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
Vvi4g1102 . . Bda04g00267 . . Bpe13g00420 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0721 . . . . . . . . Bda11g01840 . . . . Bma06g00100 . . . . . . . . . . . . . . . . . . . . . . . Lsi07g01108 . . .
Vvi4g1103 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1104 . . . Bda10g00180 . . . Bma15g00948 . . . Cma07g00432 . Car07g00381 Sed14g1183 Cpe19g00853 . Bhi03g00876 Tan03g2064 Cmetu04g2634 . Hepe04g1584 . . Cla01g01972 Cam01g2064 Cec04g1723 Cco04g1789 Clacu01g2085 Cmu01g1962 Cre04g1636 Cone8ag0845 . . . Lsi01g00609 . . Cme08g00918 . . . . . . . . . . Cmo07g00431 . . . . . . . . . . . . . . . . . . . . . Csa06g03316 Chy02g00582 .
Vvi4g1105 . . . Bda10g00181 . . . . . . Cma03g00691 . Car03g00636 Car07g00380 Sed14g1184 Cpe19g00854 Cpe10g00658 Bhi03g00874 Tan03g2066 Cmetu06g2758 . Hepe04g1586 . . . . . . . . . . . . Cone9ag1602 Lsi01g00607 . . Cme08g00920 . . . . Bpe10g00151 . . . . Cmo03g00717 Cmo07g00430 . . . . . . . . . . . . . . . . . . . . . Csa06g03318 Chy02g00580 .
Vvi4g1106 . . Bda04g00024 . . . . . . . Cma03g00690 Cma07g00431 Car03g00635 Car07g00379 . . Cpe10g00659 Bhi03g00873 . . . . . . Cla01g01974 Cam01g2067 Cec04g1726 Cco04g1792 Clacu01g2088 Cmu01g1965 Cre04g1639 Cone8ag0846 Cone12ag0720 . . Lsi01g00606 . . Cme08g00921 . . . . . . . . . Cmo03g00716 Cmo07g00429 . . . . . . . . . . . . . . . . . . . . . Csa06g03319 Chy02g00579 .
Vvi4g1107 . . Bda04g00022 . . . . . . . Cma03g00688 Cma07g00430 Car03g00634 Car07g00378 Sed14g1189 Cpe19g00857 Cpe10g00661 Bhi03g00871 Tan03g2068 Cmetu04g0034 . Hepe04g1588 . . Cla01g01977 Cam01g2071 Cec04g1730 Cco04g1795 Clacu01g2092 Cmu01g1968 Cre04g1643 . . . . Lsi01g00605 . . Cme08g00924 Blo05g00828 . . . . Bpe06g00022 . . . Cmo03g00714 Cmo07g00428 . . . . . . . . . . . . . . . . . . . . . Csa06g03322 Chy02g00578 .
Vvi4g1108 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1109 . . . . . . . . . . Cma03g00687 Cma07g00429 Car03g00633 Car07g00376 Sed14g1192 Cpe19g00858 Cpe10g00662 Bhi03g00868 Tan03g2072 Cmetu01g0947 . Hepe04g1590 . . Cla01g01978 Cam01g2072 Cec04g1731 Cco04g1796 Clacu01g2093 Cmu01g1969 Cre04g1644 . . . . Lsi01g00603 . . Cme08g00925 . Blo06g00302 . . Bpe10g00154 . . . . Cmo03g00712 Cmo07g00426 . . . . . . . . . . . . . . . . . . . . . Csa06g03323 Chy02g00575 .
Vvi4g1110 . Blo16g00077 . . . Bpe13g00418 . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0849 Cone12ag0717 . . . . . . . . Bda11g01839 . . . . Bma06g00098 . . . Cma16g01236 . . . . . . . . . . . . . . . . . . . Lsi07g01106 . . .
Vvi4g1111 Blo04g00886 . . . . Bpe13g00416 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01837 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 365357 367080 + Bda018804.1 Bda04g00022 22
4 387129 388406 - Bda018802.1 Bda04g00024 24
4 32616742 32617924 - Bda019003.1 Bda04g00267 267
10 5837301 5840477 + Bda006671.1 Bda10g00180 180
10 5842876 5845629 + Bda006672.1 Bda10g00181 181
11 53591140 53592667 - Bda008774.1 Bda11g01837 1837
11 53603461 53604749 + Bda008776.1 Bda11g01839 1839
11 53606306 53608301 + Bda008777.2 Bda11g01840 1840
3 15942180 16005549 - XM_039026145.1 Bhi03g00868 868
3 16201376 16205162 + XM_039024960.1 Bhi03g00871 871
3 16214180 16216135 - XM_039027746.1 Bhi03g00873 873
3 16226418 16231281 - XM_039026225.1 Bhi03g00874 874
3 16292756 16296448 - XM_039027421.1 Bhi03g00876 876
4 10144510 10145133 - BLOR13798 Blo04g00886 886
5 30059529 30062063 - BLOR15790 Blo05g00828 828
6 17179079 17207710 + BLOR16885 Blo06g00302 302
16 2140555 2141845 - BLOR07325 Blo16g00077 77
6 1451632 1452907 + Bma022716.1 Bma06g00098 98
6 1454647 1456651 + Bma022718.2 Bma06g00100 100
15 35434740 35437886 - Bma014204.1 Bma15g00948 948
6 229661 231954 + Bpe019466.1 Bpe06g00022 22
10 3560133 3562975 + Bpe002460.1 Bpe10g00151 151
10 3650369 3676294 + Bpe002463.1 Bpe10g00154 154
13 11830161 11831665 - Bpe006541.1 Bpe13g00416 416
13 11840978 11842259 + Bpe006543.1 Bpe13g00418 418
13 11843790 11845792 + Bpe006545.2 Bpe13g00420 420
1 33701856 33704776 + CaPI482276_01g020640.1 Cam01g2064 2064
1 33723144 33725303 + CaPI482276_01g020670.1 Cam01g2067 2067
1 33742875 33746260 - CaPI482276_01g020710.1 Cam01g2071 2071
1 33750663 33786508 + CaPI482276_01g020720.1 Cam01g2072 2072
3 5748734 5777518 - Carg00593-RA Car03g00633 633
3 5778522 5779951 + Carg00594-RA Car03g00634 634
3 5784600 5785688 - Carg00595-RA Car03g00635 635
3 5788193 5792526 - Carg00596-RA Car03g00636 636
7 1878362 1904551 - Carg07956-RA Car07g00376 376
7 1907366 1912400 + Carg07958-RA Car07g00378 378
7 1914338 1915955 - Carg07959-RA Car07g00379 379
7 1921960 1925847 - Carg07960-RA Car07g00380 380
7 1926873 1930486 - Carg07961-RA Car07g00381 381
4 32768839 32771758 + CcPI632755_04g017890.1 Cco04g1789 1789
4 32790123 32792245 + CcPI632755_04g017920.1 Cco04g1792 1792
4 32815980 32819386 - CcPI632755_04g017950.1 Cco04g1795 1795
4 32821534 32859658 + CcPI632755_04g017960.1 Cco04g1796 1796
4 36258763 36261649 + CePI673135_04g017230.1 Cec04g1723 1723
4 36280308 36282446 + CePI673135_04g017260.1 Cec04g1726 1726
4 36299987 36303401 - CePI673135_04g017300.1 Cec04g1730 1730
4 36313252 36351354 + CePI673135_04g017310.1 Cec04g1731 1731
2 3463244 3493314 - Chy2G028420.1 Chy02g00575 575
2 3505521 3508642 + Chy2G028450.1 Chy02g00578 578
2 3513690 3515294 - Chy2G028460.1 Chy02g00579 579
2 3523901 3527186 - Chy2G028470.1 Chy02g00580 580
2 3529823 3532811 - Chy2G028490.1 Chy02g00582 582
1 32557988 32561441 + ClG42_01g0208500.10 Clacu01g2085 2085
1 32579382 32581529 + ClG42_01g0208800.10 Clacu01g2088 2088
1 32599101 32602468 - ClG42_01g0209200.10 Clacu01g2092 2092
1 32604588 32642575 + ClG42_01g0209300.10 Clacu01g2093 2093
1 34342224 34352422 + ClCG01G020230.2 Cla01g01972 1972
1 34366813 34371284 + ClCG01G020260.1 Cla01g01974 1974
1 34388885 34392253 - ClCG01G020290.1 Cla01g01977 1977
1 34394473 34435278 + ClCG01G020300.1 Cla01g01978 1978
3 5658268 5687482 - CmaCh03G006870.1 Cma03g00687 687
3 5687985 5689904 + CmaCh03G006880.1 Cma03g00688 688
3 5694438 5695536 - CmaCh03G006900.1 Cma03g00690 690
3 5697859 5702336 - CmaCh03G006910.1 Cma03g00691 691
7 1845481 1871237 - CmaCh07G004290.1 Cma07g00429 429
7 1872332 1879279 + CmaCh07G004300.1 Cma07g00430 430
7 1880489 1882029 - CmaCh07G004310.1 Cma07g00431 431
7 1886274 1895382 - CmaCh07G004320.1 Cma07g00432 432
16 9359839 9361170 - CmaCh16G012360.1 Cma16g01236 1236
8 6044095 6047400 + MELO3C007895.2.1 Cme08g00918 918
8 6050382 6054707 + MELO3C007897.2.1 Cme08g00920 920
8 6062201 6063881 + MELO3C007898.2.1 Cme08g00921 921
8 6080902 6083722 - MELO3C007901.2.1 Cme08g00924 924
8 6085489 6110808 + MELO3C007903.2.1 Cme08g00925 925
1 20019366 20020316 - PI0023563.1 Cmetu01g0947 947
4 3772130 3776145 + PI0020794.1 Cmetu04g0034 34
4 3797432 3800973 - PI0002433.1 Cmetu04g2634 2634
6 9494187 9495762 + PI0027595.1 Cmetu06g2758 2758
3 6153441 6183158 - CmoCh03G007120.1 Cmo03g00712 712
3 6184755 6186434 + CmoCh03G007140.1 Cmo03g00714 714
3 6191165 6192245 - CmoCh03G007160.1 Cmo03g00716 716
3 6195228 6199498 - CmoCh03G007170.1 Cmo03g00717 717
7 1934428 1960156 - CmoCh07G004260.1 Cmo07g00426 426
7 1963145 1968817 + CmoCh07G004280.1 Cmo07g00428 428
7 1970283 1971727 - CmoCh07G004290.1 Cmo07g00429 429
7 1976540 1981046 - CmoCh07G004300.1 Cmo07g00430 430
7 1982044 1985769 - CmoCh07G004310.1 Cmo07g00431 431
1 32893992 32896914 + CmPI595203_01g019620.1 Cmu01g1962 1962
1 32916834 32918981 + CmPI595203_01g019650.1 Cmu01g1965 1965
1 32936502 32939872 - CmPI595203_01g019680.1 Cmu01g1968 1968
1 32941993 32979979 + CmPI595203_01g019690.1 Cmu01g1969 1969
8 8437744 8440943 + Conep08aG0087100.1 Cone8ag0845 845
8 8444700 8445540 + Conep08aG0087200.1 Cone8ag0846 846
8 8455867 8457583 - Conep08aG0087500.1 Cone8ag0849 849
9 11477375 11480370 - Conep09aG0165200.1 Cone9ag1602 1602
12 6617201 6618987 + Conep12aG0074000.1 Cone12ag0717 717
12 6636787 6638321 - Conep12aG0074300.1 Cone12ag0720 720
12 6646836 6650173 + Conep12aG0074400.1 Cone12ag0721 721
10 3779231 3783505 + Cp4.1LG10g00320.1 Cpe10g00658 658
10 3786192 3787536 + Cp4.1LG10g00260.1 Cpe10g00659 659
10 3793348 3794707 - Cp4.1LG10g00160.1 Cpe10g00661 661
10 3796171 3826023 + Cp4.1LG10g00270.1 Cpe10g00662 662
19 6296330 6300121 + Cp4.1LG19g08910.1 Cpe19g00853 853
19 6300896 6305584 + Cp4.1LG19g08940.1 Cpe19g00854 854
19 6320179 6320968 - Cp4.1LG19g08840.1 Cpe19g00857 857
19 6322146 6348876 + Cp4.1LG19g08930.1 Cpe19g00858 858
4 34741588 34744509 + CrPI670011_04g016360.1 Cre04g1636 1636
4 34763826 34766002 + CrPI670011_04g016390.1 Cre04g1639 1639
4 34784173 34787634 - CrPI670011_04g016430.1 Cre04g1643 1643
4 34789745 34827893 + CrPI670011_04g016440.1 Cre04g1644 1644
6 27742660 27746552 + CsaV3_6G047020.1 Csa06g03316 3316
6 27748216 27752453 + CsaV3_6G047040.1 Csa06g03318 3318
6 27760270 27761892 + CsaV3_6G047050.1 Csa06g03319 3319
6 27776567 27779479 - CsaV3_6G047080.1 Csa06g03322 3322
6 27781130 27804881 + CsaV3_6G047090.1 Csa06g03323 3323
4 71324924 71328361 + Hsped.04g15840.1 Hepe04g1584 1584
4 71332015 71335751 + Hsped.04g15860.1 Hepe04g1586 1586
4 71352781 71356176 - Hsped.04g15880.1 Hepe04g1588 1588
4 71367598 71394891 + Hsped.04g15900.1 Hepe04g1590 1590
1 4820456 4856258 - Lsi01G006030.1 Lsi01g00603 603
1 4870115 4873723 + Lsi01G006050.1 Lsi01g00605 605
1 4880194 4882315 - Lsi01G006060.1 Lsi01g00606 606
1 4894336 4899607 - Lsi01G006070.1 Lsi01g00607 607
1 4900811 4905668 - Lsi01G006090.1 Lsi01g00609 609
7 16449182 16455736 + Lsi07G011060.1 Lsi07g01106 1106
7 16460755 16474355 - Lsi07G011080.1 Lsi07g01108 1108
14 21139895 21144903 + Sed0000291.4 Sed14g1183 1183
14 21149203 21153976 + Sed0005535.1 Sed14g1184 1184
14 21171929 21176805 - Sed0013451.4 Sed14g1189 1189
14 21186389 21213802 + Sed0027366.1 Sed14g1192 1192
3 75603703 75607106 + Tan0004357.2 Tan03g2064 2064
3 75609429 75614504 + Tan0002086.1 Tan03g2066 2066
3 75629558 75633271 - Tan0017585.1 Tan03g2068 2068
3 75660165 75689098 + Tan0013474.2 Tan03g2072 2072
4 19803722 19806398 - Vvi4g1102 Vvi4g1102 1102
4 19816687 19817188 - Vvi4g1103 Vvi4g1103 1103
4 19822101 19827502 + Vvi4g1104 Vvi4g1104 1104
4 19827503 19834013 + Vvi4g1105 Vvi4g1105 1105
4 19837736 19839174 + Vvi4g1106 Vvi4g1106 1106
4 19840837 19853733 - Vvi4g1107 Vvi4g1107 1107
4 19853973 19859314 + Vvi4g1108 Vvi4g1108 1108
4 19868018 19922607 + Vvi4g1109 Vvi4g1109 1109
4 19923028 19924620 - Vvi4g1110 Vvi4g1110 1110
4 19929608 19931425 + Vvi4g1111 Vvi4g1111 1111
       

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