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
Vvi4g982 . . Bda04g00046 . . . Bma09g00077 . . . Cma03g00742 Cma07g00483 Car03g00678 Car07g00425 Sed14g1124 Cpe19g00813 Cpe10g00618 Bhi03g01304 Tan03g1985 Cmetu08g0193 . Hepe04g1520 . . Cla01g01914 Cam01g2001 Cec04g1657 Cco04g1719 Clacu01g2021 Cmu01g1897 Cre04g1573 . . Cone6ag1626 Cone9ag1551 Lsi01g00670 . . Cme08g00853 Blo05g00798 . . . . Bpe06g00044 . . . Cmo03g00770 Cmo07g00481 . . . . . . . . . . . . . . . . . . . . . Csa06g03245 Chy02g00643 .
Vvi4g983 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1627 Cone9ag1552 . . . . . . . . . . . . . . . . Cma20g00850 . . . . . . . . . . . . . . . . . . . . . .
Vvi4g984 Blo04g00915 Blo16g00047 . . . Bpe13g00442 . . . Cmo16g00674 . . . . . . . . . . . . . . . . . . . . . Cone8ag0814 Cone12ag0712 Cone6ag1628 Cone9ag1553 . . Chy07g01240 . . . Bda11g01864 . . . . Bma06g00119 . . . Cma16g00618 . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g985 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed05g3618 . . . Cma20g00847 . . . . Bhi10g02008 Tan05g1303 . . Hepe08g1014 . . . . . . . . . . . . .
Vvi4g986 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0815 Cone12ag0766 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g987 . Blo16g00048 . . . . . . . . . Cma07g00481 . Car07g00424 . Cpe19g00814 . Bhi03g01306 . . . Hepe04g1521 . . Cla01g01915 Cam01g2002 Cec04g1658 Cco04g1720 Clacu01g2022 Cmu01g1898 Cre04g1574 . . Cone6ag1629 Cone9ag1554 Lsi01g00669 . Chy07g01239 Cme08g00854 . . Bda11g01863 . . . . . . . Cmo07g00480 . . . . . . . . . . . . . . . . . . . . Lsi07g00258 Csa06g03246 Chy02g00642 .
Vvi4g988 Blo04g00914 Blo16g00049 . . Bpe15g00426 Bpe13g00441 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1630 Cone9ag1555 . . . . . . Bda11g01862 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g989 . Blo16g00050 . . . Bpe13g00440 . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0817 . . . . . Chy07g01232 . . . Bda11g01861 . . . . Bma06g00118 . . . . . . . . Cpe14g00477 . . . . . . . . . . . . . . . Csa04g00577 . .
Vvi4g990 Blo04g00912 Blo16g00051 . . Bpe15g00424 . . . . . Cma03g00740 . Car03g00676 . Sed14g1127 . Cpe10g00620 Bhi03g01315 Tan03g1990 Cmetu08g1065 . Hepe04g1076 . . . . . . . . . . . . . . . . . . . Bda11g01860 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa06g03248 Chy02g00640 .
Vvi4g991 . . Bda04g00043 . . . Bma09g00081 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1633 . . . . . Blo05g00800 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 745507 747851 + Bda018780.1 Bda04g00043 43
4 758935 762964 + Bda018777.1 Bda04g00046 46
11 53717274 53718158 + Bda008798.1 Bda11g01860 1860
11 53718380 53720909 - Bda008799.1 Bda11g01861 1861
11 53722812 53725189 - Bda008800.1 Bda11g01862 1862
11 53727722 53729352 + Bda008801.1 Bda11g01863 1863
11 53729966 53732880 - Bda008802.1 Bda11g01864 1864
3 27028177 27032116 - XM_039027937.1 Bhi03g01304 1304
3 27034614 27037925 - XM_039025634.1 Bhi03g01306 1306
3 27049194 27050658 - XM_039027477.1 Bhi03g01315 1315
10 50176855 50181531 - XM_039046032.1 Bhi10g02008 2008
4 10701857 10702717 + BLOR13824 Blo04g00912 912
4 10706325 10708452 - BLOR13826 Blo04g00914 914
4 10711448 10715422 - BLOR13827 Blo04g00915 915
5 29297380 29301290 - BLOR15760 Blo05g00798 798
5 29312310 29314713 - BLOR15762 Blo05g00800 800
16 1887921 1891090 + BLOR07295 Blo16g00047 47
16 1891899 1893452 - BLOR07296 Blo16g00048 48
16 1896281 1898692 + BLOR07297 Blo16g00049 49
16 1899421 1902807 + BLOR07298 Blo16g00050 50
16 1903083 1903967 - BLOR07299 Blo16g00051 51
6 1615449 1622132 - Bma031267 Bma06g00118 118
6 1626872 1629973 - Bma022737.3 Bma06g00119 119
9 1922614 1926521 - Bma028762.1 Bma09g00077 77
9 1998722 2001056 - Bma028768.1 Bma09g00081 81
6 511668 515695 + Bpe019489.1 Bpe06g00044 44
13 11948590 11952277 - Bpe024943 Bpe13g00440 440
13 11953027 11955408 - Bpe006564.6 Bpe13g00441 441
13 11960303 11962087 - Bpe006565.1 Bpe13g00442 442
15 15775983 15776855 + Bpe001360.1 Bpe15g00424 424
15 15780045 15781980 - Bpe001362.1 Bpe15g00426 426
1 33250872 33255607 - CaPI482276_01g020010.1 Cam01g2001 2001
1 33257866 33259862 - CaPI482276_01g020020.1 Cam01g2002 2002
3 6006696 6007783 + Carg00636-RA Car03g00676 676
3 6011605 6015815 + Carg00638-RA Car03g00678 678
7 2158858 2160932 + Carg16051-RA Car07g00424 424
7 2164491 2167680 + Carg16050-RA Car07g00425 425
4 32303154 32309592 - CcPI632755_04g017190.1 Cco04g1719 1719
4 32309656 32313860 - CcPI632755_04g017200.1 Cco04g1720 1720
4 35798022 35801709 - CePI673135_04g016570.1 Cec04g1657 1657
4 35803965 35805961 - CePI673135_04g016580.1 Cec04g1658 1658
2 3907457 3908374 + Chy2G029070.1 Chy02g00640 640
2 3917442 3919458 + Chy2G029090.1 Chy02g00642 642
2 3921095 3924692 + Chy2G029100.1 Chy02g00643 643
7 17116820 17121700 + Chy7G140620.1 Chy07g01232 1232
7 17147729 17150364 + Chy7G140690.1 Chy07g01239 1239
7 17152391 17160038 - Chy7G140700.1 Chy07g01240 1240
1 32100070 32103760 - ClG42_01g0202100.10 Clacu01g2021 2021
1 32105999 32107995 - ClG42_01g0202200.10 Clacu01g2022 2022
1 33863982 33868593 - ClCG01G019640.2 Cla01g01914 1914
1 33870182 33872178 - ClCG01G019650.2 Cla01g01915 1915
3 5887631 5888548 + CmaCh03G007400.1 Cma03g00740 740
3 5891880 5896603 + CmaCh03G007420.1 Cma03g00742 742
7 2099589 2102617 + CmaCh07G004810.1 Cma07g00481 481
7 2106419 2106784 + CmaCh07G004830.1 Cma07g00483 483
16 3193789 3198254 - CmaCh16G006180.1 Cma16g00618 618
20 4056892 4059201 - CmaCh20G008470.1 Cma20g00847 847
20 4067706 4069472 - CmaCh20G008500.1 Cma20g00850 850
8 5621355 5625471 - MELO3C007833.2.1 Cme08g00853 853
8 5627200 5630655 - MELO3C007834.2.1 Cme08g00854 854
8 21680704 21684717 - PI0024809.1 Cmetu08g0193 193
8 21696904 21697821 - PI0027690.1 Cmetu08g1065 1065
3 6398705 6402941 + CmoCh03G007700.1 Cmo03g00770 770
7 2191845 2194884 + CmoCh07G004800.1 Cmo07g00480 480
7 2195919 2199345 + CmoCh07G004810.1 Cmo07g00481 481
16 3336796 3341210 - CmoCh16G006740.1 Cmo16g00674 674
1 32448568 32452258 - CmPI595203_01g018970.1 Cmu01g1897 1897
1 32454499 32456495 - CmPI595203_01g018980.1 Cmu01g1898 1898
6 12530362 12533529 - Conep06aG0169000.1 Cone6ag1626 1626
6 12534155 12534784 - Conep06aG0169100.1 Cone6ag1627 1627
6 12536070 12539532 + Conep06aG0169200.1 Cone6ag1628 1628
6 12539797 12541830 - Conep06aG0169300.1 Cone6ag1629 1629
6 12545457 12549747 + Conep06aG0169400.1 Cone6ag1630 1630
6 12551616 12552840 - Conep06aG0169700.1 Cone6ag1633 1633
8 8171749 8177937 + Conep08aG0084000.1 Cone8ag0814 814
8 8178328 8180839 + Conep08aG0084100.1 Cone8ag0815 815
8 8182810 8185847 + Conep08aG0084300.1 Cone8ag0817 817
9 11261109 11264225 - Conep09aG0159900.1 Cone9ag1551 1551
9 11264527 11264757 - Conep09aG0160000.1 Cone9ag1552 1552
9 11266669 11269827 + Conep09aG0160100.1 Cone9ag1553 1553
9 11270251 11272983 - Conep09aG0160200.1 Cone9ag1554 1554
9 11275737 11280824 + Conep09aG0160300.1 Cone9ag1555 1555
12 6553517 6558516 - Conep12aG0073500.1 Cone12ag0712 712
12 7045263 7046544 + Conep12aG0078900.1 Cone12ag0766 766
10 3586627 3590913 - Cp4.1LG10g00540.1 Cpe10g00618 618
10 3594324 3595699 - Cp4.1LG10g00590.1 Cpe10g00620 620
14 2998798 3003942 - Cp4.1LG14g02350.1 Cpe14g00477 477
19 6089570 6093428 - Cp4.1LG19g09220.1 Cpe19g00813 813
19 6094376 6097185 - Cp4.1LG19g09210.1 Cpe19g00814 814
4 34294915 34298609 - CrPI670011_04g015730.1 Cre04g1573 1573
4 34300866 34302863 - CrPI670011_04g015740.1 Cre04g1574 1574
4 3784057 3789478 - CsaV3_4G005770.1 Csa04g00577 577
6 27382662 27386858 - CsaV3_6G046310.1 Csa06g03245 3245
6 27387767 27391500 - CsaV3_6G046320.1 Csa06g03246 3246
6 27399246 27400604 - CsaV3_6G046340.1 Csa06g03248 3248
4 65401673 65404754 + Hsped.04g10760.1 Hepe04g1076 1076
4 70735247 70739990 - Hsped.04g15200.1 Hepe04g1520 1520
4 70741379 70744604 - Hsped.04g15210.1 Hepe04g1521 1521
8 9657898 9661882 - Hsped.08g10140.1 Hepe08g1014 1014
1 5398418 5400979 + Lsi01G006690.1 Lsi01g00669 669
1 5402990 5407171 + Lsi01G006700.1 Lsi01g00670 670
7 2829163 2832345 - Lsi07G002580.1 Lsi07g00258 258
5 44510229 44512531 + Sed0007212.1 Sed05g3618 3618
14 20711489 20715474 - Sed0003603.1 Sed14g1124 1124
14 20742460 20747704 - Sed0025954.1 Sed14g1127 1127
3 74911793 74916117 - Tan0005907.1 Tan03g1985 1985
3 74930080 74934548 - Tan0011635.1 Tan03g1990 1990
5 15486171 15489336 - Tan0019417.2 Tan05g1303 1303
4 18459753 18488584 - Vvi4g982 Vvi4g982 982
4 18489565 18491019 - Vvi4g983 Vvi4g983 983
4 18499215 18507148 + Vvi4g984 Vvi4g984 984
4 18512509 18514390 + Vvi4g985 Vvi4g985 985
4 18515916 18518002 + Vvi4g986 Vvi4g986 986
4 18518532 18521845 - Vvi4g987 Vvi4g987 987
4 18526670 18529110 + Vvi4g988 Vvi4g988 988
4 18530893 18534713 + Vvi4g989 Vvi4g989 989
4 18535064 18535964 - Vvi4g990 Vvi4g990 990
4 18537010 18542602 - Vvi4g991 Vvi4g991 991
       

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