303 Bpe04g00287 Bma04g00294 Bma01g02414 . . Cma01g02027 Cma09g00041 Car01g01594 . . Cpe06g00012 . . . . . . . . . . . . . . . . Cone7ag1942 . . Lsi04g01822 Csa04g02719 . . . . Bda11g00979 . . . . . Sed01g2420 Cmo01g02082 Cmo09g00041 . . . Car09g00033 . Cpe02g00026 Bhi09g02846 Tan01g5129 Cmetu07g1792 . Hepe01g2353 Mch11g0044 . Cla11g01835 Cam11g1902 Cec11g1929 Cco11g1938 Clacu11g2066 Cmu11g1871 Cre11g2280 . . Chy07g00407 Cme07g00041
Vvi18g73 Blo01g01640 Blo12g00849 . Bda03g00326 . Bpe04g00286 Bma04g00293 . . . . Cma09g00043 Car01g01593 . . Cpe06g00013 . . . . . . . . . . . . . . . Cone4ag2027 . . . Lsi04g01821 Csa04g02718 . . . . Bda11g00978 . . . . . . Cmo01g02081 Cmo09g00043 . . . Car09g00034 . Cpe02g00027 Bhi09g02848 . . . . Mch11g0045 . Cla11g01834 Cam11g1901 Cec11g1927 Cco11g1936 Clacu11g2065 Cmu11g1870 Cre11g2278 . . Chy07g00406 Cme07g00042
Vvi18g74 . . . . . . . . Cmo05g00989 Cmo12g00622 . . . Car12g00663 . . Cpe07g00596 Bhi04g01221 . . . . . . Cla08g00935 Cam08g1382 Cec08g0963 Cco08g1082 Clacu08g1089 . Cre08g0872 . . Cone17ag1463 Cone20ag0013 . . . Cme03g01334 . Blo18g00741 . Bda01g01565 Bpe02g01759 . Bma01g00698 . . . . Cma12g00686 Cma05g00969 Car05g00853 . Cpe11g00781 . . . . . . . . . . . . . . . Lsi08g00777 . . .
Vvi18g75 Blo01g01639 . . . Bpe02g00304 . . Bma01g02413 Cmo05g00990 . . . . . . . . Bhi04g01222 . . . . . . Cla08g00936 Cam08g1383 Cec08g0964 Cco08g1083 Clacu08g1090 . Cre08g0873 . . Cone17ag1462 . . . . Cme03g01335 . Blo18g00742 Bda11g00977 Bda01g01564 Bpe02g01758 . Bma01g00699 . . . . . Cma05g00970 Car05g00854 . Cpe11g00782 . . . . . . . . . . . . . . . Lsi08g00778 . Chy03g00609 .
Vvi18g76 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1461 Cone20ag0014 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g77 . . . . . . . . . . Cma01g02026 . Car01g01592 . . . . . . . . . . . . . . . . . . . . Cone17ag1460 . Lsi04g01820 Csa04g02717 . . . . . . . . . . Sed01g2422 Cmo01g02080 . . . . . . Cpe02g00028 Bhi09g02851 Tan01g5127 Cmetu07g1293 . Hepe01g2351 Mch11g0046 . Cla11g01833 Cam11g1900 Cec11g1926 Cco11g1935 Clacu11g2064 Cmu11g1869 Cre11g2277 . . Chy07g00405 Cme07g00043
Vvi18g78 . . . . . . . . . . Cma01g02025 Cma09g00044 Car01g01591 . . Cpe06g00014 . . . . . . . . . . . . . . . . . Cone17ag1459 Cone20ag0016 Lsi04g01819 Csa04g02715 . . . . . . . . . . . . Cmo09g00045 . . . Car09g00036 . Cpe02g00029 Bhi09g02853 Tan01g5126 Cmetu07g1818 . Hepe01g2350 Mch11g0047 . Cla11g01832 Cam11g1899 Cec11g1925 Cco11g1934 Clacu11g2063 Cmu11g1868 Cre11g2276 . . Chy07g00404 Cme07g00044
Vvi18g79 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 51521042 51524782 + Bda003833.1 Bda01g01564 1564
1 51525299 51527044 - Bda003834.1 Bda01g01565 1565
3 2776009 2777744 + Bda016286.1 Bda03g00326 326
3 2778851 2781061 - Bda016287.1 Bda03g00327 327
11 9508778 9512018 + Bda005740.1 Bda11g00977 977
11 9512622 9515057 + Bda005741.1 Bda11g00978 978
11 9516047 9517894 - Bda005742.1 Bda11g00979 979
11 9538303 9541743 + Bda005744.2 Bda11g00980 980
4 29502570 29505581 + XM_039029612.1 Bhi04g01221 1221
4 29519630 29545954 - XM_039028641.1 Bhi04g01222 1222
9 75411244 75416166 - XM_039041585.1 Bhi09g02845 2845
9 75479118 75483337 + XM_039042597.1 Bhi09g02846 2846
9 75483987 75488222 - XM_039041059.1 Bhi09g02848 2848
9 75521594 75523758 + XM_039043240.1 Bhi09g02851 2851
9 75523955 75543006 - XM_039043237.1 Bhi09g02853 2853
1 56211543 56214816 + BLOR01639 Blo01g01639 1639
1 56215990 56218761 + BLOR01640 Blo01g01640 1640
1 56219899 56221827 - BLOR01641 Blo01g01641 1641
1 56222839 56229189 + BLOR01642 Blo01g01642 1642
12 26748581 26767143 + BLOR04867 Blo12g00848 848
12 26768364 26770959 - BLOR04868 Blo12g00849 849
18 19983922 19985658 + BLOR09229 Blo18g00741 741
18 19986181 19989894 - BLOR09230 Blo18g00742 742
1 6397742 6399487 + Bma000908.1 Bma01g00698 698
1 6399953 6403666 - Bma000909.1 Bma01g00699 699
1 81708023 81711276 + Bma003285.1 Bma01g02413 2413
1 81713453 81715302 - Bma003286.1 Bma01g02414 2414
1 81763424 81766867 + Bma003288.2 Bma01g02415 2415
4 2353802 2355536 + Bma018747.1 Bma04g00293 293
4 2356598 2358717 - Bma018748.1 Bma04g00294 294
2 1988917 1992348 - Bpe008144.2 Bpe02g00302 302
2 1997928 1999776 + Bpe008145.1 Bpe02g00303 303
2 2003848 2007133 - Bpe008146.2 Bpe02g00304 304
2 19917990 19921369 + Bpe009589.1 Bpe02g01758 1758
2 19921861 19923606 - Bpe009590.1 Bpe02g01759 1759
4 1834737 1837296 + Bpe014989.1 Bpe04g00286 286
4 1838362 1840584 - Bpe014990.1 Bpe04g00287 287
8 20108974 20110716 + CaPI482276_08g013820.1 Cam08g1382 1382
8 20113040 20122670 - CaPI482276_08g013830.1 Cam08g1383 1383
11 31516574 31530318 + CaPI482276_11g018990.1 Cam11g1899 1899
11 31530934 31532787 - CaPI482276_11g019000.1 Cam11g1900 1900
11 31535006 31538615 + CaPI482276_11g019010.1 Cam11g1901 1901
11 31539920 31543214 - CaPI482276_11g019020.1 Cam11g1902 1902
11 31544418 31553443 + CaPI482276_11g019030.1 Cam11g1903 1903
1 13153913 13161035 + Carg21364-RA Car01g01591 1591
1 13160641 13163267 - Carg21363-RA Car01g01592 1592
1 13163580 13167289 + Carg21362-RA Car01g01593 1593
1 13166860 13170517 - Carg21361-RA Car01g01594 1594
1 13172205 13176642 + Carg21360-RA Car01g01595 1595
5 8384557 8387237 + Carg21886-RA Car05g00853 853
5 8389883 8401205 - Carg21885-RA Car05g00854 854
9 157713 160926 - Carg08615-RA Car09g00032 32
9 162494 166666 + Carg08616-RA Car09g00033 33
9 167131 170725 - Carg08617-RA Car09g00034 34
9 182054 183539 - Carg08619-RA Car09g00036 36
12 4491176 4492915 - Carg17639-RA Car12g00663 663
8 22618323 22620065 + CcPI632755_08g010820.1 Cco08g1082 1082
8 22622286 22623851 - CcPI632755_08g010830.1 Cco08g1083 1083
11 31989399 32002743 + CcPI632755_11g019340.1 Cco11g1934 1934
11 32003350 32006409 - CcPI632755_11g019350.1 Cco11g1935 1935
11 32007154 32010965 + CcPI632755_11g019360.1 Cco11g1936 1936
11 32012260 32015521 - CcPI632755_11g019380.1 Cco11g1938 1938
11 32016696 32025796 + CcPI632755_11g019390.1 Cco11g1939 1939
8 21461336 21463078 + CePI673135_08g009630.1 Cec08g0963 963
8 21465409 21475208 - CePI673135_08g009640.1 Cec08g0964 964
11 33437952 33449134 + CePI673135_11g019250.1 Cec11g1925 1925
11 33449752 33451600 - CePI673135_11g019260.1 Cec11g1926 1926
11 33453812 33457419 + CePI673135_11g019270.1 Cec11g1927 1927
11 33458689 33461978 - CePI673135_11g019290.1 Cec11g1929 1929
11 33463121 33472305 + CePI673135_11g019300.1 Cec11g1930 1930
3 8656921 8672423 - Chy3G055890.1 Chy03g00609 609
7 3209181 3219575 + Chy7G132340.1 Chy07g00404 404
7 3220191 3222136 - Chy7G132350.1 Chy07g00405 405
7 3222245 3225367 + Chy7G132360.1 Chy07g00406 406
7 3226570 3229733 - Chy7G132370.1 Chy07g00407 407
7 3234623 3238443 + Chy7G132380.1 Chy07g00408 408
8 20880896 20882638 + ClG42_08g0108900.10 Clacu08g1089 1089
8 20885007 20894721 - ClG42_08g0109000.10 Clacu08g1090 1090
11 31554779 31568451 + ClG42_11g0206300.10 Clacu11g2063 2063
11 31569069 31572185 - ClG42_11g0206400.10 Clacu11g2064 2064
11 31573105 31576702 + ClG42_11g0206500.10 Clacu11g2065 2065
11 31577997 31582296 - ClG42_11g0206600.10 Clacu11g2066 2066
11 31582500 31591435 + ClG42_11g0206700.10 Clacu11g2067 2067
8 21880101 21891905 + ClCG08G009270.2 Cla08g00935 935
8 21887805 21906282 - ClCG08G009290.2 Cla08g00936 936
11 31963190 31977160 + ClCG11G018820.2 Cla11g01832 1832
11 31977299 31979421 - ClCG11G018840.1 Cla11g01833 1833
11 31981546 31985141 + ClCG11G018850.2 Cla11g01834 1834
11 31986111 31990570 - ClCG11G018860.1 Cla11g01835 1835
11 31994387 31999870 + ClCG11G018870.2 Cla11g01836 1836
1 12926790 12939481 + CmaCh01G020250.1 Cma01g02025 2025
1 12933546 12935877 - CmaCh01G020260.1 Cma01g02026 2026
1 12939420 12943215 - CmaCh01G020270.1 Cma01g02027 2027
1 12944004 12948842 + CmaCh01G020280.1 Cma01g02028 2028
5 7822328 7824010 + CmaCh05G009690.1 Cma05g00969 969
5 7829293 7841996 - CmaCh05G009700.1 Cma05g00970 970
9 166741 169960 - CmaCh09G000380.1 Cma09g00038 38
9 172537 175409 + CmaCh09G000410.1 Cma09g00041 41
9 175904 179882 - CmaCh09G000430.1 Cma09g00043 43
9 180144 190421 - CmaCh09G000440.1 Cma09g00044 44
12 3716587 3718326 - CmaCh12G006860.1 Cma12g00686 686
3 22892011 22895026 + MELO3C026526.2.1 Cme03g01334 1334
3 22896656 22909657 - MELO3C026527.2.1 Cme03g01335 1335
7 249588 254980 - MELO3C017043.2.1 Cme07g00040 40
7 257040 261095 + MELO3C017042.2.1 Cme07g00041 41
7 261965 265434 - MELO3C017041.2.1 Cme07g00042 42
7 265661 268071 + MELO3C017040.2.1 Cme07g00043 43
7 268257 279625 - MELO3C017039.2.1 Cme07g00044 44
7 24555535 24560923 + PI0019899.2 Cmetu07g0277 277
7 24541570 24543433 - PI0006223.1 Cmetu07g1293 1293
7 24548319 24552919 - PI0002667.1 Cmetu07g1792 1792
7 24530765 24540962 + PI0018679.1 Cmetu07g1818 1818
1 14479197 14481489 - CmoCh01G020800.1 Cmo01g02080 2080
1 14481637 14485062 + CmoCh01G020810.1 Cmo01g02081 2081
1 14485174 14488759 - CmoCh01G020820.1 Cmo01g02082 2082
1 14490476 14495176 + CmoCh01G020830.1 Cmo01g02083 2083
5 7965608 7967290 + CmoCh05G009890.1 Cmo05g00989 989
5 7970495 7981678 - CmoCh05G009900.1 Cmo05g00990 990
9 167186 170801 - CmoCh09G000380.1 Cmo09g00038 38
9 173255 176440 + CmoCh09G000410.1 Cmo09g00041 41
9 178369 181475 - CmoCh09G000430.1 Cmo09g00043 43
9 182454 192049 - CmoCh09G000450.1 Cmo09g00045 45
12 3898186 3900936 - CmoCh12G006220.1 Cmo12g00622 622
11 30804354 30818025 + CmPI595203_11g018680.1 Cmu11g1868 1868
11 30818643 30821759 - CmPI595203_11g018690.1 Cmu11g1869 1869
11 30822679 30826276 + CmPI595203_11g018700.1 Cmu11g1870 1870
11 30827571 30830866 - CmPI595203_11g018710.1 Cmu11g1871 1871
11 30832073 30841007 + CmPI595203_11g018730.1 Cmu11g1873 1873
4 14082077 14086122 + Conep04aG0209200.1 Cone4ag2027 2027
4 14092024 14094685 + Conep04aG0209500.1 Cone4ag2030 2030
7 12392172 12394262 - Conep07aG0200000.1 Cone7ag1942 1942
7 12406799 12408596 - Conep07aG0200300.1 Cone7ag1945 1945
17 9898274 9905049 + Conep17aG0150000.1 Cone17ag1459 1459
17 9905838 9907906 - Conep17aG0150100.1 Cone17ag1460 1460
17 9908095 9909226 + Conep17aG0150200.1 Cone17ag1461 1461
17 9910382 9914282 + Conep17aG0150300.1 Cone17ag1462 1462
17 9914662 9917256 - Conep17aG0150400.1 Cone17ag1463 1463
20 100589 103606 + Conep20aG0001300.1 Cone20ag0013 13
20 111676 118287 - Conep20aG0001400.1 Cone20ag0014 14
20 121124 126956 - Conep20aG0001600.1 Cone20ag0016 16
2 134377 139980 - Cp4.1LG02g08280.1 Cpe02g00025 25
2 140957 145017 + Cp4.1LG02g08360.1 Cpe02g00026 26
2 143263 147526 - Cp4.1LG02g08260.1 Cpe02g00027 27
2 147684 150686 + Cp4.1LG02g08370.1 Cpe02g00028 28
2 149020 157012 - Cp4.1LG02g08290.1 Cpe02g00029 29
6 38883 44199 - Cp4.1LG06g00140.1 Cpe06g00011 11
6 44878 49043 + Cp4.1LG06g00020.1 Cpe06g00012 12
6 49542 53311 - Cp4.1LG06g00180.1 Cpe06g00013 13
6 53576 65412 - Cp4.1LG06g00170.1 Cpe06g00014 14
7 4001473 4003212 - Cp4.1LG07g05780.1 Cpe07g00596 596
11 6323049 6324731 + Cp4.1LG11g07760.1 Cpe11g00781 781
11 6327751 6340140 - Cp4.1LG11g07790.1 Cpe11g00782 782
8 21848919 21850661 + CrPI670011_08g008720.1 Cre08g0872 872
8 21852984 21864508 - CrPI670011_08g008730.1 Cre08g0873 873
11 34488883 34502413 + CrPI670011_11g022760.1 Cre11g2276 2276
11 34503031 34506973 - CrPI670011_11g022770.1 Cre11g2277 2277
11 34507080 34510697 + CrPI670011_11g022780.1 Cre11g2278 2278
11 34511999 34515142 - CrPI670011_11g022800.1 Cre11g2280 2280
11 34516349 34525306 + CrPI670011_11g022810.1 Cre11g2281 2281
4 26218771 26230606 + CsaV3_4G037410.1 Csa04g02715 2715
4 26229876 26231992 - CsaV3_4G037430.1 Csa04g02717 2717
4 26232159 26238866 + CsaV3_4G037440.1 Csa04g02718 2718
4 26235116 26240820 - CsaV3_4G037450.1 Csa04g02719 2719
4 26244040 26247853 + CsaV3_4G037470.1 Csa04g02721 2721
1 88019712 88039682 + Hsped.01g23500.1 Hepe01g2350 2350
1 88040145 88042425 - Hsped.01g23510.1 Hepe01g2351 2351
1 88046733 88050151 - Hsped.01g23530.1 Hepe01g2353 2353
1 88051313 88056218 + Hsped.01g23540.1 Hepe01g2354 2354
4 25374676 25388674 + Lsi04G018190.1 Lsi04g01819 1819
4 25388482 25390948 - Lsi04G018200.1 Lsi04g01820 1820
4 25392116 25397485 + Lsi04G018210.1 Lsi04g01821 1821
4 25398019 25402899 - Lsi04G018220.1 Lsi04g01822 1822
4 25427138 25430822 + Lsi04G018260.1 Lsi04g01826 1826
8 16153387 16155129 + Lsi08G007770.1 Lsi08g00777 777
8 16156667 16168334 - Lsi08G007780.1 Lsi08g00778 778
11 274252 281223 - MC11g0038 Mch11g0043 43
11 286097 290569 + MC11g0039 Mch11g0044 44
11 291388 294388 - MC11g0040 Mch11g0045 45
11 294900 297142 + MC11g0041 Mch11g0046 46
11 297296 306915 - MC11g0042 Mch11g0047 47
1 18063391 18068087 - Sed0024131.2 Sed01g2417 2417
1 18074297 18076719 + Sed0027823.3 Sed01g2420 2420
1 18082994 18085871 + Sed0018366.1 Sed01g2422 2422
1 116595125 116618589 + Tan0004442.1 Tan01g5126 5126
1 116619186 116621009 - Tan0008555.1 Tan01g5127 5127
1 116626684 116630782 - Tan0008900.1 Tan01g5129 5129
1 116637833 116641666 + Tan0015513.1 Tan01g5130 5130
18 691255 696212 + Vvi18g70 Vvi18g70 70
18 696906 703692 - Vvi18g71 Vvi18g71 71
18 708206 712862 + Vvi18g72 Vvi18g72 72
18 713318 722594 - Vvi18g73 Vvi18g73 73
18 727430 730939 + Vvi18g74 Vvi18g74 74
18 731591 736822 - Vvi18g75 Vvi18g75 75
18 740651 743702 - Vvi18g76 Vvi18g76 76
18 745956 749097 + Vvi18g77 Vvi18g77 77
18 749851 760246 - Vvi18g78 Vvi18g78 78
18 761516 764467 - Vvi18g79 Vvi18g79 79
       

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