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
Vvi19g984 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g985 . . . . Bpe09g00295 . . Bma13g00894 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone15ag0978 . . . . Blo07g01003 . . Bda12g00775 . . . . . . . Cma04g00630 . . . Cpe14g00395 Cpe01g00569 . . . . . . . . . . . . . . . . . .
Vvi19g986 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g987 . . . . . . . . . . Cma01g01299 Cma09g00745 . . . . Cpe02g00631 . . . . . . . Cla11g01591 Cam11g1659 Cec11g1687 Cco11g1683 Clacu11g1816 Cmu11g1629 Cre11g2045 . . . . Lsi04g01870 . . Cme07g00760 . . . . . . . . . Cmo01g01354 Cmo09g00737 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g988 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g989 . . . . . . . . Cmo16g00524 Cmo04g00665 Cma01g01303 Cma09g00740 Car01g01110 Car09g00650 . . Cpe02g00629 . . . . . . . Cla11g01597 Cam11g1663 Cec11g1692 Cco11g1688 Clacu11g1821 Cmu11g1633 Cre11g2049 . . . . Lsi04g01874 . . Cme07g00754 . . . . . . . . . Cmo01g01358 Cmo09g00732 Cma04g00618 Cma16g00483 Car04g00578 Car16g00439 Cpe14g00410 Cpe01g00557 . . . . . . . Cla07g01031 Cam07g1474 Cec07g1183 Cco07g1160 Clacu07g1085 Cmu07g1073 Cre07g1449 . . Chy07g01071 .
Vvi19g990 . . . . . . . . . . Cma01g01304 Cma09g00739 Car01g01111 Car09g00649 . . Cpe02g00628 . . . . . . . Cla11g01598 Cam11g1664 Cec11g1693 Cco11g1689 Clacu11g1822 Cmu11g1634 Cre11g2050 Cone6ag0279 Cone9ag0315 . . Lsi04g01876 . . Cme07g00745 . . . . . . . . . Cmo01g01359 Cmo09g00731 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g991 . . . . . . . . . . Cma01g01305 Cma09g00737 Car01g01113 Car09g00647 . . Cpe02g00626 . . . . . . . Cla11g01600 Cam11g1666 Cec11g1695 Cco11g1690 Clacu11g1824 Cmu11g1636 Cre11g2051 Cone6ag0278 . . . Lsi04g01878 . . . . . . . . . . . . Cmo01g01362 Cmo09g00729 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g992 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g993 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
12 36435832 36445904 - Bda009269.1 Bda12g00775 775
7 29611452 29621269 + BLOR18935 Blo07g01003 1003
13 38900101 38906068 - Bma009968.1 Bma13g00894 894
9 2365818 2372930 + Bpe023964.1 Bpe09g00295 295
7 29373167 29384172 + CaPI482276_07g014740.1 Cam07g1474 1474
11 29286107 29292687 + CaPI482276_11g016590.1 Cam11g1659 1659
11 29315720 29321946 - CaPI482276_11g016630.1 Cam11g1663 1663
11 29325572 29335535 + CaPI482276_11g016640.1 Cam11g1664 1664
11 29353548 29360071 + CaPI482276_11g016660.1 Cam11g1666 1666
1 10352919 10358134 - Carg14775-RA Car01g01110 1110
1 10359601 10362177 + Carg14776-RA Car01g01111 1111
1 10377662 10381463 + Carg14778-RA Car01g01113 1113
4 3298654 3307822 + Carg13127-RA Car04g00578 578
9 3779867 3783746 - Carg20053-RA Car09g00647 647
9 3795794 3804501 - Carg20055-RA Car09g00649 649
9 3805713 3811650 + Carg20057-RA Car09g00650 650
16 2732161 2740427 - Carg11406-RA Car16g00439 439
7 25336407 25347491 - CcPI632755_07g011600.1 Cco07g1160 1160
11 29661571 29673506 + CcPI632755_11g016830.1 Cco11g1683 1683
11 29696288 29702673 - CcPI632755_11g016880.1 Cco11g1688 1688
11 29706491 29717339 + CcPI632755_11g016890.1 Cco11g1689 1689
11 29734844 29741271 + CcPI632755_11g016900.1 Cco11g1690 1690
7 27223979 27235073 - CePI673135_07g011830.1 Cec07g1183 1183
11 31123179 31129091 + CePI673135_11g016870.1 Cec11g1687 1687
11 31151451 31157675 - CePI673135_11g016920.1 Cec11g1692 1692
11 31161309 31170013 + CePI673135_11g016930.1 Cec11g1693 1693
11 31188414 31196252 + CePI673135_11g016950.1 Cec11g1695 1695
7 15676110 15684220 - Chy7G139010.1 Chy07g01071 1071
7 25405264 25416251 - ClG42_07g0108500.10 Clacu07g1085 1085
11 29310385 29315955 + ClG42_11g0181600.10 Clacu11g1816 1816
11 29338815 29345019 - ClG42_11g0182100.10 Clacu11g1821 1821
11 29348652 29357371 + ClG42_11g0182200.10 Clacu11g1822 1822
11 29376872 29383387 + ClG42_11g0182400.10 Clacu11g1824 1824
7 26758478 26771077 - ClCG07G010860.2 Cla07g01031 1031
11 29609183 29616948 + ClCG11G016330.2 Cla11g01591 1591
11 29640507 29647490 - ClCG11G016390.1 Cla11g01597 1597
11 29650796 29659836 + ClCG11G016400.1 Cla11g01598 1598
11 29683150 29691149 + ClCG11G016420.2 Cla11g01600 1600
1 9302287 9305539 + CmaCh01G012990.1 Cma01g01299 1299
1 9315054 9321203 - CmaCh01G013030.1 Cma01g01303 1303
1 9322797 9324758 + CmaCh01G013040.1 Cma01g01304 1304
1 9336574 9342713 + CmaCh01G013050.1 Cma01g01305 1305
4 3155567 3170249 + CmaCh04G006180.1 Cma04g00618 618
4 3234786 3239479 + CmaCh04G006300.1 Cma04g00630 630
9 3508509 3513104 - CmaCh09G007370.1 Cma09g00737 737
9 3523098 3531937 - CmaCh09G007390.1 Cma09g00739 739
9 3534014 3540853 + CmaCh09G007400.1 Cma09g00740 740
9 3555291 3559530 - CmaCh09G007450.1 Cma09g00745 745
16 2448627 2458339 - CmaCh16G004830.1 Cma16g00483 483
7 6751218 6771910 - MELO3C010569.2.1 Cme07g00745 745
7 6840247 6847544 + MELO3C010566.2.1 Cme07g00754 754
7 6913460 6915011 - MELO3C010559.2.1 Cme07g00760 760
1 10697561 10701497 + CmoCh01G013540.1 Cmo01g01354 1354
1 10710482 10717047 - CmoCh01G013580.1 Cmo01g01358 1358
1 10716866 10725326 + CmoCh01G013590.1 Cmo01g01359 1359
1 10735433 10739216 + CmoCh01G013620.1 Cmo01g01362 1362
4 3298998 3313469 + CmoCh04G006650.1 Cmo04g00665 665
9 3636443 3642554 - CmoCh09G007290.1 Cmo09g00729 729
9 3652402 3661510 - CmoCh09G007310.1 Cmo09g00731 731
9 3662546 3669509 + CmoCh09G007320.1 Cmo09g00732 732
9 3684485 3688945 - CmoCh09G007370.1 Cmo09g00737 737
16 2531128 2540159 - CmoCh16G005240.1 Cmo16g00524 524
7 25655783 25666755 - CmPI595203_07g010730.1 Cmu07g1073 1073
11 28563220 28568790 + CmPI595203_11g016290.1 Cmu11g1629 1629
11 28591569 28597772 - CmPI595203_11g016330.1 Cmu11g1633 1633
11 28601405 28610109 + CmPI595203_11g016340.1 Cmu11g1634 1634
11 28629598 28636118 + CmPI595203_11g016360.1 Cmu11g1636 1636
6 1280758 1284488 - Conep06aG0028000.1 Cone6ag0278 278
6 1292228 1295426 - Conep06aG0028100.1 Cone6ag0279 279
9 1372487 1377482 - Conep09aG0031800.1 Cone9ag0315 315
15 7807511 7812902 - Conep15aG0099900.1 Cone15ag0978 978
1 3229013 3238863 + Cp4.1LG01g01050.1 Cpe01g00557 557
1 3300820 3308758 + Cp4.1LG01g00940.1 Cpe01g00569 569
2 3803007 3810455 - Cp4.1LG02g02470.1 Cpe02g00626 626
2 3820553 3823640 - Cp4.1LG02g02510.1 Cpe02g00628 628
2 3825577 3831402 + Cp4.1LG02g02530.1 Cpe02g00629 629
2 3844275 3845438 - Cp4.1LG02g02330.1 Cpe02g00631 631
14 2440068 2446466 - Cp4.1LG14g03230.1 Cpe14g00395 395
14 2534282 2543596 - Cp4.1LG14g03140.1 Cpe14g00410 410
7 29582486 29593480 - CrPI670011_07g014490.1 Cre07g1449 1449
11 32226945 32233250 + CrPI670011_11g020450.1 Cre11g2045 2045
11 32255605 32261819 - CrPI670011_11g020490.1 Cre11g2049 2049
11 32265551 32278334 + CrPI670011_11g020500.1 Cre11g2050 2050
11 32293421 32299741 + CrPI670011_11g020510.1 Cre11g2051 2051
4 25843833 25845116 + Lsi04G018700.1 Lsi04g01870 1870
4 25871282 25880247 - Lsi04G018740.1 Lsi04g01874 1874
4 25891276 25898028 + Lsi04G018760.1 Lsi04g01876 1876
4 25915049 25922267 + Lsi04G018780.1 Lsi04g01878 1878
19 19222698 19224725 - Vvi19g984 Vvi19g984 984
19 19247389 19265696 - Vvi19g985 Vvi19g985 985
19 19293517 19296332 - Vvi19g986 Vvi19g986 986
19 19354125 19365820 + Vvi19g987 Vvi19g987 987
19 19433698 19434875 - Vvi19g988 Vvi19g988 988
19 19442859 19461262 - Vvi19g989 Vvi19g989 989
19 19485256 19493771 + Vvi19g990 Vvi19g990 990
19 19501040 19517554 - Vvi19g991 Vvi19g991 991
19 19529947 19532156 + Vvi19g992 Vvi19g992 992
19 19539044 19540048 - Vvi19g993 Vvi19g993 993
       

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