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
Vvi19g564 . . . . Bpe09g00157 . Bma10g00572 Bma13g01075 Cmo16g00944 . . . . . . . . . . . . . . . Cla10g00484 Cam10g0471 Cec10g0491 Cco10g0478 Clacu10g0490 Cmu10g1318 Cre10g0724 . Cone10ag1399 Cone8ag1554 Cone12ag1475 . Csa03g00483 . Cme06g02844 Blo07g00887 . Bda05g00702 Bda12g00930 . Bpe03g00777 . . . . . . Cma16g00908 . Car16g00883 . . Bhi11g00585 Tan01g1742 Cmetu06g0936 . Hepe06g0015 . . . . . . . . . Lsi05g00571 . Chy06g01839 .
Vvi19g565 Blo03g00544 . Bda07g00377 . . . . . . . Cma01g01116 . Car01g00986 . Sed01g2008 . Cpe02g00787 Bhi09g01690 Tan01g3117 Cmetu12g0552 . Hepe01g1252 Mch11g1210 . . . . . . . . Cone6ag0045 Cone9ag0054 . . . Csa07g01027 . . . . . . . . . Bma14g00325 . Cmo01g01162 . . . . . . . . . . . . . . Cla09g01029 Cam09g1084 Cec09g1083 Cco09g1104 . . Cre09g1049 . . Chy01g01051 Cme01g01003
Vvi19g566 . Blo03g01458 . Bda09g00407 Bpe09g00155 Bpe08g01114 . Bma13g01076 Cmo16g00945 Cmo06g00894 . . . . . . . . . . . . . . Cla10g00481 Cam10g0468 Cec10g0488 Cco10g0476 Clacu10g0488 Cmu10g1316 Cre10g0721 . Cone9ag0053 Cone14ag1175 Cone15ag1188 . Csa03g00482 . Cme06g02843 . Blo10g00846 . Bda12g00931 . . Bma07g01286 . Sed08g2983 . . . Cma16g00910 . Car16g00884 Cpe14g00735 . Bhi11g00583 Tan01g1744 Cmetu12g0825 . Hepe07g1278 . . . . . . . . . Lsi05g00569 . Chy06g01840 .
Vvi19g567 . . . . Bpe09g00154 . Bma10g00573 Bma13g01077 . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1176 Cone15ag1189 . . . . Blo07g00886 . . Bda12g00932 . Bpe03g00775 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g568 . . . . . . Bma10g00574 . . . Cma01g01115 . Car01g00985 . . . Cpe02g00788 Bhi09g01691 Tan01g3119 . . Hepe01g1251 Mch11g1212 . . . . . . . . . . Cone14ag1177 Cone15ag1190 Lsi02g01883 . . . Blo07g00885 . Bda05g00700 . . . . . . Cmo01g01161 . . . . . . . . . . . . . . Cla09g01031 Cam09g1086 Cec09g1085 Cco09g1106 . . Cre09g1051 . . Chy01g01052 Cme01g01002
Vvi19g569 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe03g00774 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g570 . . . . . . Bma10g00575 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1178 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g571 . . . . Bpe09g00153 . Bma10g00576 Bma13g01078 Cmo16g00946 Cmo06g00893 . Cma09g00968 . Car09g00883 Sed04g3701 Cpe06g00783 . Bhi09g01692 Tan01g3121 Cmetu01g0613 . Hepe01g1250 Mch11g1215 . Cla10g00480 Cam10g0467 Cec10g0487 Cco10g0475 Clacu10g0487 Cmu10g1315 Cre10g0720 Cone6ag0044 Cone9ag0052 Cone14ag1179 Cone15ag1191 Lsi02g01882 Csa03g00481 . Cme06g02842 Blo07g00884 Blo10g00848 Bda05g00699 Bda12g00933 . Bpe03g00773 . . Sed08g2981 . Cmo09g00969 . Cma16g00911 . Car16g00885 Cpe14g00736 . Bhi11g00582 Tan01g1745 Cmetu06g0127 . Hepe06g0017 . . Cla09g01032 Cam09g1087 Cec09g1086 Cco09g1107 . . Cre09g1052 Lsi05g00568 . Chy06g01841 .
Vvi19g572 . . . . . . Bma10g00577 Bma13g01079 . . . Cma09g00970 Car01g00984 Car09g00884 Sed08g1927 Cpe06g00784 Cpe02g00789 Bhi09g01693 Tan01g3123 Cmetu01g0215 . Hepe01g1249 Mch11g1216 . . . . . . . . . . . . Lsi02g01881 . . . . . Bda05g00698 Bda12g00934 . . . . . Cmo01g01160 Cmo09g00970 . . . . . . . . . . . . . Cla09g01033 Cam09g1088 Cec09g1087 Cco09g1108 . . Cre09g1053 . . Chy01g01054 Cme01g00999
Vvi19g573 . . . . . . Bma10g00578 . . Cmo06g00892 . . . . . . . . . . . . . . Cla10g00479 Cam10g0466 Cec10g0486 Cco10g0474 Clacu10g0486 Cmu10g1314 Cre10g0718 . . . Cone15ag1194 . Csa03g00480 . Cme06g02841 . . Bda05g00697 . . Bpe03g00772 . . Sed08g2980 . . . . . . . . Bhi11g00581 Tan01g1746 Cmetu06g1014 . Hepe06g0018 . . . . . . . . . Lsi05g00567 . Chy06g01842 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 55275650 55280033 - Bda021834.1 Bda05g00697 697
5 55282908 55283201 + Bda021835.1 Bda05g00698 698
5 55284756 55287959 - Bda021836.1 Bda05g00699 699
5 55291927 55293434 + Bda021837.1 Bda05g00700 700
5 55301536 55302288 - Bda021839.1 Bda05g00702 702
7 4768831 4771136 + Bda025463.1 Bda07g00377 377
9 5088201 5090591 + Bda030986.1 Bda09g00407 407
12 40421460 40422209 + Bda009475.1 Bda12g00930 930
12 40426887 40431713 + Bda009476.1 Bda12g00931 931
12 40442666 40443032 + Bda009477.1 Bda12g00932 932
12 40445432 40448581 + Bda009478.2 Bda12g00933 933
12 40449720 40450476 - Bda009479.1 Bda12g00934 934
9 45280825 45287836 + XM_039042270.1 Bhi09g01690 1690
9 45333948 45337665 - XM_039042273.1 Bhi09g01691 1691
9 45381381 45384822 + XM_039042271.1 Bhi09g01692 1692
9 45385755 45388276 - XM_039042274.1 Bhi09g01693 1693
11 13177700 13183957 - XM_039047169.1 Bhi11g00581 581
11 13198602 13202922 - XM_039047495.1 Bhi11g00582 582
11 13216714 13229007 - XM_039048731.1 Bhi11g00583 583
11 13309705 13310839 - XM_039047255.1 Bhi11g00585 585
3 21304521 21306750 - BLOR11725 Blo03g00544 544
3 41200009 41203639 + BLOR12639 Blo03g01458 1458
7 27602554 27605782 - BLOR18816 Blo07g00884 884
7 27613391 27618663 + BLOR18817 Blo07g00885 885
7 27619267 27619639 - BLOR18818 Blo07g00886 886
7 27634893 27635645 - BLOR18819 Blo07g00887 887
10 26957829 26962684 + BLOR02636 Blo10g00846 846
10 26971831 26975159 + BLOR02638 Blo10g00848 848
7 48502083 48509687 - Bma026558.1 Bma07g01286 1286
10 7101937 7102689 + Bma004277.1 Bma10g00572 572
10 7125140 7125503 + Bma030361 Bma10g00573 573
10 7126254 7127725 - Bma004279.2 Bma10g00574 574
10 7128773 7130112 + Bma004280.1 Bma10g00575 575
10 7131258 7134433 + Bma004281.2 Bma10g00576 576
10 7135969 7136262 - Bma004282.1 Bma10g00577 577
10 7138988 7143373 + Bma004283.1 Bma10g00578 578
13 43608302 43609054 + Bma010197.1 Bma13g01075 1075
13 43613466 43618290 + Bma010198.1 Bma13g01076 1076
13 43619957 43620321 + Bma010199.1 Bma13g01077 1077
13 43622710 43625766 + Bma010200.3 Bma13g01078 1078
13 43626896 43627678 - Bma010201.1 Bma13g01079 1079
14 4048103 4049270 - Bma010746.1 Bma14g00325 325
3 27722601 27726953 - Bpe012682.1 Bpe03g00772 772
3 27732158 27735310 - Bpe012683.1 Bpe03g00773 773
3 27737095 27738403 - Bpe012684.1 Bpe03g00774 774
3 27741607 27741952 - Bpe012685.1 Bpe03g00775 775
3 27747543 27748295 - Bpe012687.1 Bpe03g00777 777
8 13147235 13151158 - Bpe023240.1 Bpe08g01114 1114
9 1041049 1044233 - Bpe023826.1 Bpe09g00153 153
9 1045898 1046259 - Bpe026206 Bpe09g00154 154
9 1048257 1053102 - Bpe023827.2 Bpe09g00155 155
9 1059463 1060095 - Bpe023829.1 Bpe09g00157 157
9 11278403 11284787 + CaPI482276_09g010840.1 Cam09g1084 1084
9 11290324 11291764 - CaPI482276_09g010860.1 Cam09g1086 1086
9 11293730 11296034 + CaPI482276_09g010870.1 Cam09g1087 1087
9 11299654 11301839 - CaPI482276_09g010880.1 Cam09g1088 1088
10 7080610 7086644 - CaPI482276_10g004660.1 Cam10g0466 466
10 7090575 7095064 - CaPI482276_10g004670.1 Cam10g0467 467
10 7103458 7109562 - CaPI482276_10g004680.1 Cam10g0468 468
10 7144111 7144761 - CaPI482276_10g004710.1 Cam10g0471 471
1 9351986 9354762 + Carg22378-RA Car01g00984 984
1 9357427 9359203 + Carg22377-RA Car01g00985 985
1 9360653 9363210 - Carg22376-RA Car01g00986 986
9 5425859 5427743 + Carg12837-RA Car09g00883 883
9 5428070 5430252 - Carg12838-RA Car09g00884 884
16 6806077 6806742 + Carg27286-RA Car16g00883 883
16 6878531 6885112 + Carg26943-RA Car16g00884 884
16 6893524 6895591 + Carg26942-RA Car16g00885 885
9 10611258 10617652 + CcPI632755_09g011040.1 Cco09g1104 1104
9 10621452 10625209 - CcPI632755_09g011060.1 Cco09g1106 1106
9 10627031 10629329 + CcPI632755_09g011070.1 Cco09g1107 1107
9 10632925 10635109 - CcPI632755_09g011080.1 Cco09g1108 1108
10 5644616 5650638 - CcPI632755_10g004740.1 Cco10g0474 474
10 5656290 5660853 - CcPI632755_10g004750.1 Cco10g0475 475
10 5668453 5674906 - CcPI632755_10g004760.1 Cco10g0476 476
10 5710605 5711255 - CcPI632755_10g004780.1 Cco10g0478 478
9 10640753 10647272 + CePI673135_09g010830.1 Cec09g1083 1083
9 10652828 10654978 - CePI673135_09g010850.1 Cec09g1085 1085
9 10656903 10659209 + CePI673135_09g010860.1 Cec09g1086 1086
9 10662802 10664985 - CePI673135_09g010870.1 Cec09g1087 1087
10 5848571 5854658 - CePI673135_10g004860.1 Cec10g0486 486
10 5860083 5864598 - CePI673135_10g004870.1 Cec10g0487 487
10 5872665 5878731 - CePI673135_10g004880.1 Cec10g0488 488
10 5912195 5912845 - CePI673135_10g004910.1 Cec10g0491 491
1 11571685 11576561 + Chy1G010510.1 Chy01g01051 1051
1 11607770 11611471 - Chy1G010520.1 Chy01g01052 1052
1 11654090 11655739 - Chy1G010540.1 Chy01g01054 1054
6 22151171 22151818 + Chy6G123670.1 Chy06g01839 1839
6 22161272 22167222 + Chy6G123680.1 Chy06g01840 1840
6 22170550 22174519 + Chy6G123690.1 Chy06g01841 1841
6 22176298 22182191 + Chy6G123700.1 Chy06g01842 1842
10 5915552 5921641 - ClG42_10g0048600.10 Clacu10g0486 486
10 5925432 5929925 - ClG42_10g0048700.10 Clacu10g0487 487
10 5940462 5951495 - ClG42_10g0048800.10 Clacu10g0488 488
10 5979048 5979698 - ClG42_10g0049000.10 Clacu10g0490 490
9 10887289 10893967 + ClCG09G011030.1 Cla09g01029 1029
9 10897453 10900627 - ClCG09G011050.2 Cla09g01031 1031
9 10902276 10904962 + ClCG09G011060.1 Cla09g01032 1032
9 10908265 10910592 - ClCG09G011070.1 Cla09g01033 1033
10 6295566 6302294 - ClCG10G005120.2 Cla10g00479 479
10 6305701 6310651 - ClCG10G005130.1 Cla10g00480 480
10 6318383 6325208 - ClCG10G005140.1 Cla10g00481 481
10 6360105 6361954 - ClCG10G005170.2 Cla10g00484 484
1 8157018 8163501 + CmaCh01G011150.1 Cma01g01115 1115
1 8165005 8167534 - CmaCh01G011160.1 Cma01g01116 1116
9 4907174 4914564 + CmaCh09G009680.1 Cma09g00968 968
9 4915018 4917220 - CmaCh09G009700.1 Cma09g00970 970
16 6781618 6782283 + CmaCh16G009080.1 Cma16g00908 908
16 6805758 6812482 + CmaCh16G009100.1 Cma16g00910 910
16 6816861 6820509 + CmaCh16G009110.1 Cma16g00911 911
1 11983706 11985742 + MELO3C013128.2.1 Cme01g00999 999
1 12041787 12042960 + MELO3C013130.2.1 Cme01g01002 1002
1 12085466 12091092 - MELO3C013132.2.1 Cme01g01003 1003
6 35866375 35882484 - MELO3C014178.2.1 Cme06g02841 2841
6 35883916 35888336 - MELO3C014179.2.1 Cme06g02842 2842
6 35899186 35905751 - MELO3C014180.2.1 Cme06g02843 2843
6 35914585 35915669 - MELO3C014181.2.1 Cme06g02844 2844
1 11626255 11628665 - PI0018204.1 Cmetu01g0215 215
1 11621364 11624521 + PI0002166.1 Cmetu01g0613 613
6 26505337 26509761 + PI0015948.2 Cmetu06g0127 127
6 26487941 26488496 + PI0023041.1 Cmetu06g0936 936
6 26510769 26517414 + PI0025719.1 Cmetu06g1014 1014
12 11756662 11763814 + PI0024810.1 Cmetu12g0552 552
12 11777807 11783586 + PI0022890.1 Cmetu12g0825 825
1 9482710 9485255 + CmoCh01G011600.1 Cmo01g01160 1160
1 9487353 9490016 + CmoCh01G011610.1 Cmo01g01161 1161
1 9491669 9494323 - CmoCh01G011620.1 Cmo01g01162 1162
6 5248904 5253670 - CmoCh06G008920.1 Cmo06g00892 892
6 5255599 5258884 - CmoCh06G008930.1 Cmo06g00893 893
6 5271004 5283109 - CmoCh06G008940.1 Cmo06g00894 894
9 5115562 5127190 + CmoCh09G009690.1 Cmo09g00969 969
9 5126620 5128969 - CmoCh09G009700.1 Cmo09g00970 970
16 6074249 6074914 + CmoCh16G009440.1 Cmo16g00944 944
16 6114152 6120874 + CmoCh16G009450.1 Cmo16g00945 945
16 6125817 6128979 + CmoCh16G009460.1 Cmo16g00946 946
10 6039071 6045164 - CmPI595203_10g013140.1 Cmu10g1314 1314
10 6048960 6053453 - CmPI595203_10g013150.1 Cmu10g1315 1315
10 6061772 6075026 - CmPI595203_10g013160.1 Cmu10g1316 1316
10 6102580 6103230 - CmPI595203_10g013180.1 Cmu10g1318 1318
6 264119 267192 - Conep06aG0004400.1 Cone6ag0044 44
6 269272 271024 - Conep06aG0004500.1 Cone6ag0045 45
8 11648898 11650178 + Conep08aG0160700.1 Cone8ag1554 1554
9 262621 264719 - Conep09aG0005200.1 Cone9ag0052 52
9 266989 268434 - Conep09aG0005300.1 Cone9ag0053 53
9 268790 270526 - Conep09aG0005400.1 Cone9ag0054 54
10 10886244 10887600 + Conep10aG0144100.1 Cone10ag1399 1399
12 10549137 10550193 - Conep12aG0152700.1 Cone12ag1475 1475
14 9639992 9640372 + Conep14aG0119900.1 Cone14ag1175 1175
14 9640671 9641904 + Conep14aG0120000.1 Cone14ag1176 1176
14 9642178 9643828 - Conep14aG0120100.1 Cone14ag1177 1177
14 9644344 9646605 + Conep14aG0120200.1 Cone14ag1178 1178
14 9647390 9649506 + Conep14aG0120300.1 Cone14ag1179 1179
15 9543008 9546934 + Conep15aG0121700.1 Cone15ag1188 1188
15 9547380 9550575 + Conep15aG0121800.1 Cone15ag1189 1189
15 9548845 9550544 - Conep15aG0121900.1 Cone15ag1190 1190
15 9551535 9553607 + Conep15aG0122000.1 Cone15ag1191 1191
15 9560584 9564859 + Conep15aG0122300.1 Cone15ag1194 1194
2 5037682 5040443 + Cp4.1LG02g00810.1 Cpe02g00787 787
2 5041637 5044377 - Cp4.1LG02g00750.1 Cpe02g00788 788
2 5046029 5048521 - Cp4.1LG02g00720.1 Cpe02g00789 789
6 4970937 4973932 + Cp4.1LG06g08790.1 Cpe06g00783 783
6 4972712 4975869 - Cp4.1LG06g08710.1 Cpe06g00784 784
14 5493342 5500225 + Cp4.1LG14g07360.1 Cpe14g00735 735
14 5504346 5507737 + Cp4.1LG14g07350.1 Cpe14g00736 736
9 10821713 10828043 + CrPI670011_09g010490.1 Cre09g1049 1049
9 10831884 10837359 - CrPI670011_09g010510.1 Cre09g1051 1051
9 10837496 10839798 + CrPI670011_09g010520.1 Cre09g1052 1052
9 10842446 10844576 - CrPI670011_09g010530.1 Cre09g1053 1053
10 6935214 6941246 - CrPI670011_10g007180.1 Cre10g0718 718
10 6946818 6951288 - CrPI670011_10g007200.1 Cre10g0720 720
10 6959443 6965513 - CrPI670011_10g007210.1 Cre10g0721 721
10 7001235 7001885 - CrPI670011_10g007240.1 Cre10g0724 724
3 4047496 4053873 - CsaV3_3G004800.1 Csa03g00480 480
3 4054879 4059641 - CsaV3_3G004810.1 Csa03g00481 481
3 4062082 4068820 - CsaV3_3G004820.1 Csa03g00482 482
3 4074143 4076200 - CsaV3_3G004830.1 Csa03g00483 483
7 9593215 9604597 - CsaV3_7G021170.1 Csa07g01027 1027
1 77747062 77749252 + Hsped.01g12490.1 Hepe01g1249 1249
1 77751156 77753839 - Hsped.01g12500.1 Hepe01g1250 1250
1 77759219 77761842 + Hsped.01g12510.1 Hepe01g1251 1251
1 77766310 77772006 - Hsped.01g12520.1 Hepe01g1252 1252
6 466507 467124 + Hsped.06g00150.1 Hepe06g0015 15
6 507785 511864 + Hsped.06g00170.1 Hepe06g0017 17
6 519859 526950 + Hsped.06g00180.1 Hepe06g0018 18
7 38658413 38660080 - Hsped.07g12780.1 Hepe07g1278 1278
2 24686313 24688557 + Lsi02G018810.1 Lsi02g01881 1881
2 24687815 24692393 - Lsi02G018820.1 Lsi02g01882 1882
2 24695568 24698316 + Lsi02G018830.1 Lsi02g01883 1883
5 7027206 7034265 - Lsi05G005670.1 Lsi05g00567 567
5 7036514 7041950 - Lsi05G005680.1 Lsi05g00568 568
5 7044925 7051729 - Lsi05G005690.1 Lsi05g00569 569
5 7088026 7088676 - Lsi05G005710.1 Lsi05g00571 571
11 8575591 8580721 + MC11g1000 Mch11g1210 1210
11 8583417 8585559 - MC11g1001 Mch11g1212 1212
11 8597683 8600770 + MC11g1004 Mch11g1215 1215
11 8601544 8603883 - MC11g1005 Mch11g1216 1216
1 15022377 15031323 + Sed0016166.1 Sed01g2008 2008
4 45912552 45916091 - Sed0003517.1 Sed04g3701 3701
8 33690329 33698811 - Sed0024160.1 Sed08g1927 1927
8 40361954 40366650 - Sed0026759.2 Sed08g2980 2980
8 40368896 40379153 - Sed0010116.1 Sed08g2981 2981
8 40381126 40400244 - Sed0017318.2 Sed08g2983 2983
1 18603400 18604769 + Tan0018932.1 Tan01g1742 1742
1 18635900 18641999 + Tan0016799.1 Tan01g1744 1744
1 18644543 18648176 + Tan0001831.1 Tan01g1745 1745
1 18650024 18657353 + Tan0018179.1 Tan01g1746 1746
1 83999540 84007375 + Tan0015557.1 Tan01g3117 3117
1 84040061 84042073 - Tan0010717.1 Tan01g3119 3119
1 84094136 84096711 + Tan0006305.1 Tan01g3121 3121
1 84099830 84102694 - Tan0007298.1 Tan01g3123 3123
19 7169434 7170792 + Vvi19g564 Vvi19g564 564
19 7199187 7201533 + Vvi19g565 Vvi19g565 565
19 7211955 7217656 + Vvi19g566 Vvi19g566 566
19 7220527 7222925 + Vvi19g567 Vvi19g567 567
19 7223202 7225703 - Vvi19g568 Vvi19g568 568
19 7228122 7230884 + Vvi19g569 Vvi19g569 569
19 7231711 7233558 - Vvi19g570 Vvi19g570 570
19 7236472 7240677 + Vvi19g571 Vvi19g571 571
19 7244481 7247977 - Vvi19g572 Vvi19g572 572
19 7248620 7255469 + Vvi19g573 Vvi19g573 573
       

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