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
Vvi2g62 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g63 Blo02g01127 . . Bda08g00498 Bpe05g00666 . . . . Cmo16g00624 . . . . . Cpe14g00486 Cpe05g00632 . . . . . . . Cla07g00737 Cam07g0790 Cec07g0855 Cco07g0825 Clacu07g0771 Cmu07g0780 Cre07g1131 . . Cone6ag0820 Cone9ag0819 . . . Cme07g01607 . . . . . . Bma05g00841 . . Cmo02g01109 . . Cma16g00575 . . . . . . . . . . . . . . . . . . . Csa04g00619 Chy07g01193 .
Vvi2g64 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g65 . Blo03g00231 Bda06g00126 . . Bpe07g00089 . . . . . . . . . . Cpe05g00630 . . . . . . . . . . . . . . . Cone12ag0274 . Cone9ag0820 . . . . . . . . . . . . . Cmo02g01113 Cmo15g01113 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g66 . . Bda06g00127 . . Bpe07g00088 . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0267 Cone12ag0273 Cone6ag0821 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g67 Blo02g01128 . Bda06g00128 Bda08g00496 Bpe05g00667 Bpe07g00087 . . . . . . . . . . . . . . . . . . Cla07g00736 Cam07g0789 Cec07g0854 Cco07g0824 Clacu07g0770 Cmu07g0779 Cre07g1130 . . . . . . . Cme07g01606 . . . . . . Bma05g00842 Bma12g00059 . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00620 Chy07g01192 .
Vvi2g68 . . . . . . . . . . Cma02g01415 . Car02g01185 . . . Cpe05g00367 . . . . . . . . . . . . . . . . Cone6ag0822 Cone9ag0822 . Csa05g00228 Chy09g01272 . . Blo19g00352 . . . . . . . Cmo02g01444 . . . . . . . Bhi12g00172 . . . . . . Cla01g00211 Cam01g0216 Cec01g0210 Cco01g0214 Clacu01g0211 Cmu01g0205 Cre09g2302 Lsi09g00199 . . Cme09g01815
Vvi2g69 Blo02g01129 . . Bda08g00495 Bpe05g00668 . Bma07g01676 Bma14g00620 . . Cma02g01414 Cma15g01258 Car02g01184 Car15g01135 . . Cpe05g00368 . . . . . . . . . . . . . . Cone8ag0266 Cone12ag0271 . . . Csa05g00227 Chy09g01273 . . Blo19g00353 Bda07g00470 Bda09g00022 Bpe08g01511 Bpe11g00648 Bma05g00843 . . Cmo02g01443 Cmo15g01326 . . . . . Cpe13g00127 Bhi12g00171 . . Lac11g2032 Hepe06g1501 . Lcy12g1594 Cla01g00210 Cam01g0215 Cec01g0209 Cco01g0213 Clacu01g0210 Cmu01g0204 Cre09g2303 Lsi09g00198 . . Cme09g01816
Vvi2g70 . . . . . . . Bma14g00621 . . Cma02g01412 Cma15g01259 Car02g01183 Car15g01136 . . . . . . . . . . . . . . . . . Cone8ag0265 Cone12ag0270 . . . Csa05g00225 Chy09g01275 . . . . . . Bpe11g00647 . . . Cmo02g01441 Cmo15g01328 . . . . . . Bhi12g00170 . . Lac11g2031 Hepe06g1500 . Lcy12g1593 Cla01g00208 Cam01g0213 Cec01g0208 Cco01g0211 Clacu01g0208 Cmu01g0203 Cre09g2304 Lsi09g00196 . . Cme09g01818
Vvi2g71 . Blo03g00233 Bda06g00130 . Bpe05g00670 Bpe07g00085 . Bma14g00622 . Cmo16g00622 . . . . . Cpe14g00484 . . . . . . . . Cla07g00729 Cam07g0783 Cec07g0848 Cco07g0819 Clacu07g0766 Cmu07g0773 Cre07g1125 . Cone12ag0269 . Cone9ag0824 . . . Cme07g01600 . . Bda07g00469 . . Bpe11g00646 . Bma12g00058 . . . . Cma16g00570 . . . . . . . . . . . . . . . . . . . Csa04g00624 Chy07g01190 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 1941965 1943465 - Bda023321.1 Bda06g00126 126
6 1946449 1951748 - Bda023322.1 Bda06g00127 127
6 1953920 1957174 - Bda023323.2 Bda06g00128 128
6 1979836 1980327 - Bda023326.1 Bda06g00130 130
7 5972933 5973508 + Bda025570.1 Bda07g00469 469
7 5980642 5982600 + Bda025571.1 Bda07g00470 470
8 5061305 5063074 + Bda024947.1 Bda08g00495 495
8 5064205 5069719 + Bda024948.1 Bda08g00496 496
8 5073205 5078022 + Bda033808 Bda08g00498 498
9 362728 364730 + Bda030541.3 Bda09g00022 22
12 4940567 4948214 + XM_039019290.1 Bhi12g00170 170
12 4962884 4967816 + XM_039020134.1 Bhi12g00171 171
12 4967972 4973404 - XM_039020135.1 Bhi12g00172 172
2 42570842 42575592 - BLOR10857 Blo02g01127 1127
2 42626011 42629081 - BLOR10858 Blo02g01128 1128
2 42630962 42633016 - BLOR10859 Blo02g01129 1129
3 5123770 5138837 - BLOR11412 Blo03g00231 231
3 5145758 5146327 - BLOR11414 Blo03g00233 233
19 22685567 22690182 + BLOR09695 Blo19g00352 352
19 22719825 22721855 - BLOR09696 Blo19g00353 353
5 45960657 45965482 - Bma021956.1 Bma05g00841 841
5 45967363 45970046 - Bma021957.1 Bma05g00842 842
5 45971441 45972559 - Bma021958.1 Bma05g00843 843
7 52323820 52325847 - Bma026973.1 Bma07g01676 1676
12 1129864 1130442 + Bma006928.1 Bma12g00058 58
12 1144942 1148190 + Bma006929.1 Bma12g00059 59
14 6697194 6699161 - Bma011060.1 Bma14g00620 620
14 6700975 6703437 - Bma011061.1 Bma14g00621 621
14 6719072 6719593 - Bma011064.1 Bma14g00622 622
5 20372967 20377796 - Bpe018079.1 Bpe05g00666 666
5 20380044 20383061 - Bpe018080.1 Bpe05g00667 667
5 20383985 20386009 - Bpe018081.1 Bpe05g00668 668
5 20392141 20392476 - Bpe018083.1 Bpe05g00670 670
7 632406 633074 + Bpe020898.1 Bpe07g00085 85
7 641315 644579 + Bpe020900.1 Bpe07g00087 87
7 646425 651860 + Bpe020901.1 Bpe07g00088 88
7 653025 655199 + Bpe020902.1 Bpe07g00089 89
8 15787523 15789523 - Bpe023622.2 Bpe08g01511 1511
11 4979467 4979955 + Bpe024775 Bpe11g00646 646
11 4984657 4987286 + Bpe004003.1 Bpe11g00647 647
11 4989073 4991034 + Bpe004004.1 Bpe11g00648 648
1 2466214 2473273 + CaPI482276_01g002130.1 Cam01g0213 213
1 2489053 2491071 + CaPI482276_01g002150.1 Cam01g0215 215
1 2492578 2499030 - CaPI482276_01g002160.1 Cam01g0216 216
7 19599165 19599743 + CaPI482276_07g007830.1 Cam07g0783 783
7 19791871 19795886 + CaPI482276_07g007890.1 Cam07g0789 789
7 19800412 19810850 + CaPI482276_07g007900.1 Cam07g0790 790
2 8059171 8064488 + Carg02565-RA Car02g01183 1183
2 8067533 8071660 + Carg02564-RA Car02g01184 1184
2 8072173 8075452 - Carg02563-RA Car02g01185 1185
15 8946945 8948960 - Carg21259-RA Car15g01135 1135
15 8955302 8962904 - Carg21260-RA Car15g01136 1136
1 2063020 2070094 + CcPI632755_01g002110.1 Cco01g0211 211
1 2092341 2094359 + CcPI632755_01g002130.1 Cco01g0213 213
1 2095811 2102335 - CcPI632755_01g002140.1 Cco01g0214 214
7 18884472 18884789 + CcPI632755_07g008190.1 Cco07g0819 819
7 19066962 19071008 + CcPI632755_07g008240.1 Cco07g0824 824
7 19074383 19080449 + CcPI632755_07g008250.1 Cco07g0825 825
1 2064022 2071057 + CePI673135_01g002080.1 Cec01g0208 208
1 2086669 2088687 + CePI673135_01g002090.1 Cec01g0209 209
1 2090195 2096556 - CePI673135_01g002100.1 Cec01g0210 210
7 20827084 20827662 + CePI673135_07g008480.1 Cec07g0848 848
7 20990192 20994243 + CePI673135_07g008540.1 Cec07g0854 854
7 20997626 21005686 + CePI673135_07g008550.1 Cec07g0855 855
7 16760609 16763395 + Chy7G140200.1 Chy07g01190 1190
7 16775357 16779522 + Chy7G140220.1 Chy07g01192 1192
7 16782405 16787811 + Chy7G140230.1 Chy07g01193 1193
9 14731851 14735928 + Chy9G169880.1 Chy09g01272 1272
9 14737279 14739291 - Chy9G169890.1 Chy09g01273 1273
9 14751470 14758436 - Chy9G169910.1 Chy09g01275 1275
1 2083291 2090337 + ClG42_01g0020800.10 Clacu01g0208 208
1 2106006 2108024 + ClG42_01g0021000.10 Clacu01g0210 210
1 2109526 2115894 - ClG42_01g0021100.10 Clacu01g0211 211
7 19261093 19261671 + ClG42_07g0076600.10 Clacu07g0766 766
7 19454610 19458632 + ClG42_07g0077000.10 Clacu07g0770 770
7 19461858 19467948 + ClG42_07g0077100.10 Clacu07g0771 771
1 2106098 2113308 + ClCG01G002130.1 Cla01g00208 208
1 2129348 2131366 + ClCG01G002150.1 Cla01g00210 210
1 2132868 2139920 - ClCG01G002160.2 Cla01g00211 211
7 20336631 20337209 + ClCG07G007650.1 Cla07g00729 729
7 20533736 20537758 + ClCG07G007740.2 Cla07g00736 736
7 20540932 20547204 + ClCG07G007750.2 Cla07g00737 737
2 8153476 8158815 + CmaCh02G014120.1 Cma02g01412 1412
2 8164543 8166564 + CmaCh02G014140.1 Cma02g01414 1414
2 8167068 8171607 - CmaCh02G014150.1 Cma02g01415 1415
15 7990729 7993080 - CmaCh15G012580.1 Cma15g01258 1258
15 7999446 8007699 - CmaCh15G012590.1 Cma15g01259 1259
16 2936259 2936828 + CmaCh16G005700.1 Cma16g00570 570
16 2963731 2969562 + CmaCh16G005750.1 Cma16g00575 575
7 21789416 21790255 + MELO3C016325.2.1 Cme07g01600 1600
7 21853197 21857723 + MELO3C016330.2.1 Cme07g01606 1606
7 21860264 21866335 + MELO3C016331.2.1 Cme07g01607 1607
9 22470824 22474493 + MELO3C005726.2.1 Cme09g01815 1815
9 22475524 22480493 - MELO3C005727.2.1 Cme09g01816 1816
9 22490599 22497538 - MELO3C005729.2.1 Cme09g01818 1818
2 6698916 6705964 - CmoCh02G011090.1 Cmo02g01109 1109
2 6722890 6726936 - CmoCh02G011130.1 Cmo02g01113 1113
2 8501254 8506445 + CmoCh02G014410.1 Cmo02g01441 1441
2 8511871 8513892 + CmoCh02G014430.1 Cmo02g01443 1443
2 8514396 8517645 - CmoCh02G014440.1 Cmo02g01444 1444
15 7707420 7711805 + CmoCh15G011130.1 Cmo15g01113 1113
15 9096400 9098938 - CmoCh15G013260.1 Cmo15g01326 1326
15 9105487 9113613 - CmoCh15G013280.1 Cmo15g01328 1328
16 3054006 3054584 + CmoCh16G006220.1 Cmo16g00622 622
16 3064166 3071067 + CmoCh16G006240.1 Cmo16g00624 624
1 2036450 2043497 + CmPI595203_01g002030.1 Cmu01g0203 203
1 2059160 2061178 + CmPI595203_01g002040.1 Cmu01g0204 204
1 2062680 2069054 - CmPI595203_01g002050.1 Cmu01g0205 205
7 19471800 19472378 + CmPI595203_07g007730.1 Cmu07g0773 773
7 19665252 19669275 + CmPI595203_07g007790.1 Cmu07g0779 779
7 19672498 19678578 + CmPI595203_07g007800.1 Cmu07g0780 780
6 4175897 4180519 - Conep06aG0084400.1 Cone6ag0820 820
6 4183029 4188921 - Conep06aG0084500.1 Cone6ag0821 821
6 4196410 4204023 + Conep06aG0084600.1 Cone6ag0822 822
8 1540852 1543209 + Conep08aG0027800.1 Cone8ag0265 265
8 1547171 1551594 + Conep08aG0027900.1 Cone8ag0266 266
8 1552476 1557016 + Conep08aG0028000.1 Cone8ag0267 267
9 3950168 3955074 - Conep09aG0083700.1 Cone9ag0819 819
9 3963510 3966528 - Conep09aG0083800.1 Cone9ag0820 820
9 3979252 3981475 + Conep09aG0084000.1 Cone9ag0822 822
9 3987362 3988217 - Conep09aG0084200.1 Cone9ag0824 824
12 1452283 1452929 + Conep12aG0027900.1 Cone12ag0269 269
12 1453637 1459732 + Conep12aG0028000.1 Cone12ag0270 270
12 1463553 1467964 + Conep12aG0028100.1 Cone12ag0271 271
12 1472244 1475939 + Conep12aG0028300.1 Cone12ag0273 273
12 1476518 1479130 + Conep12aG0028400.1 Cone12ag0274 274
5 2073891 2078102 + Cp4.1LG05g03080.1 Cpe05g00367 367
5 2078624 2080645 - Cp4.1LG05g02970.1 Cpe05g00368 368
5 3845536 3855121 + Cp4.1LG05g06310.1 Cpe05g00630 630
5 3863595 3871930 + Cp4.1LG05g06300.1 Cpe05g00632 632
13 921310 923325 + Cp4.1LG13g01280.1 Cpe13g00127 127
14 3069444 3070031 + Cp4.1LG14g02290.1 Cpe14g00484 484
14 3079211 3088297 + Cp4.1LG14g02320.1 Cpe14g00486 486
7 22838183 22838764 + CrPI670011_07g011250.1 Cre07g1125 1125
7 23013885 23017935 + CrPI670011_07g011300.1 Cre07g1130 1130
7 23021300 23027485 + CrPI670011_07g011310.1 Cre07g1131 1131
9 42219932 42226485 + CrPI670011_09g023020.1 Cre09g2302 2302
9 42227991 42230009 - CrPI670011_09g023030.1 Cre09g2303 2303
9 42245694 42252824 - CrPI670011_09g023040.1 Cre09g2304 2304
4 4100956 4107788 - CsaV3_4G006190.1 Csa04g00619 619
4 4109551 4114326 - CsaV3_4G006200.1 Csa04g00620 620
4 4146573 4148757 - CsaV3_4G006240.1 Csa04g00624 624
5 1368619 1375888 + CsaV3_5G002250.1 Csa05g00225 225
5 1385520 1390734 + CsaV3_5G002270.1 Csa05g00227 227
5 1391557 1395469 - CsaV3_5G002280.1 Csa05g00228 228
6 65617585 65625312 + Hsped.06g15000.1 Hepe06g1500 1500
6 65636823 65638838 + Hsped.06g15010.1 Hepe06g1501 1501
11 35958290 35966174 + Lag0032669.1 Lac11g2031 2031
11 35981249 35983260 + Lag0032670.1 Lac11g2032 2032
12 36096057 36102741 + Maker00029181 Lcy12g1593 1593
12 36113298 36117931 + Maker00029277 Lcy12g1594 1594
9 2073879 2081422 + Lsi09G001960.1 Lsi09g00196 196
9 2095327 2097339 + Lsi09G001980.1 Lsi09g00198 198
9 2099048 2111197 - Lsi09G001990.1 Lsi09g00199 199
2 709706 709739 + Vvi2g62 Vvi2g62 62
2 709762 719214 - Vvi2g63 Vvi2g63 63
2 721667 721817 + Vvi2g64 Vvi2g64 64
2 722226 726962 - Vvi2g65 Vvi2g65 65
2 727513 734302 - Vvi2g66 Vvi2g66 66
2 734376 743551 - Vvi2g67 Vvi2g67 67
2 753240 756161 + Vvi2g68 Vvi2g68 68
2 757935 763421 - Vvi2g69 Vvi2g69 69
2 765534 773252 - Vvi2g70 Vvi2g70 70
2 775164 779587 - Vvi2g71 Vvi2g71 71
       

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