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
Vvi19g584 . . . . Bpe09g00146 . . . . Cmo06g00885 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy06g01863 .
Vvi19g585 . . . . . . Bma10g00581 Bma13g01095 . Cmo06g00884 . . . . . . . . . . . . . . Cla10g00460 Cam10g0446 Cec10g0469 Cco10g0457 Clacu10g0467 Cmu10g1296 Cre10g0701 Cone6ag0040 Cone9ag0046 . . . Csa03g00458 . Cme06g02820 Blo07g00880 Blo10g00853 . Bda12g00939 . . . . . . . . . . . . . Bhi11g00549 . . . . Mch10g1390 . . . . . . . . Lsi05g00545 . . .
Vvi19g586 . . . . . . . . . . Cma01g01110 Cma09g00976 . . Sed07g2707 . . Bhi09g01702 Tan01g3133 Cmetu01g0078 . . . . . . . . . . . . Cone9ag0045 . . Lsi02g01876 . . . . . . . . . . . . Cmo01g01154 Cmo09g00975 . . . . . . . . . . . . . Cla09g01037 . . Cco09g1114 . . . . . Chy01g01060 Cme01g00993
Vvi19g587 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g588 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g589 . . . . . . . . . . Cma01g01108 Cma09g00978 Car01g00979 . Sed05g3441 . Cpe02g00793 Bhi09g01704 Tan01g3135 Cmetu01g0339 . Hepe01g1242 Mch11g1222 . . . . . . . . . . . . Lsi02g01873 Csa07g01001 . . . . . . Bpe11g00560 . . Bma14g00177 . Cmo01g01153 Cmo09g00977 . . . . . . . . . . . . . Cla09g01038 Cam09g1093 Cec09g1093 Cco09g1115 . . . . . Chy01g01065 Cme01g00989
Vvi19g590 . . Bda07g00382 . . . . . . . Cma01g01106 Cma09g00979 . . . Cpe06g00789 Cpe02g00794 Bhi09g01707 Tan01g3137 . . . Mch11g1224 . . . . . . . . . Cone9ag0042 . . Lsi02g01871 Csa07g00999 . . . . . . . . . . . Cmo01g01152 Cmo09g00980 . . . . . . . . . . . . . Cla09g01039 Cam09g1094 Cec09g1094 Cco09g1117 . . Cre09g1059 . . Chy01g01067 Cme01g00987
Vvi19g591 Blo03g00537 . Bda07g00383 . . . . . . . Cma01g01105 . Car01g00978 . . . Cpe02g00796 Bhi09g01710 . . . . . . . . . . . . . . . Cone14ag1189 Cone15ag1208 Lsi02g01869 Csa07g00996 . . . . . . Bpe11g00561 . . . . Cmo01g01151 . . . . . . . . . . . . . . Cla09g02036 Cam09g2125 Cec09g2190 . . . . . . Chy01g01070 .
Vvi19g592 . . . . Bpe09g00144 . . Bma13g01098 Cmo16g00964 Cmo06g00881 . . . . . . . . . . . . . . Cla10g00455 Cam10g0441 Cec10g0463 Cco10g0453 Clacu10g0461 Cmu10g1291 Cre10g0697 . . Cone14ag1190 Cone15ag1209 . Csa03g00452 . Cme06g02815 Blo07g00877 . Bda05g00691 Bda12g00942 . Bpe03g00765 . . . . . . Cma16g00930 . Car16g00900 Cpe14g00751 . Bhi11g00521 Tan01g1786 . . . . . . . . . . . . Lsi05g00540 . Chy06g01867 .
Vvi19g593 Blo03g00535 Blo03g01462 Bda07g00384 Bda09g00413 . Bpe08g01108 . . . . Cma01g01104 . Car01g00976 . . . Cpe02g00797 Bhi09g01716 . . . . . . . . . . . . . Cone6ag0039 Cone9ag0041 . . Lsi02g01868 Csa07g00991 . . . . . . Bpe11g00562 . Bma07g01280 Bma14g00318 . Cmo01g01150 . . . . . . . . . . . . . . Cla09g02037 Cam09g2126 . . . . . . . Chy01g01071 Cme01g00979
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 55206855 55211773 + Bda021826.1 Bda05g00691 691
7 4812681 4813838 - Bda025467.1 Bda07g00382 382
7 4816791 4838353 - Bda025468.4 Bda07g00383 383
7 4839515 4843543 + Bda033839 Bda07g00384 384
9 5127291 5129444 + Bda034094 Bda09g00413 413
12 40478091 40482124 + Bda009484.1 Bda12g00939 939
12 40498125 40502759 - Bda009487.3 Bda12g00942 942
9 45681705 45685349 - XM_039044015.1 Bhi09g01702 1702
9 46033317 46034548 + XM_039043878.1 Bhi09g01704 1704
9 46218747 46222445 - XM_039041156.1 Bhi09g01707 1707
9 46359658 46400668 - XM_039042883.1 Bhi09g01710 1710
9 46517213 46521633 + XM_039044246.1 Bhi09g01716 1716
11 12307950 12313213 + XM_039049216.1 Bhi11g00521 521
11 12579567 12584315 - XM_039050336.1 Bhi11g00549 549
3 20627580 20632620 - BLOR11716 Blo03g00535 535
3 20636327 20659179 + BLOR11718 Blo03g00537 537
3 41240347 41245143 + BLOR12643 Blo03g01462 1462
7 27486945 27492048 + BLOR18809 Blo07g00877 877
7 27540022 27543381 - BLOR18812 Blo07g00880 880
10 27015561 27018782 + BLOR02643 Blo10g00853 853
7 48463550 48465723 - Bma026551.1 Bma07g01280 1280
10 7151541 7154415 + Bma004286.1 Bma10g00581 581
13 43884904 43887963 + Bma010221.1 Bma13g01095 1095
13 43905030 43907970 - Bma010224.1 Bma13g01098 1098
14 2326765 2333975 + Bma010588.1 Bma14g00177 177
14 3954943 3957540 - Bma010741.1 Bma14g00318 318
3 27674316 27679141 + Bpe012675.1 Bpe03g00765 765
8 13119454 13121607 - Bpe023235.1 Bpe08g01108 1108
9 985116 989832 + Bpe023818.1 Bpe09g00144 144
9 1005315 1010223 + Bpe023820.1 Bpe09g00146 146
11 4300990 4302057 - Bpe003927.1 Bpe11g00560 560
11 4304535 4322430 - Bpe003928.1 Bpe11g00561 561
11 4323604 4327608 + Bpe024763 Bpe11g00562 562
9 11355793 11356734 - CaPI482276_09g010930.1 Cam09g1093 1093
9 11378564 11379568 - CaPI482276_09g010940.1 Cam09g1094 1094
9 35795702 35816985 - CaPI482276_09g021250.1 Cam09g2125 2125
9 35822578 35826617 + CaPI482276_09g021260.1 Cam09g2126 2126
10 6809564 6814545 + CaPI482276_10g004410.1 Cam10g0441 441
10 6868990 6873283 - CaPI482276_10g004460.1 Cam10g0446 446
1 9288025 9293450 - Carg22386-RA Car01g00976 976
1 9295998 9313646 + Carg22384-RA Car01g00978 978
1 9314659 9315741 + Carg22383-RA Car01g00979 979
16 7150609 7155730 - Carg22354-RA Car16g00900 900
9 10683093 10686304 - CcPI632755_09g011140.1 Cco09g1114 1114
9 10690291 10691232 - CcPI632755_09g011150.1 Cco09g1115 1115
9 10708880 10709884 - CcPI632755_09g011170.1 Cco09g1117 1117
10 5361776 5367077 + CcPI632755_10g004530.1 Cco10g0453 453
10 5430070 5434636 - CcPI632755_10g004570.1 Cco10g0457 457
9 10722947 10723888 - CePI673135_09g010930.1 Cec09g1093 1093
9 10745681 10746685 - CePI673135_09g010940.1 Cec09g1094 1094
9 38818523 38839786 - CePI673135_09g021900.1 Cec09g2190 2190
10 5561127 5566443 + CePI673135_10g004630.1 Cec10g0463 463
10 5620531 5625072 - CePI673135_10g004690.1 Cec10g0469 469
1 11780220 11783733 - Chy1G010600.1 Chy01g01060 1060
1 11855974 11856984 - Chy1G010650.1 Chy01g01065 1065
1 11947004 11948041 - Chy1G010670.1 Chy01g01067 1067
1 11998816 12052383 - Chy1G010700.1 Chy01g01070 1070
1 12052576 12055185 + Chy1G010710.1 Chy01g01071 1071
6 22511495 22519423 - Chy6G123910.1 Chy06g01863 1863
6 22549187 22553646 - Chy6G123950.1 Chy06g01867 1867
10 5641805 5646790 + ClG42_10g0046100.10 Clacu10g0461 461
10 5701811 5706116 - ClG42_10g0046700.10 Clacu10g0467 467
9 10959648 10963429 - ClCG09G011120.1 Cla09g01037 1037
9 10965176 10970613 - ClCG09G011130.2 Cla09g01038 1038
9 10991971 10993314 - ClCG09G011140.2 Cla09g01039 1039
9 37924136 37945878 - ClCG09G020910.2 Cla09g02036 2036
9 37951455 37955943 + ClCG09G020920.1 Cla09g02037 2037
10 6020205 6026651 + ClCG10G004860.2 Cla10g00455 455
10 6082601 6087614 - ClCG10G004930.2 Cla10g00460 460
1 8087994 8091018 - CmaCh01G011040.1 Cma01g01104 1104
1 8093463 8111895 + CmaCh01G011050.1 Cma01g01105 1105
1 8113578 8114660 + CmaCh01G011060.1 Cma01g01106 1106
1 8121325 8122161 - CmaCh01G011080.1 Cma01g01108 1108
1 8127523 8130542 + CmaCh01G011100.1 Cma01g01110 1110
9 4950327 4953943 - CmaCh09G009760.1 Cma09g00976 976
9 4962417 4963349 - CmaCh09G009780.1 Cma09g00978 978
9 4967338 4968378 - CmaCh09G009790.1 Cma09g00979 979
16 7076658 7082191 - CmaCh16G009300.1 Cma16g00930 930
1 11546228 11550835 - MELO3C013104.2.1 Cme01g00979 979
1 11795192 11796590 + MELO3C013118.2.1 Cme01g00987 987
1 11852353 11853638 + MELO3C013120.2.1 Cme01g00989 989
1 11890755 11894215 + MELO3C013122.2.1 Cme01g00993 993
6 35441963 35447724 + MELO3C014150.2.1 Cme06g02815 2815
6 35492818 35497221 - MELO3C014156.2.1 Cme06g02820 2820
1 11719204 11722556 - PI0000012.1 Cmetu01g0078 78
1 12450976 12452376 + PI0020815.1 Cmetu01g0339 339
1 9418943 9424916 - CmoCh01G011500.1 Cmo01g01150 1150
1 9426876 9445040 + CmoCh01G011510.1 Cmo01g01151 1151
1 9446016 9447098 + CmoCh01G011520.1 Cmo01g01152 1152
1 9448181 9449224 - CmoCh01G011530.1 Cmo01g01153 1153
1 9450805 9454463 + CmoCh01G011540.1 Cmo01g01154 1154
6 5057361 5062375 + CmoCh06G008810.1 Cmo06g00881 881
6 5121072 5127820 + CmoCh06G008840.1 Cmo06g00884 884
6 5127883 5132486 - CmoCh06G008850.1 Cmo06g00885 885
9 5162124 5165448 - CmoCh09G009750.1 Cmo09g00975 975
9 5174793 5175746 - CmoCh09G009770.1 Cmo09g00977 977
9 5184736 5185692 - CmoCh09G009800.1 Cmo09g00980 980
16 6379544 6385587 - CmoCh16G009640.1 Cmo16g00964 964
10 5778758 5783735 + CmPI595203_10g012910.1 Cmu10g1291 1291
10 5838720 5843020 - CmPI595203_10g012960.1 Cmu10g1296 1296
6 229974 232379 - Conep06aG0003900.1 Cone6ag0039 39
6 248715 250907 + Conep06aG0004000.1 Cone6ag0040 40
9 178425 180362 - Conep09aG0004100.1 Cone9ag0041 41
9 180867 182088 + Conep09aG0004200.1 Cone9ag0042 42
9 239083 240652 + Conep09aG0004500.1 Cone9ag0045 45
9 241206 243077 + Conep09aG0004600.1 Cone9ag0046 46
14 9707466 9714694 - Conep14aG0121300.1 Cone14ag1189 1189
14 9715101 9719200 - Conep14aG0121400.1 Cone14ag1190 1190
15 9613201 9620263 - Conep15aG0123700.1 Cone15ag1208 1208
15 9621021 9625932 - Conep15aG0123800.1 Cone15ag1209 1209
2 5080446 5081492 + Cp4.1LG02g00790.1 Cpe02g00793 793
2 5083128 5083727 - Cp4.1LG02g00770.1 Cpe02g00794 794
2 5086275 5104203 - Cp4.1LG02g00740.1 Cpe02g00796 796
2 5106724 5111756 + Cp4.1LG02g00820.1 Cpe02g00797 797
6 5018677 5027339 - Cp4.1LG06g08690.1 Cpe06g00789 789
14 5728686 5734825 - Cp4.1LG14g07510.1 Cpe14g00751 751
9 10919000 10920004 - CrPI670011_09g010590.1 Cre09g1059 1059
10 6664315 6669646 + CrPI670011_10g006970.1 Cre10g0697 697
10 6731920 6737096 - CrPI670011_10g007010.1 Cre10g0701 701
3 3805928 3812120 + CsaV3_3G004520.1 Csa03g00452 452
3 3847900 3852392 - CsaV3_3G004580.1 Csa03g00458 458
7 8802671 8805281 - CsaV3_7G018820.1 Csa07g00991 991
7 9096184 9118575 + CsaV3_7G019860.1 Csa07g00996 996
7 9126835 9128453 + CsaV3_7G019890.1 Csa07g00999 999
7 9153111 9156855 + CsaV3_7G019910.1 Csa07g01001 1001
1 77676247 77677293 + Hsped.01g12420.1 Hepe01g1242 1242
2 24442793 24447289 - Lsi02G018680.1 Lsi02g01868 1868
2 24453382 24477621 + Lsi02G018690.1 Lsi02g01869 1869
2 24494413 24497792 + Lsi02G018710.1 Lsi02g01871 1871
2 24529337 24530471 + Lsi02G018730.1 Lsi02g01873 1873
2 24582531 24586767 + Lsi02G018760.1 Lsi02g01876 1876
5 6705611 6712221 + Lsi05G005400.1 Lsi05g00540 540
5 6765044 6769914 - Lsi05G005450.1 Lsi05g00545 545
10 12732618 12747931 + MC10g1109 Mch10g1390 1390
11 8650613 8651621 - MC11g1011 Mch11g1222 1222
11 8659715 8660734 - MC11g1013 Mch11g1224 1224
5 43330994 43331977 - Sed0009386.1 Sed05g3441 3441
7 42315823 42319184 - Sed0022155.2 Sed07g2707 2707
1 19087310 19093738 - Tan0001139.3 Tan01g1786 1786
1 84204512 84207233 - Tan0017935.1 Tan01g3133 3133
1 84344267 84345205 - Tan0008043.1 Tan01g3135 3135
1 84446826 84447809 - Tan0006514.1 Tan01g3137 3137
19 7378798 7386028 + Vvi19g584 Vvi19g584 584
19 7386092 7390777 - Vvi19g585 Vvi19g585 585
19 7392199 7394238 - Vvi19g586 Vvi19g586 586
19 7399627 7400371 + Vvi19g587 Vvi19g587 587
19 7430875 7431705 + Vvi19g588 Vvi19g588 588
19 7454668 7455712 - Vvi19g589 Vvi19g589 589
19 7471402 7478122 - Vvi19g590 Vvi19g590 590
19 7478513 7493598 - Vvi19g591 Vvi19g591 591
19 7494805 7501203 - Vvi19g592 Vvi19g592 592
19 7512780 7517479 + Vvi19g593 Vvi19g593 593
       

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