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
Vvi1g591 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0710 Cone12ag0688 . . . . . . . . . . . . . Cmo04g02791 . . Cma05g00056 . Car05g00044 . . . . . . . . . . . . . . . . . . . .
Vvi1g592 . . . . . Bpe10g00853 Bma14g01835 Bma15g00232 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo06g00834 Blo11g01032 Bda07g01650 . . . . . . . . . Cma05g00055 . Car05g00043 . . . . . . . . . . . . . . . . . . . .
Vvi1g593 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g594 . . . . . . . Bma15g00231 . Cmo18g00718 . Cma18g00730 . Car18g00679 Sed06g1711 Cpe09g00558 Cpe01g01581 Bhi07g01840 Tan04g0128 Cmetu10g1498 Lac13g0112 Hepe10g1562 . . Cla05g02622 Cam05g2810 Cec05g2846 Cco05g2877 Clacu05g2814 Cmu05g2662 Cre05g2778 . . . . Lsi04g00634 Csa05g02253 Chy10g00822 Cme10g00608 Blo06g00835 . . . . . . . . . . Cma04g01794 . Car04g01808 . . . . . . . . . . . . . . . . . . . Chy09g00409 .
Vvi1g595 . . . . . . . Bma15g00230 . . . . . . Sed01g3038 . Cpe01g01580 Bhi07g01839 Tan04g0129 Cmetu09g0131 Lac13g0113 Hepe10g1564 . . Cla05g02620 Cam05g2807 Cec05g2843 Cco05g2875 Clacu05g2811 Cmu05g2659 Cre05g2775 Cone13ag1096 Cone19ag1086 . . Lsi04g00633 Csa05g02254 Chy10g00824 Cme10g00607 Blo06g00836 . . . . . . . . . . Cma04g01792 . Car04g01807 . . . . . . . . . . . . . . . . . . . . .
Vvi1g596 Blo01g00379 . Bda01g02201 . Bpe13g00513 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0708 Cone12ag0686 . . . . . . . . . . Bma01g00031 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g597 . . . . . . Bma14g01834 . . Cmo18g00719 . Cma18g00731 . Car18g00681 . Cpe09g00557 . Bhi07g01837 . . Lac13g0114 Hepe10g1565 . . Cla05g02619 Cam05g2806 Cec05g2842 Cco05g2874 Clacu05g2810 Cmu05g2658 Cre05g2774 Cone13ag1095 Cone19ag1085 . . Lsi04g00632 Csa05g02255 Chy10g00825 Cme10g00606 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g598 . . . . . . Bma14g01833 . . . . . . . Sed04g0552 . Cpe01g01579 Bhi07g01835 Tan04g0132 Cmetu10g1346 Lac13g0115 Hepe10g0058 . . Cla05g02618 Cam05g2805 Cec05g2841 Cco05g2873 Clacu05g2809 Cmu05g2657 Cre05g2773 . . . . Lsi04g00631 Csa05g02256 Chy10g00826 Cme10g00605 Blo06g00838 . Bda07g01649 . . . . . . . . Cma04g01791 Cma05g00053 Car04g01806 Car05g00041 . . . . . . . . . . . . . . . . . . . .
Vvi1g599 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma05g00052 . Car05g00040 . . . . . . . . . . . . . . . . . . . .
Vvi1g600 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57908369 57913541 - Bda004541.1 Bda01g02201 2201
7 30716752 30717247 - Bda028530.1 Bda07g01649 1649
7 30728927 30732173 + Bda028531.1 Bda07g01650 1650
7 49803504 49806838 - XM_039035963.1 Bhi07g01835 1835
7 49815855 49820705 - XM_039037400.1 Bhi07g01837 1837
7 49990208 49997446 - XM_039036258.1 Bhi07g01839 1839
7 50097381 50102488 + XM_039037112.1 Bhi07g01840 1840
1 4353969 4359043 - BLOR00379 Blo01g00379 379
6 31576443 31579635 - BLOR17417 Blo06g00834 834
6 31581290 31585901 - BLOR17418 Blo06g00835 835
6 31592069 31600932 + BLOR17419 Blo06g00836 836
6 31622888 31625278 + BLOR17421 Blo06g00838 838
11 27382642 27387294 - BLOR03908 Blo11g01032 1032
1 400214 404533 - Bma000200.1 Bma01g00031 31
14 39249713 39252259 - Bma012612.1 Bma14g01833 1833
14 39255011 39257548 - Bma012613.1 Bma14g01834 1834
14 39265101 39268380 + Bma030743 Bma14g01835 1835
15 2272975 2277172 - Bma013214.1 Bma15g00230 230
15 2324138 2329507 + Bma013217.1 Bma15g00231 231
15 2331081 2334217 + Bma013218.1 Bma15g00232 232
10 14421885 14424869 - Bpe003157.1 Bpe10g00853 853
13 12484004 12489229 + Bpe010222.2 Bpe13g00513 513
5 35186012 35198182 - CaPI482276_05g028050.1 Cam05g2805 2805
5 35203274 35207682 - CaPI482276_05g028060.1 Cam05g2806 2806
5 35208855 35215018 - CaPI482276_05g028070.1 Cam05g2807 2807
5 35220651 35224993 + CaPI482276_05g028100.1 Cam05g2810 2810
4 10479348 10482040 - Carg14299-RA Car04g01806 1806
4 10489551 10495739 - Carg14298-RA Car04g01807 1807
4 10500347 10505823 + Carg14297-RA Car04g01808 1808
5 216021 217367 + Carg21840-RA Car05g00040 40
5 218314 220951 - Carg21841-RA Car05g00041 41
5 223614 229425 + Carg21843-RA Car05g00043 43
5 230257 232086 - Carg21844-RA Car05g00044 44
18 7971451 7978826 - Carg27651-RA Car18g00679 679
18 7984819 7985735 + Carg27649-RA Car18g00681 681
5 36342965 36356026 - CcPI632755_05g028730.1 Cco05g2873 2873
5 36360879 36366591 - CcPI632755_05g028740.1 Cco05g2874 2874
5 36368004 36374231 - CcPI632755_05g028750.1 Cco05g2875 2875
5 36379907 36384255 + CcPI632755_05g028770.1 Cco05g2877 2877
5 38657075 38668452 - CePI673135_05g028410.1 Cec05g2841 2841
5 38671933 38678044 - CePI673135_05g028420.1 Cec05g2842 2842
5 38679660 38685860 - CePI673135_05g028430.1 Cec05g2843 2843
5 38693597 38697939 + CePI673135_05g028460.1 Cec05g2846 2846
9 3590471 3591972 - Chy9G161250.1 Chy09g00409 409
10 14179138 14183769 - Chy10G180160.1 Chy10g00822 822
10 14193921 14199862 + Chy10G180180.1 Chy10g00824 824
10 14201357 14205979 + Chy10G180190.1 Chy10g00825 825
10 14210804 14213472 + Chy10G180200.1 Chy10g00826 826
5 35410430 35422094 - ClG42_05g0280900.10 Clacu05g2809 2809
5 35425859 35431593 - ClG42_05g0281000.10 Clacu05g2810 2810
5 35432755 35438944 - ClG42_05g0281100.10 Clacu05g2811 2811
5 35444380 35448729 + ClG42_05g0281400.10 Clacu05g2814 2814
5 37393069 37396531 - ClCG05G026100.1 Cla05g02618 2618
5 37401439 37406634 - ClCG05G026110.2 Cla05g02619 2619
5 37407069 37414564 - ClCG05G026120.2 Cla05g02620 2620
5 37418935 37424205 + ClCG05G026140.2 Cla05g02622 2622
4 9038282 9041402 - CmaCh04G017910.1 Cma04g01791 1791
4 9047947 9054520 - CmaCh04G017920.1 Cma04g01792 1792
4 9058593 9063735 + CmaCh04G017940.1 Cma04g01794 1794
5 211386 212739 + CmaCh05G000520.1 Cma05g00052 52
5 213722 218217 - CmaCh05G000530.1 Cma05g00053 53
5 218821 225041 + CmaCh05G000550.1 Cma05g00055 55
5 225612 227514 - CmaCh05G000560.1 Cma05g00056 56
18 6592489 6599809 - CmaCh18G007300.1 Cma18g00730 730
18 6601875 6606557 + CmaCh18G007310.1 Cma18g00731 731
10 3871314 3874697 - MELO3C011917.2.1 Cme10g00605 605
10 3878807 3883368 - MELO3C011916.2.1 Cme10g00606 606
10 3884215 3891074 - MELO3C011915.2.1 Cme10g00607 607
10 3897317 3902855 + MELO3C011913.2.1 Cme10g00608 608
9 14013202 14021911 - PI0018430.1 Cmetu09g0131 131
10 18061576 18064812 + PI0011290.1 Cmetu10g1346 1346
10 18032779 18038424 - PI0028400.1 Cmetu10g1498 1498
4 20087052 20090039 - CmoCh04G027910.1 Cmo04g02791 2791
18 8985471 8992658 - CmoCh18G007180.1 Cmo18g00718 718
18 8994895 8999405 + CmoCh18G007190.1 Cmo18g00719 719
5 35148735 35160398 - CmPI595203_05g026570.1 Cmu05g2657 2657
5 35165251 35169883 - CmPI595203_05g026580.1 Cmu05g2658 2658
5 35171041 35177223 - CmPI595203_05g026590.1 Cmu05g2659 2659
5 35182656 35187017 + CmPI595203_05g026620.1 Cmu05g2662 2662
8 7107798 7112879 + Conep08aG0073100.1 Cone8ag0708 708
8 7123264 7124696 - Conep08aG0073300.1 Cone8ag0710 710
12 6263536 6268918 + Conep12aG0070900.1 Cone12ag0686 686
12 6283813 6285469 - Conep12aG0071100.1 Cone12ag0688 688
13 8868614 8871770 - Conep13aG0112700.1 Cone13ag1095 1095
13 8872117 8876541 - Conep13aG0112800.1 Cone13ag1096 1096
19 7904127 7906480 - Conep19aG0111900.1 Cone19ag1085 1085
19 7906599 7911264 - Conep19aG0112000.1 Cone19ag1086 1086
1 9645947 9649354 - Cp4.1LG01g15880.1 Cpe01g01579 1579
1 9654994 9662420 - Cp4.1LG01g15890.1 Cpe01g01580 1580
1 9667653 9673285 + Cp4.1LG01g15850.1 Cpe01g01581 1581
9 3852015 3856563 - Cp4.1LG09g06240.1 Cpe09g00557 557
9 3857267 3864549 + Cp4.1LG09g06270.1 Cpe09g00558 558
5 38513146 38524755 - CrPI670011_05g027730.1 Cre05g2773 2773
5 38530717 38535110 - CrPI670011_05g027740.1 Cre05g2774 2774
5 38536772 38542977 - CrPI670011_05g027750.1 Cre05g2775 2775
5 38548975 38553331 + CrPI670011_05g027780.1 Cre05g2778 2778
5 25182312 25188225 - CsaV3_5G030720.1 Csa05g02253 2253
5 25193679 25200966 + CsaV3_5G030730.1 Csa05g02254 2254
5 25201442 25206585 + CsaV3_5G030740.1 Csa05g02255 2255
5 25210618 25214151 + CsaV3_5G030750.1 Csa05g02256 2256
10 550817 553379 - Hsped.10g00580.1 Hepe10g0058 58
10 52332469 52337134 - Hsped.10g15620.1 Hepe10g1562 1562
10 52345426 52353047 + Hsped.10g15640.1 Hepe10g1564 1564
10 52354259 52358587 + Hsped.10g15650.1 Hepe10g1565 1565
13 769239 773787 - Lag0039908.1 Lac13g0112 112
13 777712 788489 + Lag0039909.1 Lac13g0113 113
13 789921 795394 + Lag0039910.1 Lac13g0114 114
13 799248 801913 + Lag0039911.1 Lac13g0115 115
4 5788627 5791556 - Lsi04G006310.1 Lsi04g00631 631
4 5796041 5802602 - Lsi04G006320.1 Lsi04g00632 632
4 5805054 5812123 - Lsi04G006330.1 Lsi04g00633 633
4 5820813 5825586 + Lsi04G006340.1 Lsi04g00634 634
1 33469366 33480172 - Sed0002623.2 Sed01g3038 3038
4 4102171 4105094 + Sed0012446.1 Sed04g0552 552
6 41827311 41840907 + Sed0008942.1 Sed06g1711 1711
4 818357 825089 - Tan0012038.1 Tan04g0128 128
4 838004 845589 + Tan0008058.1 Tan04g0129 129
4 856534 859471 + Tan0019362.1 Tan04g0132 132
1 6744492 6746449 + Vvi1g591 Vvi1g591 591
1 6748930 6767400 - Vvi1g592 Vvi1g592 592
1 6772857 6781078 - Vvi1g593 Vvi1g593 593
1 6782563 6810457 - Vvi1g594 Vvi1g594 594
1 6819901 6830379 + Vvi1g595 Vvi1g595 595
1 6831273 6842487 - Vvi1g596 Vvi1g596 596
1 6843365 6852105 + Vvi1g597 Vvi1g597 597
1 6863498 6866630 + Vvi1g598 Vvi1g598 598
1 6869576 6871249 - Vvi1g599 Vvi1g599 599
1 6875153 6876150 - Vvi1g600 Vvi1g600 600
       

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