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
Vvi18g90 . Blo12g00852 . Bda03g00321 . Bpe04g00282 Bma04g00288 . Cmo05g00994 . Cma01g02016 Cma09g00051 Car01g01585 . . . . Bhi04g01225 . . . . . . Cla08g00940 . . . . . . . . Cone17ag1456 Cone20ag0021 Lsi04g01809 Csa04g02704 . Cme03g01340 . . . . . . . . . Cmo01g02074 Cmo09g00054 Cma12g00680 Cma05g00975 . Car09g00044 . . Bhi09g02877 . . . . . . Cla11g01825 . . . . . . Lsi08g00783 . Chy07g00395 Cme07g00052
Vvi18g91 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g92 . . . . . . . . . Cmo12g00617 . . . Car12g00659 . . Cpe07g00590 . . . . . . . . . . . . . . . . Cone17ag1455 . . . . . Blo17g00905 . . . . . . . . . . Cma12g00679 . Car05g00857 . . . . . . . . . . . . . . . . . . . . .
Vvi18g93 . . . . . . . . Cmo05g00995 . . . . . . . . Bhi04g01226 . . . . . . Cla08g00941 . . . . . . . . . Cone20ag0022 . . . Cme03g01341 . . . . . . . . . . . . Cma05g00976 . . Cpe11g00786 . . . . . . . . . . . . . . . Lsi08g00786 . Chy03g00616 .
Vvi18g94 . . . . . . . . . . Cma01g02015 Cma09g00052 Car01g01584 . . Cpe06g00021 . . . . . . . . . . . . . . . . Cone7ag1937 . . Lsi04g01807 Csa04g02702 . . Blo17g00904 . . . . . . . . Cmo01g02072 . . . . Car09g00045 . Cpe02g00034 Bhi09g02880 . . . . . . Cla11g01824 Cam11g1890 Cec11g1915 Cco11g1923 Clacu11g2055 Cmu11g1860 Cre11g2266 . . Chy07g00394 Cme07g00053
Vvi18g95 Blo01g01637 Blo12g00853 . Bda03g00320 Bpe02g00307 Bpe04g00281 . Bma01g02411 . . Cma01g02014 Cma09g00053 Car01g01583 . . Cpe06g00022 . . . . . . . . . . . . . . . Cone4ag2020 Cone7ag1936 . Cone20ag0023 Lsi04g01806 Csa04g02701 . . Blo17g00903 . Bda11g00974 . . . . . Sed01g2434 Cmo01g02071 Cmo09g00055 . . . Car09g00046 . Cpe02g00035 Bhi09g02885 Tan01g5108 Cmetu07g0208 . . Mch11g0056 . Cla11g01823 Cam11g1889 Cec11g1914 Cco11g1922 Clacu11g2054 Cmu11g1859 Cre11g2265 . . Chy07g00393 Cme07g00054
Vvi18g96 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g97 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g98 Blo01g01636 Blo12g00854 . Bda03g00319 Bpe02g00309 Bpe04g00280 Bma04g00287 Bma01g02409 Cmo05g00996 Cmo12g00616 Cma01g02012 Cma09g00054 Car01g01582 Car12g00658 . Cpe06g00023 Cpe07g00589 Bhi04g01227 . . . Hepe08g1506 . . Cla08g00942 Cam08g1392 Cec08g0974 Cco08g1097 Clacu08g1099 . Cre08g0883 . . . . Lsi04g01805 Csa04g02699 . Cme03g01342 . . Bda11g00972 . . . . . Sed08g1839 . . Cma12g00678 Cma05g00977 Car05g00858 Car09g00047 Cpe11g00788 Cpe02g00036 Bhi09g02890 Tan01g5104 Cmetu03g1562 . Hepe01g2339 Mch11g0058 . Cla11g01822 Cam11g1888 Cec11g1913 Cco11g1920 Clacu11g2052 Cmu11g1857 Cre11g2263 Lsi08g00787 . Chy07g00390 Cme07g00057
Vvi18g99 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 2735043 2738456 + Bda016279.1 Bda03g00319 319
3 2741407 2744307 + Bda016280.1 Bda03g00320 320
3 2745793 2747953 - Bda016281.2 Bda03g00321 321
11 9478513 9481821 + Bda005735.1 Bda11g00972 972
11 9496242 9499466 + Bda005737.1 Bda11g00974 974
4 29810543 29815464 + XM_039030510.1 Bhi04g01225 1225
4 29868026 29872220 + XM_039030541.1 Bhi04g01226 1226
4 29898102 29902635 - XM_039028471.1 Bhi04g01227 1227
9 75720020 75723302 + XM_039041389.1 Bhi09g02877 2877
9 75811647 75827632 + XM_039041975.1 Bhi09g02880 2880
9 75833559 75839329 - XM_039041798.1 Bhi09g02885 2885
9 75843887 75847448 - XM_039041779.1 Bhi09g02890 2890
1 56186099 56188911 + BLOR01636 Blo01g01636 1636
1 56197879 56205282 + BLOR01637 Blo01g01637 1637
12 26794248 26802833 + BLOR04871 Blo12g00852 852
12 26805869 26809387 - BLOR04872 Blo12g00853 853
12 26812460 26817369 - BLOR04873 Blo12g00854 854
17 29779574 29786434 + BLOR08449 Blo17g00903 903
17 29786702 29799713 - BLOR08450 Blo17g00904 904
17 29807608 29809866 - BLOR08451 Blo17g00905 905
1 81654999 81658048 + Bma003280.1 Bma01g02409 2409
1 81688236 81690002 + Bma003282.1 Bma01g02411 2411
4 2312251 2315807 + Bma018741.1 Bma04g00287 287
4 2323193 2325361 - Bma018742.3 Bma04g00288 288
2 2017591 2020778 - Bpe008149.1 Bpe02g00307 307
2 2035691 2039130 - Bpe008151.1 Bpe02g00309 309
4 1798995 1801997 + Bpe025597 Bpe04g00280 280
4 1805006 1807927 + Bpe014985.3 Bpe04g00281 281
4 1809372 1811551 - Bpe025598 Bpe04g00282 282
8 20201762 20206133 - CaPI482276_08g013920.1 Cam08g1392 1392
11 31422808 31438033 + CaPI482276_11g018880.1 Cam11g1888 1888
11 31438056 31441791 + CaPI482276_11g018890.1 Cam11g1889 1889
11 31444509 31460366 - CaPI482276_11g018900.1 Cam11g1890 1890
1 13109931 13113980 + Carg21373-RA Car01g01582 1582
1 13115602 13118959 + Carg21372-RA Car01g01583 1583
1 13118287 13130623 - Carg21371-RA Car01g01584 1584
1 13138239 13140634 - Carg21370-RA Car01g01585 1585
5 8427923 8436672 + Carg21882-RA Car05g00857 857
5 8438371 8443015 - Carg21881-RA Car05g00858 858
9 208991 212016 + Carg08627-RA Car09g00044 44
9 214172 229194 + Carg08628-RA Car09g00045 45
9 230493 234675 - Carg08629-RA Car09g00046 46
9 237302 241118 - Carg08630-RA Car09g00047 47
12 4443165 4446166 + Carg17644-RA Car12g00658 658
12 4446374 4455700 - Carg17643-RA Car12g00659 659
8 22717225 22721428 - CcPI632755_08g010970.1 Cco08g1097 1097
11 31889123 31900215 + CcPI632755_11g019200.1 Cco11g1920 1920
11 31906420 31910155 + CcPI632755_11g019220.1 Cco11g1922 1922
11 31912901 31928670 - CcPI632755_11g019230.1 Cco11g1923 1923
8 21553742 21557677 - CePI673135_08g009740.1 Cec08g0974 974
11 33342008 33358372 + CePI673135_11g019130.1 Cec11g1913 1913
11 33358395 33362130 + CePI673135_11g019140.1 Cec11g1914 1914
11 33364792 33380291 - CePI673135_11g019150.1 Cec11g1915 1915
3 8724666 8727140 + Chy3G055960.1 Chy03g00616 616
7 3115465 3118549 + Chy7G132200.1 Chy07g00390 390
7 3133948 3137623 + Chy7G132230.1 Chy07g00393 393
7 3139784 3154019 - Chy7G132240.1 Chy07g00394 394
7 3164790 3166890 - Chy7G132250.1 Chy07g00395 395
8 20974457 20978857 - ClG42_08g0109900.10 Clacu08g1099 1099
11 31461830 31471815 + ClG42_11g0205200.10 Clacu11g2052 2052
11 31477322 31481129 + ClG42_11g0205400.10 Clacu11g2054 2054
11 31483819 31499461 - ClG42_11g0205500.10 Clacu11g2055 2055
8 21956257 21964984 + ClCG08G009340.2 Cla08g00940 940
8 21979379 21982200 + ClCG08G009350.1 Cla08g00941 941
8 21983570 21989322 - ClCG08G009360.2 Cla08g00942 942
11 31869724 31879287 + ClCG11G018720.2 Cla11g01822 1822
11 31885237 31889547 + ClCG11G018730.2 Cla11g01823 1823
11 31891302 31907461 - ClCG11G018740.1 Cla11g01824 1824
11 31921672 31926731 - ClCG11G018750.2 Cla11g01825 1825
1 12884453 12888011 + CmaCh01G020120.1 Cma01g02012 2012
1 12889584 12893117 + CmaCh01G020140.1 Cma01g02014 2014
1 12891245 12908439 - CmaCh01G020150.1 Cma01g02015 2015
1 12910712 12913482 - CmaCh01G020160.1 Cma01g02016 2016
5 7870534 7873951 + CmaCh05G009750.1 Cma05g00975 975
5 7876417 7878534 + CmaCh05G009760.1 Cma05g00976 976
5 7879843 7884378 - CmaCh05G009770.1 Cma05g00977 977
9 217016 218680 + CmaCh09G000510.1 Cma09g00051 51
9 219585 237772 + CmaCh09G000520.1 Cma09g00052 52
9 238376 243909 - CmaCh09G000530.1 Cma09g00053 53
9 245537 249556 - CmaCh09G000540.1 Cma09g00054 54
12 3665565 3669765 + CmaCh12G006780.1 Cma12g00678 678
12 3670396 3672550 - CmaCh12G006790.1 Cma12g00679 679
12 3678680 3681785 - CmaCh12G006800.1 Cma12g00680 680
3 22943619 22948376 + MELO3C026531.2.1 Cme03g01340 1340
3 22969561 22971468 + MELO3C027420.2.1 Cme03g01341 1341
3 22972354 22976386 - MELO3C026532.2.1 Cme03g01342 1342
7 319325 322201 + MELO3C017028.2.1 Cme07g00052 52
7 331093 346331 + MELO3C017027.2.1 Cme07g00053 53
7 347490 351816 - MELO3C017025.2.1 Cme07g00054 54
7 362879 366635 - MELO3C017023.2.1 Cme07g00057 57
3 6404710 6409163 + PI0015519.1 Cmetu03g1562 1562
7 24436172 24439880 + PI0002611.1 Cmetu07g0208 208
1 14430546 14438974 + CmoCh01G020710.1 Cmo01g02071 2071
1 14440588 14442920 - CmoCh01G020720.1 Cmo01g02072 2072
1 14456723 14459125 - CmoCh01G020740.1 Cmo01g02074 2074
5 8007821 8010918 + CmoCh05G009940.1 Cmo05g00994 994
5 8014224 8016815 + CmoCh05G009950.1 Cmo05g00995 995
5 8023898 8028772 - CmoCh05G009960.1 Cmo05g00996 996
9 219005 240860 + CmoCh09G000540.1 Cmo09g00054 54
9 241552 253002 - CmoCh09G000550.1 Cmo09g00055 55
12 3848542 3853492 + CmoCh12G006160.1 Cmo12g00616 616
12 3853610 3855368 - CmoCh12G006170.1 Cmo12g00617 617
11 30711475 30720996 + CmPI595203_11g018570.1 Cmu11g1857 1857
11 30727036 30730771 + CmPI595203_11g018590.1 Cmu11g1859 1859
11 30733462 30749223 - CmPI595203_11g018600.1 Cmu11g1860 1860
4 14057012 14060986 + Conep04aG0208500.1 Cone4ag2020 2020
7 12353709 12357301 + Conep07aG0199400.1 Cone7ag1936 1936
7 12357562 12371284 - Conep07aG0199500.1 Cone7ag1937 1937
17 9881338 9883497 - Conep17aG0149600.1 Cone17ag1455 1455
17 9885707 9888624 - Conep17aG0149700.1 Cone17ag1456 1456
20 137719 139917 + Conep20aG0002100.1 Cone20ag0021 21
20 141578 145708 + Conep20aG0002200.1 Cone20ag0022 22
20 143717 147018 - Conep20aG0002300.1 Cone20ag0023 23
2 175193 191762 + Cp4.1LG02g08430.1 Cpe02g00034 34
2 189705 194219 - Cp4.1LG02g08270.1 Cpe02g00035 35
2 195001 199226 - Cp4.1LG02g08310.1 Cpe02g00036 36
6 97580 112479 + Cp4.1LG06g00230.1 Cpe06g00021 21
6 113524 117766 - Cp4.1LG06g00330.1 Cpe06g00022 22
6 120430 124497 - Cp4.1LG06g00300.1 Cpe06g00023 23
7 3950751 3954065 + Cp4.1LG07g05850.1 Cpe07g00589 589
7 3954274 3956313 - Cp4.1LG07g05800.1 Cpe07g00590 590
11 6375438 6376721 + Cp4.1LG11g07890.1 Cpe11g00786 786
11 6379414 6383782 - Cp4.1LG11g07970.1 Cpe11g00788 788
8 21941661 21946048 - CrPI670011_08g008830.1 Cre08g0883 883
11 34394444 34404011 + CrPI670011_11g022630.1 Cre11g2263 2263
11 34410140 34413865 + CrPI670011_11g022650.1 Cre11g2265 2265
11 34416602 34432325 - CrPI670011_11g022660.1 Cre11g2266 2266
4 26130038 26134144 + CsaV3_4G037250.1 Csa04g02699 2699
4 26143290 26148646 + CsaV3_4G037270.1 Csa04g02701 2701
4 26150103 26164876 - CsaV3_4G037280.1 Csa04g02702 2702
4 26173294 26177620 - CsaV3_4G037300.1 Csa04g02704 2704
1 87930515 87934988 + Hsped.01g23390.1 Hepe01g2339 2339
8 18856974 18861350 + Hsped.08g15060.1 Hepe08g1506 1506
4 25268800 25279233 + Lsi04G018050.1 Lsi04g01805 1805
4 25286568 25292132 + Lsi04G018060.1 Lsi04g01806 1806
4 25294658 25296969 - Lsi04G018070.1 Lsi04g01807 1807
4 25327852 25331257 - Lsi04G018090.1 Lsi04g01809 1809
8 16217990 16221614 + Lsi08G007830.1 Lsi08g00783 783
8 16245337 16249074 + Lsi08G007860.1 Lsi08g00786 786
8 16250999 16255415 - Lsi08G007870.1 Lsi08g00787 787
11 367262 373128 - MC11g0051 Mch11g0056 56
11 376539 381047 - MC11g0052 Mch11g0058 58
1 18131605 18136747 - Sed0020896.2 Sed01g2434 2434
8 33089288 33094165 + Sed0008332.2 Sed08g1839 1839
1 116432998 116437253 + Tan0006113.1 Tan01g5104 5104
1 116441307 116446990 + Tan0000010.2 Tan01g5108 5108
18 836206 838752 + Vvi18g90 Vvi18g90 90
18 838798 839349 + Vvi18g91 Vvi18g91 91
18 852592 859459 + Vvi18g92 Vvi18g92 92
18 859573 862780 + Vvi18g93 Vvi18g93 93
18 874265 900936 + Vvi18g94 Vvi18g94 94
18 908407 914042 - Vvi18g95 Vvi18g95 95
18 914533 922269 - Vvi18g96 Vvi18g96 96
18 922457 926763 - Vvi18g97 Vvi18g97 97
18 927340 932130 - Vvi18g98 Vvi18g98 98
18 932503 935155 - Vvi18g99 Vvi18g99 99
       

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