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
Vvi1g451 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g452 . . . . . Bpe10g00983 Bma14g01888 . . . . Cma04g00062 . Car04g00059 . . Cpe01g01844 . . . . . . . . . . . . . . Cone13ag0750 . . . . Csa05g02017 Chy10g00230 . . . . . . . . . . . . . . . . . Cpe04g01368 Bhi12g00911 . . . . . . Cla01g00614 Cam01g0643 Cec01g0635 Cco01g0662 Clacu01g0632 Cmu01g0605 Cre09g1896 Lsi09g00665 . . .
Vvi1g453 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo11g00976 . . . . . . . . Cmo15g00998 . . . Car15g00904 Cpe13g00365 . . . . . . . . . . . . . . . . . Chy09g00847 Cme09g01380
Vvi1g454 . . . . . . . . . . . . . . . . Cpe01g01843 . . . . . . . . . . . . . . . . . . . Csa05g02016 . . . . . . . . . . . . Cmo15g01000 . Cma15g00959 . Car15g00905 Cpe13g00364 . Bhi12g00914 . . . Hepe02g2646 . . Cla01g00615 Cam01g0644 Cec01g0636 Cco01g0663 Clacu01g0633 Cmu01g0606 Cre09g1895 Lsi09g00666 . Chy09g00844 Cme09g01376
Vvi1g455 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo15g01001 . Cma15g00961 . Car15g00907 Cpe13g00363 . Bhi12g00916 . . . . . . Cla01g00618 Cam01g0646 Cec01g0638 Cco01g0664 Clacu01g0634 . . Lsi09g00668 . . .
Vvi1g456 . . . . . . . . Cmo04g01088 . Cma04g01010 Cma04g00064 Car04g00946 Car04g00061 Sed06g0178 . . Bhi07g00361 Tan04g1544 Cmetu10g1184 Lac13g1416 Hepe01g0553 . . Cla07g00573 Cam07g0600 Cec07g0669 Cco07g0640 Clacu07g0602 Cmu07g0639 Cre07g0975 . . . Cone9ag0416 Lsi04g01122 . . Cme10g01588 Blo06g01010 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g457 . . . . . . . . . . . Cma04g00104 . . . . Cpe01g01842 . . . . . . . . . . . . . . . . Cone6ag0389 . . Csa05g02015 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy09g00843 Cme09g01375
Vvi1g458 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g02014 . . . . . . . . . . . . Cmo15g00939 . Cma15g00902 . Car15g00841 Cpe13g00362 . Bhi12g00918 . . . Hepe02g2639 . . Cla01g00619 Cam01g0647 Cec01g0639 Cco01g0665 Clacu01g0635 Cmu01g0608 Cre09g1893 Lsi09g00669 . Chy09g00841 Cme09g01373
Vvi1g459 . . . . . . . . Cmo04g01090 . Cma04g01012 . Car04g00947 . Sed04g3023 . . Bhi07g00362 Tan04g1541 Cmetu10g0424 . Hepe01g0554 . . Cla07g00572 Cam07g0599 Cec07g0668 Cco07g0639 Clacu07g0601 Cmu07g0638 Cre07g0974 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g460 . . . . . . . . Cmo04g01091 . Cma04g01013 Cma04g00065 Car04g00949 Car04g00062 . . . . . . . . . . Cla07g00570 Cam07g0596 Cec07g0663 Cco07g0636 Clacu07g0599 Cmu07g0633 Cre07g0972 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01148 . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 16217521 16222520 + XM_039036935.1 Bhi07g00361 361
7 16256011 16260748 + XM_039037396.1 Bhi07g00362 362
12 27444596 27447647 + XM_039020348.1 Bhi12g00911 911
12 27533345 27535994 - XM_039018485.1 Bhi12g00914 914
12 27609655 27613511 + XM_039050741.1 Bhi12g00916 916
12 27615901 27627127 + XM_039018474.1 Bhi12g00918 918
6 33334507 33338427 - BLOR17593 Blo06g01010 1010
11 23222501 23223472 + BLOR03852 Blo11g00976 976
14 40383250 40384424 + Bma012674.1 Bma14g01888 1888
10 15275567 15276474 - Bpe003288.1 Bpe10g00983 983
1 7019347 7021195 + CaPI482276_01g006430.1 Cam01g0643 643
1 7032622 7034382 - CaPI482276_01g006440.1 Cam01g0644 644
1 7071658 7074053 + CaPI482276_01g006460.1 Cam01g0646 646
1 7075760 7082614 + CaPI482276_01g006470.1 Cam01g0647 647
7 10471473 10482916 + CaPI482276_07g005960.1 Cam07g0596 596
7 10530147 10532242 - CaPI482276_07g005990.1 Cam07g0599 599
7 10535573 10539952 - CaPI482276_07g006000.1 Cam07g0600 600
4 314989 316803 + Carg22007-RA Car04g00059 59
4 321412 326168 + Carg22009-RA Car04g00061 61
4 327008 333471 + Carg22010-RA Car04g00062 62
4 5450311 5455129 + Carg00121-RA Car04g00946 946
4 5458977 5459643 - Carg00122-RA Car04g00947 947
4 5465953 5474218 - Carg00124-RA Car04g00949 949
15 4868631 4870711 + Carg27990-RA Car15g00841 841
15 5493357 5495137 - Carg26340-RA Car15g00904 904
15 5503250 5504992 - Carg26339-RA Car15g00905 905
15 5517459 5520042 + Carg26337-RA Car15g00907 907
1 6774740 6776962 + CcPI632755_01g006620.1 Cco01g0662 662
1 6788263 6790023 - CcPI632755_01g006630.1 Cco01g0663 663
1 6821318 6830200 + CcPI632755_01g006640.1 Cco01g0664 664
1 6831914 6838351 + CcPI632755_01g006650.1 Cco01g0665 665
7 10068496 10072629 + CcPI632755_07g006360.1 Cco07g0636 636
7 10132558 10134638 - CcPI632755_07g006390.1 Cco07g0639 639
7 10138014 10142397 - CcPI632755_07g006400.1 Cco07g0640 640
1 6825989 6828970 + CePI673135_01g006350.1 Cec01g0635 635
1 6840444 6842201 - CePI673135_01g006360.1 Cec01g0636 636
1 6877615 6880040 + CePI673135_01g006380.1 Cec01g0638 638
1 6881763 6888217 + CePI673135_01g006390.1 Cec01g0639 639
7 10887254 10895572 + CePI673135_07g006630.1 Cec07g0663 663
7 10956722 10958791 - CePI673135_07g006680.1 Cec07g0668 668
7 10962179 10966570 - CePI673135_07g006690.1 Cec07g0669 669
9 11215621 11221362 - Chy9G165570.1 Chy09g00841 841
9 11227994 11256136 - Chy9G165590.1 Chy09g00843 843
9 11256207 11257967 + Chy9G165600.1 Chy09g00844 844
9 11274399 11275111 + Chy9G165630.1 Chy09g00847 847
10 5786478 5787203 + Chy10G174240.1 Chy10g00230 230
1 6653568 6655446 + ClG42_01g0063200.10 Clacu01g0632 632
1 6666773 6668533 - ClG42_01g0063300.10 Clacu01g0633 633
1 6698057 6708139 + ClG42_01g0063400.10 Clacu01g0634 634
1 6709858 6716377 + ClG42_01g0063500.10 Clacu01g0635 635
7 9397120 9423484 + ClG42_07g0059900.10 Clacu07g0599 599
7 9469046 9471139 - ClG42_07g0060100.10 Clacu07g0601 601
7 9474511 9478878 - ClG42_07g0060200.10 Clacu07g0602 602
1 7017547 7019984 + ClCG01G006300.1 Cla01g00614 614
1 7031201 7032961 - ClCG01G006310.1 Cla01g00615 615
1 7070945 7074176 + ClCG01G006340.2 Cla01g00618 618
1 7075553 7082358 + ClCG01G006350.1 Cla01g00619 619
7 9682631 9712162 + ClCG07G005930.2 Cla07g00570 570
7 9759915 9762214 - ClCG07G005970.2 Cla07g00572 572
7 9765296 9770440 - ClCG07G005980.2 Cla07g00573 573
4 293140 294741 + CmaCh04G000620.1 Cma04g00062 62
4 300503 305368 + CmaCh04G000640.1 Cma04g00064 64
4 305979 312306 + CmaCh04G000650.1 Cma04g00065 65
4 513356 517082 + CmaCh04G001040.1 Cma04g00104 104
4 5230416 5235212 + CmaCh04G010100.1 Cma04g01010 1010
4 5245261 5249684 - CmaCh04G010120.1 Cma04g01012 1012
4 5252443 5263154 - CmaCh04G010130.1 Cma04g01013 1013
15 4650006 4650962 - CmaCh15G009020.1 Cma15g00902 902
15 5172627 5174351 - CmaCh15G009590.1 Cma15g00959 959
15 5185288 5188429 + CmaCh15G009610.1 Cma15g00961 961
9 18986610 18992519 - MELO3C005295.2.1 Cme09g01373 1373
9 18998029 19000014 - MELO3C005297.2.1 Cme09g01375 1375
9 19022258 19024452 + MELO3C005298.2.1 Cme09g01376 1376
9 19042948 19046228 + MELO3C005301.2.1 Cme09g01380 1380
10 21005177 21009960 + MELO3C026422.2.1 Cme10g01588 1588
10 6216999 6221868 + PI0007354.1 Cmetu10g0424 424
10 6198820 6203958 + PI0002577.1 Cmetu10g1184 1184
4 5484057 5489592 + CmoCh04G010880.1 Cmo04g01088 1088
4 5510873 5515233 - CmoCh04G010900.1 Cmo04g01090 1090
4 5518387 5526944 - CmoCh04G010910.1 Cmo04g01091 1091
15 4813333 4814289 - CmoCh15G009390.1 Cmo15g00939 939
15 5378409 5379482 - CmoCh15G009980.1 Cmo15g00998 998
15 5387954 5389696 - CmoCh15G010000.1 Cmo15g01000 1000
15 5402358 5405847 + CmoCh15G010010.1 Cmo15g01001 1001
1 6610995 6612878 + CmPI595203_01g006050.1 Cmu01g0605 605
1 6624201 6625961 - CmPI595203_01g006060.1 Cmu01g0606 606
1 6666605 6677244 + CmPI595203_01g006080.1 Cmu01g0608 608
7 9561286 9564427 + CmPI595203_07g006330.1 Cmu07g0633 633
7 9627509 9629602 - CmPI595203_07g006380.1 Cmu07g0638 638
7 9632966 9637331 - CmPI595203_07g006390.1 Cmu07g0639 639
6 1894274 1895611 - Conep06aG0039700.1 Cone6ag0389 389
9 1919206 1923034 + Conep09aG0042600.1 Cone9ag0416 416
13 7118508 7120472 + Conep13aG0077400.1 Cone13ag0750 750
1 15673876 15675304 - Cp4.1LG01g18410.1 Cpe01g01842 1842
1 15723496 15725259 + Cp4.1LG01g18440.1 Cpe01g01843 1843
1 15729256 15731602 - Cp4.1LG01g18510.1 Cpe01g01844 1844
4 11123228 11126212 + Cp4.1LG04g13650.1 Cpe04g01368 1368
13 3926926 3933456 - Cp4.1LG13g03630.1 Cpe13g00362 362
13 3934112 3936335 - Cp4.1LG13g03640.1 Cpe13g00363 363
13 3951163 3952905 + Cp4.1LG13g03610.1 Cpe13g00364 364
13 3962129 3963864 + Cp4.1LG13g03650.1 Cpe13g00365 365
7 11432628 11438255 + CrPI670011_07g009720.1 Cre07g0972 972
7 11514265 11516363 - CrPI670011_07g009740.1 Cre07g0974 974
7 11521600 11525966 - CrPI670011_07g009750.1 Cre07g0975 975
9 37634185 37640664 - CrPI670011_09g018930.1 Cre09g1893 1893
9 37683600 37685360 + CrPI670011_09g018950.1 Cre09g1895 1895
9 37696717 37698605 - CrPI670011_09g018960.1 Cre09g1896 1896
5 11793475 11810308 - CsaV3_5G014720.1 Csa05g01148 1148
5 23513918 23520244 - CsaV3_5G028330.1 Csa05g02014 2014
5 23524501 23530825 - CsaV3_5G028340.1 Csa05g02015 2015
5 23548902 23552351 + CsaV3_5G028350.1 Csa05g02016 2016
5 23557147 23560019 - CsaV3_5G028360.1 Csa05g02017 2017
1 65175561 65180593 + Hsped.01g05530.1 Hepe01g0553 553
1 65187055 65190435 - Hsped.01g05540.1 Hepe01g0554 554
2 73907356 73914093 - Hsped.02g26390.1 Hepe02g2639 2639
2 73957125 73959629 + Hsped.02g26460.1 Hepe02g2646 2646
13 13812755 13817137 + Lag0041212.1 Lac13g1416 1416
4 14674875 14679985 - Lsi04G011220.1 Lsi04g01122 1122
9 7443141 7445538 + Lsi09G006650.1 Lsi09g00665 665
9 7460521 7462281 - Lsi09G006660.1 Lsi09g00666 666
9 7508830 7511934 + Lsi09G006680.1 Lsi09g00668 668
9 7513534 7519585 + Lsi09G006690.1 Lsi09g00669 669
4 41405152 41408757 + Sed0010427.1 Sed04g3023 3023
6 1234736 1240821 - Sed0027263.1 Sed06g0178 178
4 23182860 23187473 + Tan0019203.2 Tan04g1541 1541
4 23213442 23218608 - Tan0008724.1 Tan04g1544 1544
1 4858516 4862023 - Vvi1g451 Vvi1g451 451
1 4866663 4868192 - Vvi1g452 Vvi1g452 452
1 4878610 4879983 + Vvi1g453 Vvi1g453 453
1 4894993 4897616 - Vvi1g454 Vvi1g454 454
1 4904272 4911526 - Vvi1g455 Vvi1g455 455
1 4912272 4918899 + Vvi1g456 Vvi1g456 456
1 4918965 4920189 - Vvi1g457 Vvi1g457 457
1 4920368 4928008 + Vvi1g458 Vvi1g458 458
1 4928288 4931588 + Vvi1g459 Vvi1g459 459
1 4934359 4949025 + Vvi1g460 Vvi1g460 460
       

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