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
Vvi4g942 . . . . . Bpe13g00453 . . . Cmo16g00710 . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1611 Cone9ag1539 . . Chy07g01284 . . . Bda11g01875 . . . . Bma06g00129 . . . Cma16g00653 . . . . Cpe14g00557 . . . . . . . Cla07g00859 Cam07g0931 Cec07g0996 Cco07g0972 Clacu07g0905 Cmu07g0905 Cre07g1273 Lsi07g00214 Csa04g00517 . .
Vvi4g943 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g944 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g945 Blo04g00923 Blo16g00038 . . . . . . Cmo04g00834 . . . . . . . . . . . . . . . . . . . . . . Cone8ag0800 Cone12ag0753 . . . . Chy07g01287 . . . . . . . Bma03g00994 . . . . . . . . . . . . . . . . . Cla07g00862 Cam07g0934 Cec07g0999 Cco07g0977 Clacu07g0908 Cmu07g0908 Cre07g1276 Lsi07g00211 Csa04g00514 . .
Vvi4g946 . . . . . . . . . . . Cma07g00497 . Car07g00437 . Cpe19g00803 . Bhi03g01277 . . . Hepe04g1496 . . Cla01g01894 Cam01g1984 Cec04g1636 Cco04g1702 Clacu01g2004 Cmu01g1875 Cre04g1556 . . . . Lsi01g00690 . . Cme08g00834 Blo05g00789 . . . . . . . Sed14g1103 . . . . . . . . Bhi10g02034 Tan05g1329 Cmetu01g1244 . Hepe08g1031 . . . . . . . . . . Csa06g03226 Chy02g00662 .
Vvi4g947 . . . . . . . . . . . Cma07g00496 . Car07g00436 Sed14g1106 Cpe19g00804 . Bhi03g01281 Tan03g1967 Cmetu08g1547 . Hepe04g1498 . . Cla01g01895 Cam01g1985 Cec04g1637 Cco04g1703 Clacu01g2005 Cmu01g1876 Cre04g1557 . . . . Lsi01g00688 . . Cme08g00836 . . . . Bpe10g00114 . . . . . Cmo07g00498 . . . . . . . . . . . . . . . . . . . . . Csa06g03228 Chy02g00660 .
Vvi4g948 Blo04g00922 . . . . . Bma09g00072 . . . Cma03g00761 Cma07g00495 Car03g00695 Car07g00435 Sed14g1107 Cpe19g00805 Cpe10g00602 Bhi03g01282 Tan03g1968 Cmetu08g1737 . Hepe04g1499 . . Cla01g01896 . . . . . . Cone8ag0801 Cone12ag0751 Cone6ag1612 . Lsi01g00686 . . Cme08g00837 Blo05g00790 . . . . Bpe06g00049 . . . Cmo03g00789 Cmo07g00497 . . . . . . . . . . . . . . . . . . . . . Csa06g03229 Chy02g00659 .
Vvi4g949 Blo04g00921 . . . Bpe15g00434 . . . . . Cma03g00760 . Car03g00694 . Sed14g1109 . Cpe10g00603 Bhi03g01283 Tan03g1969 Cmetu08g1776 . Hepe04g1500 . . Cla01g01897 Cam01g1987 Cec04g1638 Cco04g1704 Clacu01g2006 Cmu01g1877 Cre04g1558 . . . . Lsi01g00685 . . Cme08g00838 . . . . . . . . . Cmo03g00787 . . . . . . . . . . . . . . . . . . . . . . Csa06g03230 Chy02g00658 .
Vvi4g950 . . Bda04g00056 Bda10g00127 . . Bma09g00073 Bma15g01001 . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0802 Cone12ag0748 . . . . . . Blo05g00791 Blo06g00131 . . . Bpe06g00048 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g951 . . . . . . . . Cmo04g00835 . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1614 Cone9ag1540 . . Chy07g01289 . . . . . . . . . . . . . . . . . . . . . . . . . Cla07g00863 Cam07g0936 Cec07g1002 Cco07g0979 Clacu07g0909 Cmu07g0909 Cre07g1279 Lsi07g00209 Csa04g00512 . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 895035 898084 - Bda018766.2 Bda04g00056 56
10 3549732 3552018 + Bda006587.1 Bda10g00127 127
11 53808083 53808934 - Bda008812.1 Bda11g01875 1875
3 26425914 26428232 + XM_039027982.1 Bhi03g01277 1277
3 26443236 26445056 + XM_039027983.1 Bhi03g01281 1281
3 26489592 26492995 + XM_039027985.1 Bhi03g01282 1282
3 26498232 26501830 + XM_039026234.1 Bhi03g01283 1283
10 50839367 50841493 - XM_039046125.1 Bhi10g02034 2034
4 10914660 10916979 - BLOR13833 Blo04g00921 921
4 10918697 10926755 - BLOR13834 Blo04g00922 922
4 10927365 10928387 + BLOR13835 Blo04g00923 923
5 29050689 29052323 + BLOR15751 Blo05g00789 789
5 29063283 29065949 + BLOR15752 Blo05g00790 790
5 29067385 29069715 + BLOR15753 Blo05g00791 791
6 5264761 5267075 - BLOR16714 Blo06g00131 131
16 1770577 1771572 - BLOR07286 Blo16g00038 38
3 10795646 10796191 + Bma017338.1 Bma03g00994 994
6 1731076 1731768 - Bma022747.1 Bma06g00129 129
9 1804818 1805398 + Bma028757.1 Bma09g00072 72
9 1820267 1822597 + Bma028758.1 Bma09g00073 73
15 38941687 38943924 + Bma014285.3 Bma15g01001 1001
6 578508 580809 - Bpe019493.1 Bpe06g00048 48
6 584106 584688 - Bpe019494.1 Bpe06g00049 49
10 1974529 1976285 - Bpe002416.1 Bpe10g00114 114
13 12046527 12047732 - Bpe006577.2 Bpe13g00453 453
15 15833262 15835664 - Bpe001370.1 Bpe15g00434 434
1 33127806 33129323 + CaPI482276_01g019840.1 Cam01g1984 1984
1 33131691 33133716 + CaPI482276_01g019850.1 Cam01g1985 1985
1 33138848 33147539 + CaPI482276_01g019870.1 Cam01g1987 1987
7 23004507 23005739 + CaPI482276_07g009310.1 Cam07g0931 931
7 23023512 23024444 - CaPI482276_07g009340.1 Cam07g0934 934
7 23045540 23046703 + CaPI482276_07g009360.1 Cam07g0936 936
3 6075787 6079270 - Carg00654-RA Car03g00694 694
3 6079845 6083289 - Carg00655-RA Car03g00695 695
7 2203173 2206467 - Carg16040-RA Car07g00435 435
7 2207602 2209145 - Carg16039-RA Car07g00436 436
7 2210370 2212395 - Carg16038-RA Car07g00437 437
4 32177104 32178621 + CcPI632755_04g017020.1 Cco04g1702 1702
4 32180866 32182898 + CcPI632755_04g017030.1 Cco04g1703 1703
4 32193599 32202339 + CcPI632755_04g017040.1 Cco04g1704 1704
7 22550849 22552069 + CcPI632755_07g009720.1 Cco07g0972 972
7 22575197 22576123 - CcPI632755_07g009770.1 Cco07g0977 977
7 22597591 22598754 + CcPI632755_07g009790.1 Cco07g0979 979
4 35669975 35671492 + CePI673135_04g016360.1 Cec04g1636 1636
4 35673825 35675860 + CePI673135_04g016370.1 Cec04g1637 1637
4 35680952 35688636 + CePI673135_04g016380.1 Cec04g1638 1638
7 24369257 24370489 + CePI673135_07g009960.1 Cec07g0996 996
7 24386436 24387362 - CePI673135_07g009990.1 Cec07g0999 999
7 24435329 24436492 + CePI673135_07g010020.1 Cec07g1002 1002
2 3997386 4001313 - Chy2G029250.1 Chy02g00658 658
2 4002654 4005475 - Chy2G029260.1 Chy02g00659 659
2 4007333 4008759 - Chy2G029270.1 Chy02g00660 660
2 4014399 4015982 - Chy2G029290.1 Chy02g00662 662
7 17541505 17542743 + Chy7G141140.1 Chy07g01284 1284
7 17548813 17549721 - Chy7G141170.1 Chy07g01287 1287
7 17557630 17558823 + Chy7G141190.1 Chy07g01289 1289
1 31973944 31975461 + ClG42_01g0200400.10 Clacu01g2004 2004
1 31977805 31979849 + ClG42_01g0200500.10 Clacu01g2005 2005
1 31987470 31996195 + ClG42_01g0200600.10 Clacu01g2006 2006
7 22771661 22772893 + ClG42_07g0090500.10 Clacu07g0905 905
7 22790898 22791830 - ClG42_07g0090800.10 Clacu07g0908 908
7 22813955 22815118 + ClG42_07g0090900.10 Clacu07g0909 909
1 33729536 33735849 + ClCG01G019410.2 Cla01g01894 1894
1 33737572 33739967 + ClCG01G019430.2 Cla01g01895 1895
1 33747407 33748074 + ClCG01G019440.2 Cla01g01896 1896
1 33752255 33756292 + ClCG01G019450.1 Cla01g01897 1897
7 23972578 23973810 + ClCG07G009040.1 Cla07g00859 859
7 23991832 23992764 - ClCG07G009070.1 Cla07g00862 862
7 24017038 24018973 + ClCG07G009080.1 Cla07g00863 863
3 5960446 5963533 - CmaCh03G007600.1 Cma03g00760 760
3 5963667 5971230 - CmaCh03G007610.1 Cma03g00761 761
7 2135581 2144707 - CmaCh07G004950.1 Cma07g00495 495
7 2145502 2147119 - CmaCh07G004960.1 Cma07g00496 496
7 2148287 2149891 - CmaCh07G004970.1 Cma07g00497 497
16 3402575 3403828 + CmaCh16G006530.1 Cma16g00653 653
8 5521349 5524370 + MELO3C007815.2.1 Cme08g00834 834
8 5530025 5531550 + MELO3C007817.2.1 Cme08g00836 836
8 5533924 5537187 + MELO3C007818.2.1 Cme08g00837 837
8 5538259 5541549 + MELO3C007819.2.1 Cme08g00838 838
1 6725298 6729991 - PI0005159.1 Cmetu01g1244 1244
8 21584084 21588034 + PI0010334.1 Cmetu08g1547 1547
8 21590256 21593642 + PI0011934.1 Cmetu08g1737 1737
8 21594867 21597659 + PI0004059.1 Cmetu08g1776 1776
3 6467706 6470700 - CmoCh03G007870.1 Cmo03g00787 787
3 6473779 6474582 - CmoCh03G007890.1 Cmo03g00789 789
4 4155392 4156342 - CmoCh04G008340.1 Cmo04g00834 834
4 4159025 4160215 + CmoCh04G008350.1 Cmo04g00835 835
7 2247755 2248563 - CmoCh07G004970.1 Cmo07g00497 497
7 2249468 2250975 - CmoCh07G004980.1 Cmo07g00498 498
16 3546620 3547855 + CmoCh16G007100.1 Cmo16g00710 710
1 32322324 32323841 + CmPI595203_01g018750.1 Cmu01g1875 1875
1 32326188 32328225 + CmPI595203_01g018760.1 Cmu01g1876 1876
1 32335851 32344585 + CmPI595203_01g018770.1 Cmu01g1877 1877
7 23002640 23003872 + CmPI595203_07g009050.1 Cmu07g0905 905
7 23021878 23022810 - CmPI595203_07g009080.1 Cmu07g0908 908
7 23044944 23046107 + CmPI595203_07g009090.1 Cmu07g0909 909
6 12465158 12466506 + Conep06aG0167400.1 Cone6ag1611 1611
6 12467408 12468035 + Conep06aG0167500.1 Cone6ag1612 1612
6 12471930 12474216 + Conep06aG0167700.1 Cone6ag1614 1614
8 8035463 8036335 + Conep08aG0082600.1 Cone8ag0800 800
8 8052629 8055779 - Conep08aG0082700.1 Cone8ag0801 801
8 8063015 8066900 + Conep08aG0082800.1 Cone8ag0802 802
9 11190461 11192920 + Conep09aG0158500.1 Cone9ag1539 1539
9 11193555 11195577 + Conep09aG0158600.1 Cone9ag1540 1540
12 6935022 6938442 - Conep12aG0077100.1 Cone12ag0748 748
12 6949804 6953045 + Conep12aG0077400.1 Cone12ag0751 751
12 6960497 6961603 - Conep12aG0077600.1 Cone12ag0753 753
10 3516679 3520122 + Cp4.1LG10g00820.1 Cpe10g00602 602
10 3520549 3524924 + Cp4.1LG10g00900.1 Cpe10g00603 603
14 3539003 3540259 + Cp4.1LG14g01660.1 Cpe14g00557 557
19 6045847 6047452 + Cp4.1LG19g09430.1 Cpe19g00803 803
19 6048607 6050602 + Cp4.1LG19g09450.1 Cpe19g00804 804
19 6051052 6054586 + Cp4.1LG19g09460.1 Cpe19g00805 805
4 34170995 34172512 + CrPI670011_04g015560.1 Cre04g1556 1556
4 34174988 34177008 + CrPI670011_04g015570.1 Cre04g1557 1557
4 34182170 34190840 + CrPI670011_04g015580.1 Cre04g1558 1558
7 26779310 26780554 + CrPI670011_07g012730.1 Cre07g1273 1273
7 26799596 26800525 - CrPI670011_07g012760.1 Cre07g1276 1276
7 26823665 26831205 + CrPI670011_07g012790.1 Cre07g1279 1279
4 3372076 3374115 - CsaV3_4G005120.1 Csa04g00512 512
4 3382292 3383742 + CsaV3_4G005140.1 Csa04g00514 514
4 3390581 3391825 - CsaV3_4G005170.1 Csa04g00517 517
6 27291188 27292771 + CsaV3_6G046120.1 Csa06g03226 3226
6 27297793 27299816 + CsaV3_6G046140.1 Csa06g03228 3228
6 27301228 27304055 + CsaV3_6G046150.1 Csa06g03229 3229
6 27305465 27308224 + CsaV3_6G046160.1 Csa06g03230 3230
4 70586089 70588373 + Hsped.04g14960.1 Hepe04g1496 1496
4 70600963 70602472 + Hsped.04g14980.1 Hepe04g1498 1498
4 70604331 70607184 + Hsped.04g14990.1 Hepe04g1499 1499
4 70608710 70612321 + Hsped.04g15000.1 Hepe04g1500 1500
8 9923791 9925448 - Hsped.08g10310.1 Hepe08g1031 1031
1 5500389 5503245 - Lsi01G006850.1 Lsi01g00685 685
1 5504590 5507937 - Lsi01G006870.1 Lsi01g00686 686
1 5510155 5512706 - Lsi01G006880.1 Lsi01g00688 688
1 5520153 5521786 - Lsi01G006900.1 Lsi01g00690 690
7 2266994 2268163 - Lsi07G002090.1 Lsi07g00209 209
7 2275929 2276852 + Lsi07G002110.1 Lsi07g00211 211
7 2283959 2285191 - Lsi07G002140.1 Lsi07g00214 214
14 20515451 20517653 + Sed0022643.1 Sed14g1103 1103
14 20544833 20547660 + Sed0011190.1 Sed14g1106 1106
14 20558945 20564228 + Sed0016352.1 Sed14g1107 1107
14 20575890 20581985 + Sed0022670.1 Sed14g1109 1109
3 74772023 74775001 + Tan0009076.1 Tan03g1967 1967
3 74777627 74781386 + Tan0021033.1 Tan03g1968 1968
3 74783188 74786526 + Tan0004600.1 Tan03g1969 1969
5 17007201 17009547 - Tan0019842.1 Tan05g1329 1329
4 18009480 18011045 + Vvi4g942 Vvi4g942 942
4 18012559 18022101 + Vvi4g943 Vvi4g943 943
4 18026698 18028680 + Vvi4g944 Vvi4g944 944
4 18030229 18035626 - Vvi4g945 Vvi4g945 945
4 18045318 18047078 + Vvi4g946 Vvi4g946 946
4 18049832 18052659 + Vvi4g947 Vvi4g947 947
4 18053844 18064423 + Vvi4g948 Vvi4g948 948
4 18064982 18073658 + Vvi4g949 Vvi4g949 949
4 18074948 18081203 + Vvi4g950 Vvi4g950 950
4 18095520 18100098 + Vvi4g951 Vvi4g951 951
       

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