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
Vvi4g952 . . Bda04g00055 Bda10g00129 . . Bma09g00074 . Cmo04g00836 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy07g01290 . Blo05g00792 . . . . . . . . . . . Cma20g00855 . . . . Bhi10g02022 . . . . . . Cla07g00865 . . . . . . . Csa04g00511 . .
Vvi4g953 . . Bda04g00054 . . . Bma09g00075 . . . Cma03g00757 . Car03g00692 Car07g00434 Sed14g1110 Cpe19g00806 Cpe10g00604 Bhi03g01285 Tan03g1971 Cmetu08g0416 . Hepe04g1502 . . Cla01g01899 Cam01g1988 Cec04g1640 Cco04g1705 Clacu01g2007 Cmu01g1878 Cre04g1559 Cone8ag0804 . Cone6ag1615 . Lsi01g00682 . . Cme08g00840 Blo05g00793 . . . Bpe10g00116 . . . . Cmo03g00785 Cmo07g00496 . . . . . . . . . . . . . . . . . . . . . Csa06g03232 Chy02g00657 .
Vvi4g954 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g955 Blo04g00920 Blo16g00039 . . Bpe15g00433 Bpe13g00452 . . Cmo04g00837 Cmo16g00712 . . . . . . . . . . . . . . . . . . . . . Cone8ag0805 . . . . . Chy07g01291 . . . Bda11g01874 . . . Bma03g00992 Bma06g00128 . . . Cma16g00655 . . . . Cpe14g00559 . . . . . . . Cla07g00866 Cam07g0939 Cec07g1004 Cco07g0982 Clacu07g0912 Cmu07g0912 Cre07g1283 . Csa04g00510 . .
Vvi4g956 . . . . Bpe15g00432 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g957 Blo04g00919 Blo16g00040 . . Bpe15g00431 Bpe13g00450 . . Cmo04g00838 . . . . . . . . . . . . . . . . . . . . . . Cone8ag0806 . . . . . Chy07g01292 . . . Bda11g01873 . . . Bma03g00991 Bma06g00127 . . . . . . . . Cpe14g00428 . . . . . . . Cla07g00867 Cam07g0940 Cec07g1005 Cco07g0983 Clacu07g0913 Cmu07g0913 Cre07g1284 Lsi07g00205 Csa04g00509 . .
Vvi4g958 . . . Bda10g00132 . . . Bma15g01000 Cmo04g00839 . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1616 Cone9ag1541 . . Chy07g01293 . . Blo06g00133 . Bda14g01154 Bpe10g00117 . . . . . . . . . . . Cpe14g00560 . . . . . . . Cla07g00870 Cam07g0941 Cec07g1008 Cco07g0987 Clacu07g0917 Cmu07g0916 Cre07g1287 Lsi07g00203 Csa04g00508 . .
Vvi4g959 . . Bda04g00052 . . Bpe13g00449 . . Cmo04g00840 Cmo16g00713 Cma03g00756 Cma07g00493 Car03g00690 Car07g00433 Sed10g0914 Cpe19g00807 Cpe10g00605 Bhi03g01287 Tan03g1972 Cmetu08g0213 . Hepe04g1503 . . Cla01g01901 Cam01g1990 . . Clacu01g2009 Cmu01g1880 . . . Cone6ag1617 Cone9ag1542 Lsi01g00680 . Chy07g01294 Cme08g00842 Blo05g00794 . Bda11g01872 . . . . Bma06g00126 . Cmo03g00782 Cmo07g00492 Cma16g00656 . . . . Cpe14g00561 . . . . . . . Cla07g00872 Cam07g0944 Cec07g1011 Cco07g0988 Clacu07g0918 Cmu07g0917 Cre07g1288 Lsi07g00202 Csa06g03233 Chy02g00656 .
Vvi4g960 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g961 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 867857 869695 - Bda018770.1 Bda04g00052 52
4 880748 885460 - Bda018768.1 Bda04g00054 54
4 890864 893510 - Bda018767.1 Bda04g00055 55
10 3557155 3559706 + Bda006588.1 Bda10g00129 129
10 3664610 3670000 - Bda006595.1 Bda10g00132 132
11 53768324 53770105 - Bda008809.1 Bda11g01872 1872
11 53774640 53777056 - Bda008810.1 Bda11g01873 1873
11 53795238 53804963 - Bda033170 Bda11g01874 1874
14 10715336 10718582 + Bda027999.1 Bda14g01154 1154
3 26594969 26600298 + XM_039025554.1 Bhi03g01285 1285
3 26684067 26686348 + XM_039026809.1 Bhi03g01287 1287
10 50654272 50660401 - XM_039046045.1 Bhi10g02022 2022
4 10866597 10869279 - BLOR13831 Blo04g00919 919
4 10886248 10890911 - BLOR13832 Blo04g00920 920
5 29078656 29081239 + BLOR15754 Blo05g00792 792
5 29110396 29115197 + BLOR15755 Blo05g00793 793
5 29199863 29201701 + BLOR15756 Blo05g00794 794
6 5320172 5331635 + BLOR16716 Blo06g00133 133
16 1771705 1788055 + BLOR07287 Blo16g00039 39
16 1801737 1804168 + BLOR07288 Blo16g00040 40
3 10712519 10715183 - Bma017333.1 Bma03g00991 991
3 10721657 10726056 - Bma017334.1 Bma03g00992 992
6 1705318 1707099 - Bma022744.1 Bma06g00126 126
6 1710317 1712767 - Bma022745.1 Bma06g00127 127
6 1722979 1728153 - Bma022746.1 Bma06g00128 128
9 1824425 1827095 + Bma028759.1 Bma09g00074 74
9 1842794 1847543 + Bma028760.1 Bma09g00075 75
15 38806923 38812466 - Bma014284.2 Bma15g01000 1000
10 1990177 1995215 + Bpe002418.1 Bpe10g00116 116
10 2014623 2019997 + Bpe002420.1 Bpe10g00117 117
13 12011322 12013121 - Bpe006573.1 Bpe13g00449 449
13 12015771 12018255 - Bpe006574.1 Bpe13g00450 450
13 12033551 12038634 - Bpe006576.1 Bpe13g00452 452
15 15817334 15821034 - Bpe001367.1 Bpe15g00431 431
15 15825879 15826887 - Bpe001368.1 Bpe15g00432 432
15 15827515 15832552 - Bpe001369.1 Bpe15g00433 433
1 33150212 33154992 + CaPI482276_01g019880.1 Cam01g1988 1988
1 33163736 33168707 + CaPI482276_01g019900.1 Cam01g1990 1990
7 23074240 23086150 + CaPI482276_07g009390.1 Cam07g0939 939
7 23101027 23109607 - CaPI482276_07g009400.1 Cam07g0940 940
7 23220201 23221197 + CaPI482276_07g009410.1 Cam07g0941 941
7 23255829 23257655 + CaPI482276_07g009440.1 Cam07g0944 944
3 6063461 6065326 - Carg00650-RA Car03g00690 690
3 6069942 6074706 - Carg00652-RA Car03g00692 692
7 2192215 2194017 - Carg16042-RA Car07g00433 433
7 2196120 2201843 - Carg16041-RA Car07g00434 434
4 32204823 32209646 + CcPI632755_04g017050.1 Cco04g1705 1705
7 22627798 22640113 + CcPI632755_07g009820.1 Cco07g0982 982
7 22659311 22664394 - CcPI632755_07g009830.1 Cco07g0983 983
7 22744812 22756075 + CcPI632755_07g009870.1 Cco07g0987 987
7 22781696 22783357 + CcPI632755_07g009880.1 Cco07g0988 988
4 35691858 35696953 + CePI673135_04g016400.1 Cec04g1640 1640
7 24483903 24492041 + CePI673135_07g010040.1 Cec07g1004 1004
7 24510265 24515411 - CePI673135_07g010050.1 Cec07g1005 1005
7 24620885 24621727 + CePI673135_07g010080.1 Cec07g1008 1008
7 24661846 24663672 + CePI673135_07g010110.1 Cec07g1011 1011
2 3981224 3983053 - Chy2G029230.1 Chy02g00656 656
2 3991206 3995782 - Chy2G029240.1 Chy02g00657 657
7 17560875 17565525 + Chy7G141200.1 Chy07g01290 1290
7 17567849 17574625 + Chy7G141210.1 Chy07g01291 1291
7 17581445 17592858 - Chy7G141220.1 Chy07g01292 1292
7 17610862 17618049 + Chy7G141230.1 Chy07g01293 1293
7 17624576 17626189 + Chy7G141240.1 Chy07g01294 1294
1 31998048 32003684 + ClG42_01g0200700.10 Clacu01g2007 2007
1 32012370 32014172 + ClG42_01g0200900.10 Clacu01g2009 2009
7 22853477 22862110 + ClG42_07g0091200.10 Clacu07g0912 912
7 22881363 22886441 - ClG42_07g0091300.10 Clacu07g0913 913
7 23013908 23026286 + ClG42_07g0091700.10 Clacu07g0917 917
7 23049116 23050777 + ClG42_07g0091800.10 Clacu07g0918 918
1 33760959 33766378 + ClCG01G019460.1 Cla01g01899 1899
1 33774464 33776674 + ClCG01G019490.1 Cla01g01901 1901
7 24038856 24047067 + ClCG07G009100.2 Cla07g00865 865
7 24057474 24066350 + ClCG07G009110.1 Cla07g00866 866
7 24087472 24092803 - ClCG07G009120.1 Cla07g00867 867
7 24243030 24255408 + ClCG07G009150.2 Cla07g00870 870
7 24281159 24282985 + ClCG07G009170.2 Cla07g00872 872
3 5947647 5949506 - CmaCh03G007560.1 Cma03g00756 756
3 5954034 5958631 - CmaCh03G007570.1 Cma03g00757 757
7 2130556 2132331 - CmaCh07G004930.1 Cma07g00493 493
16 3406102 3421367 + CmaCh16G006550.1 Cma16g00655 655
16 3424282 3426054 + CmaCh16G006560.1 Cma16g00656 656
20 4104105 4121764 - CmaCh20G008550.1 Cma20g00855 855
8 5543513 5548587 + MELO3C007821.2.1 Cme08g00840 840
8 5556885 5558975 + MELO3C007823.2.1 Cme08g00842 842
8 21612447 21615414 + PI0027004.1 Cmetu08g0213 213
8 21600092 21605345 + PI0025382.1 Cmetu08g0416 416
3 6454476 6456320 - CmoCh03G007820.1 Cmo03g00782 782
3 6461285 6466004 - CmoCh03G007850.1 Cmo03g00785 785
4 4161753 4166266 + CmoCh04G008360.1 Cmo04g00836 836
4 4166756 4169460 + CmoCh04G008370.1 Cmo04g00837 837
4 4170265 4174315 - CmoCh04G008380.1 Cmo04g00838 838
4 4183510 4189570 + CmoCh04G008390.1 Cmo04g00839 839
4 4192956 4194776 + CmoCh04G008400.1 Cmo04g00840 840
7 2224850 2227516 - CmoCh07G004920.1 Cmo07g00492 492
7 2233623 2235551 - CmoCh07G004960.1 Cmo07g00496 496
16 3550543 3565256 + CmoCh16G007120.1 Cmo16g00712 712
16 3569005 3570780 + CmoCh16G007130.1 Cmo16g00713 713
1 32346410 32352044 + CmPI595203_01g018780.1 Cmu01g1878 1878
1 32360723 32362525 + CmPI595203_01g018800.1 Cmu01g1880 1880
7 23084671 23093074 + CmPI595203_07g009120.1 Cmu07g0912 912
7 23112257 23117324 - CmPI595203_07g009130.1 Cmu07g0913 913
7 23254265 23263322 + CmPI595203_07g009160.1 Cmu07g0916 916
7 23286135 23287796 + CmPI595203_07g009170.1 Cmu07g0917 917
6 12479507 12481297 + Conep06aG0167800.1 Cone6ag1615 1615
6 12482648 12487870 + Conep06aG0167900.1 Cone6ag1616 1616
6 12490663 12493007 + Conep06aG0168000.1 Cone6ag1617 1617
8 8070437 8075829 + Conep08aG0083000.1 Cone8ag0804 804
8 8080711 8086515 + Conep08aG0083100.1 Cone8ag0805 805
8 8116467 8118964 + Conep08aG0083200.1 Cone8ag0806 806
9 11199612 11204702 + Conep09aG0158700.1 Cone9ag1541 1541
9 11208012 11210429 + Conep09aG0158800.1 Cone9ag1542 1542
10 3525186 3529995 + Cp4.1LG10g00930.1 Cpe10g00604 604
10 3534018 3537003 + Cp4.1LG10g00870.1 Cpe10g00605 605
14 2689691 2692444 + Cp4.1LG14g02890.1 Cpe14g00428 428
14 3543854 3550982 + Cp4.1LG14g01690.1 Cpe14g00559 559
14 3552498 3558204 + Cp4.1LG14g01680.1 Cpe14g00560 560
14 3562009 3563784 + Cp4.1LG14g01490.1 Cpe14g00561 561
19 6055469 6061021 + Cp4.1LG19g09510.1 Cpe19g00806 806
19 6062922 6065307 + Cp4.1LG19g09550.1 Cpe19g00807 807
4 34193559 34198333 + CrPI670011_04g015590.1 Cre04g1559 1559
7 26863295 26871438 + CrPI670011_07g012830.1 Cre07g1283 1283
7 26888916 26897784 - CrPI670011_07g012840.1 Cre07g1284 1284
7 26983371 26994275 + CrPI670011_07g012870.1 Cre07g1287 1287
7 27006836 27008662 + CrPI670011_07g012880.1 Cre07g1288 1288
4 3319942 3328564 - CsaV3_4G005080.1 Csa04g00508 508
4 3345127 3350392 + CsaV3_4G005090.1 Csa04g00509 509
4 3357095 3364226 - CsaV3_4G005100.1 Csa04g00510 510
4 3365923 3370773 - CsaV3_4G005110.1 Csa04g00511 511
6 27310659 27316030 + CsaV3_6G046180.1 Csa06g03232 3232
6 27323359 27326845 + CsaV3_6G046190.1 Csa06g03233 3233
4 70615261 70619835 + Hsped.04g15020.1 Hepe04g1502 1502
4 70630850 70632691 + Hsped.04g15030.1 Hepe04g1503 1503
1 5478459 5480288 - Lsi01G006800.1 Lsi01g00680 680
1 5491119 5496668 - Lsi01G006820.1 Lsi01g00682 682
7 2173708 2175321 - Lsi07G002020.1 Lsi07g00202 202
7 2184353 2193491 - Lsi07G002030.1 Lsi07g00203 203
7 2230672 2236545 + Lsi07G002050.1 Lsi07g00205 205
10 7131592 7134379 + Sed0018218.1 Sed10g0914 914
14 20582833 20588919 + Sed0017755.1 Sed14g1110 1110
3 74789593 74795474 + Tan0010607.1 Tan03g1971 1971
3 74808985 74811350 + Tan0016777.1 Tan03g1972 1972
4 18102695 18105221 + Vvi4g952 Vvi4g952 952
4 18116505 18126495 + Vvi4g953 Vvi4g953 953
4 18131143 18134803 + Vvi4g954 Vvi4g954 954
4 18137892 18145402 + Vvi4g955 Vvi4g955 955
4 18146216 18154487 + Vvi4g956 Vvi4g956 956
4 18166916 18171198 + Vvi4g957 Vvi4g957 957
4 18184768 18192254 + Vvi4g958 Vvi4g958 958
4 18196919 18200082 + Vvi4g959 Vvi4g959 959
4 18201453 18202166 + Vvi4g960 Vvi4g960 960
4 18202173 18202332 - Vvi4g961 Vvi4g961 961
       

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