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
Vvi4g1042 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1043 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1044 . . . . . . Bma09g00091 . . . Cma03g00717 Cma07g00464 Car03g00657 Car07g00411 . Cpe19g00826 Cpe10g00639 Bhi03g00913 . . . . . . . . . . . . . . . . Cone9ag1574 Lsi01g00642 . . Cme08g00889 . . . . . . . . . Cmo03g00743 Cmo07g00462 . . . . . . . . . . . . . . . . . . . . . Csa06g03284 Chy02g00612 .
Vvi4g1045 . Blo16g00060 . . . Bpe13g00431 Bma09g00092 . . Cmo16g00691 Cma03g00716 . Car03g00656 . . . . Bhi03g00911 . . . . . . Cla01g01943 . . . . . . . Cone12ag0780 Cone6ag1651 Cone9ag1575 . . Chy07g01260 . Blo05g00810 . Bda11g01850 . . . . Bma06g00110 . . . Cma16g00634 . . . . . . . . . . . . Cla07g00832 . . . . . . . Csa06g03285 Chy02g00611 .
Vvi4g1046 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1047 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1048 . . . . . . . Bma15g00985 . . Cma03g00714 . . . . Cpe19g00828 Cpe10g00641 Bhi03g00909 . . . . . . Cla01g01945 . Cec04g1692 . Clacu01g2055 Cmu01g1932 . . Cone12ag0781 . . Lsi01g00639 . . Cme08g00891 . Blo06g00145 . . Bpe10g00131 . . . . Cmo03g00741 . . . . . . . . . . . . . . . . . . . . . . Csa06g03287 Chy02g00609 .
Vvi4g1049 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1652 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1050 . Blo16g00061 . Bda10g00150 . Bpe13g00430 . Bma15g00984 . Cmo16g00693 . . . . . . . . . . . . . . . . . . . . . Cone8ag0829 Cone12ag0782 . . . . Chy07g01261 . . Blo06g00146 Bda11g01849 . Bpe10g00132 . . Bma06g00109 . . . Cma16g00635 . . . . . . . . . . . . Cla07g00833 Cam07g0903 Cec07g0955 Cco07g0945 Clacu07g0876 Cmu07g0877 Cre07g1239 Lsi07g00235 Csa04g00542 . .
Vvi4g1051 . . . . . Bpe13g00429 . . . Cmo16g00694 . . . . . . . . . . . . . . . . . . . . . . Cone12ag0783 . . . . Chy07g01262 . . . Bda11g01848 . . . . Bma06g00108 . . . Cma16g00636 . . . . Cpe14g00543 . . . . . . . Cla07g00835 Cam07g0904 Cec07g0957 Cco07g0947 Clacu07g0879 Cmu07g0879 Cre07g1240 Lsi07g00234 Csa04g00541 . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
10 4454588 4456784 - Bda033105 Bda10g00150 150
11 53663609 53669482 + Bda008785.1 Bda11g01848 1848
11 53670889 53672671 + Bda008786.1 Bda11g01849 1849
11 53673006 53674455 - Bda008787.1 Bda11g01850 1850
3 17149704 17158873 - XM_039026042.1 Bhi03g00909 909
3 17182653 17185947 - XM_039025435.1 Bhi03g00911 911
3 17186958 17194985 - XM_039027562.1 Bhi03g00913 913
5 29632407 29653582 + BLOR15772 Blo05g00810 810
6 5741865 5745744 + BLOR16728 Blo06g00145 145
6 5745917 5751231 - BLOR16729 Blo06g00146 146
16 1954452 1955748 + BLOR07308 Blo16g00060 60
16 1956089 1964436 - BLOR07309 Blo16g00061 61
6 1526622 1537215 + Bma022727.1 Bma06g00108 108
6 1538574 1540294 + Bma031266 Bma06g00109 109
6 1540628 1542030 - Bma022728.2 Bma06g00110 110
9 2436977 2438797 + Bma028782.1 Bma09g00091 91
9 2440209 2441492 + Bma028783.1 Bma09g00092 92
15 38232607 38234786 + Bma014262.1 Bma15g00984 984
15 38236807 38237548 - Bma014263.1 Bma15g00985 985
10 2458439 2462491 + Bpe002434.1 Bpe10g00131 131
10 2467445 2469792 - Bpe002435.1 Bpe10g00132 132
13 11889102 11894687 + Bpe006553.2 Bpe13g00429 429
13 11895853 11897586 + Bpe024942 Bpe13g00430 430
13 11897912 11899376 - Bpe006554.2 Bpe13g00431 431
7 22152735 22155568 - CaPI482276_07g009030.1 Cam07g0903 903
7 22197691 22210302 - CaPI482276_07g009040.1 Cam07g0904 904
3 5882799 5884795 - Carg00616-RA Car03g00656 656
3 5886073 5893597 - Carg00617-RA Car03g00657 657
7 2079243 2084238 - Carg16064-RA Car07g00411 411
7 21636604 21639604 - CcPI632755_07g009450.1 Cco07g0945 945
7 21684233 21696994 - CcPI632755_07g009470.1 Cco07g0947 947
4 36045955 36063351 + CePI673135_04g016920.1 Cec04g1692 1692
7 23457397 23460402 - CePI673135_07g009550.1 Cec07g0955 955
7 23515074 23534786 - CePI673135_07g009570.1 Cec07g0957 957
2 3701280 3707577 - Chy2G028760.1 Chy02g00609 609
2 3712025 3713952 - Chy2G028780.1 Chy02g00611 611
2 3715829 3726810 - Chy2G028790.1 Chy02g00612 612
7 17305002 17307712 + Chy7G140900.1 Chy07g01260 1260
7 17310427 17313676 - Chy7G140910.1 Chy07g01261 1261
7 17319221 17328628 - Chy7G140920.1 Chy07g01262 1262
1 32340773 32350121 + ClG42_01g0205500.10 Clacu01g2055 2055
7 21879881 21882703 - ClG42_07g0087600.10 Clacu07g0876 876
7 21928244 21940936 - ClG42_07g0087900.10 Clacu07g0879 879
1 34110056 34112700 + ClCG01G019950.1 Cla01g01943 1943
1 34117062 34122832 + ClCG01G019970.1 Cla01g01945 1945
7 23049341 23051503 + ClCG07G008740.1 Cla07g00832 832
7 23059748 23063060 - ClCG07G008750.2 Cla07g00833 833
7 23107884 23122551 - ClCG07G008770.2 Cla07g00835 835
3 5782219 5787455 - CmaCh03G007140.1 Cma03g00714 714
3 5790882 5792773 - CmaCh03G007160.1 Cma03g00716 716
3 5794253 5801099 - CmaCh03G007170.1 Cma03g00717 717
7 2019481 2028922 - CmaCh07G004640.1 Cma07g00464 464
16 3271830 3273908 + CmaCh16G006340.1 Cma16g00634 634
16 3274769 3277946 - CmaCh16G006350.1 Cma16g00635 635
16 3280357 3291103 - CmaCh16G006360.1 Cma16g00636 636
8 5833385 5840493 + MELO3C007867.2.1 Cme08g00889 889
8 5848533 5852687 + MELO3C001466.2.1 Cme08g00891 891
3 6282873 6287504 - CmoCh03G007410.1 Cmo03g00741 741
3 6291134 6305286 - CmoCh03G007430.1 Cmo03g00743 743
7 2107826 2116953 - CmoCh07G004620.1 Cmo07g00462 462
16 3419492 3420862 + CmoCh16G006910.1 Cmo16g00691 691
16 3422327 3425611 - CmoCh16G006930.1 Cmo16g00693 693
16 3427959 3438490 - CmoCh16G006940.1 Cmo16g00694 694
1 32681236 32687186 + CmPI595203_01g019320.1 Cmu01g1932 1932
7 22100909 22103722 - CmPI595203_07g008770.1 Cmu07g0877 877
7 22146067 22163714 - CmPI595203_07g008790.1 Cmu07g0879 879
6 12612075 12613770 + Conep06aG0171600.1 Cone6ag1651 1651
6 12613661 12615139 - Conep06aG0171700.1 Cone6ag1652 1652
8 8263750 8266418 - Conep08aG0085500.1 Cone8ag0829 829
9 11332786 11336580 + Conep09aG0162400.1 Cone9ag1574 1574
9 11337036 11338323 + Conep09aG0162500.1 Cone9ag1575 1575
12 7133940 7135609 + Conep12aG0080300.1 Cone12ag0780 780
12 7136414 7143633 + Conep12aG0080400.1 Cone12ag0781 781
12 7145030 7147814 - Conep12aG0080500.1 Cone12ag0782 782
12 7157981 7164637 - Conep12aG0080600.1 Cone12ag0783 783
10 3675501 3682842 + Cp4.1LG10g00480.1 Cpe10g00639 639
10 3690407 3696024 + Cp4.1LG10g00450.1 Cpe10g00641 641
14 3414981 3430059 - Cp4.1LG14g01740.1 Cpe14g00543 543
19 6168505 6176114 + Cp4.1LG19g09160.1 Cpe19g00826 826
19 6180337 6186534 + Cp4.1LG19g09190.1 Cpe19g00828 828
7 25893619 25896755 - CrPI670011_07g012390.1 Cre07g1239 1239
7 25938124 25950737 - CrPI670011_07g012400.1 Cre07g1240 1240
4 3586391 3595878 + CsaV3_4G005410.1 Csa04g00541 541
4 3601439 3604686 + CsaV3_4G005420.1 Csa04g00542 542
6 27557602 27563922 + CsaV3_6G046700.1 Csa06g03284 3284
6 27565675 27567365 + CsaV3_6G046710.1 Csa06g03285 3285
6 27571241 27576475 + CsaV3_6G046730.1 Csa06g03287 3287
1 5147862 5161508 - Lsi01G006390.1 Lsi01g00639 639
1 5170810 5180886 - Lsi01G006420.1 Lsi01g00642 642
7 2592923 2603338 + Lsi07G002340.1 Lsi07g00234 234
7 2612435 2619270 + Lsi07G002350.1 Lsi07g00235 235
4 19076790 19078109 + Vvi4g1042 Vvi4g1042 1042
4 19107431 19110307 + Vvi4g1043 Vvi4g1043 1043
4 19116411 19130669 + Vvi4g1044 Vvi4g1044 1044
4 19132071 19133694 + Vvi4g1045 Vvi4g1045 1045
4 19134300 19137992 - Vvi4g1046 Vvi4g1046 1046
4 19138457 19141545 + Vvi4g1047 Vvi4g1047 1047
4 19143416 19150304 + Vvi4g1048 Vvi4g1048 1048
4 19151033 19152506 - Vvi4g1049 Vvi4g1049 1049
4 19153004 19160933 - Vvi4g1050 Vvi4g1050 1050
4 19164014 19178113 - Vvi4g1051 Vvi4g1051 1051
       

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