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
Vvi2g12 . . . . . Bpe07g00103 . Bma14g00607 . . Cma02g01003 Cma15g01239 . Car15g01116 . . Cpe05g00349 . . . . . . . . . . . . . . . Cone12ag0296 . . . Csa05g00265 Chy09g01243 . . . Bda07g00483 . . Bpe11g00660 . . . Cmo02g01472 Cmo15g01303 . . . . . Cpe13g00146 Bhi12g00284 . . . . . . Cla01g00249 Cam01g0254 Cec01g0246 Cco01g0260 Clacu01g0252 Cmu01g0242 Cre09g2267 Lsi09g00240 . . Cme09g01778
Vvi2g13 . . . . . . Bma07g01663 . . Cmo16g00656 . . . . . Cpe14g00511 . . . . . . . . Cla07g00785 Cam07g0845 Cec07g0897 Cco07g0880 Clacu07g0820 Cmu07g0824 Cre07g1181 . . Cone6ag0789 Cone9ag0791 . . . Cme07g01639 . . . Bda09g00033 . . . . . . . . Cma16g00601 . . . . . . . . . . . . . . . . . . . . Chy07g01224 .
Vvi2g14 Blo02g01112 . Bda06g00114 Bda08g00514 Bpe05g00648 . Bma07g01664 . Cmo06g01099 . . . Car02g01207 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma05g00821 Bma12g00072 . . . . . Car06g00910 . . . . . . . . . . . . . . . . . . . . .
Vvi2g15 Blo02g01113 Blo03g00218 Bda06g00116 Bda08g00513 Bpe05g00649 Bpe07g00102 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0791 Cone9ag0793 . . . . . . . . . . Bma05g00822 Bma12g00071 . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00586 . .
Vvi2g16 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g17 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g18 . . . . . . . . . . Cma02g01437 Cma15g01240 Car02g01205 Car15g01117 . . Cpe05g00350 . . . . . . . . . . . . . . Cone8ag0289 Cone12ag0295 Cone6ag0794 . . Csa05g00264 Chy09g01244 . . Blo19g00330 . . . . . . . Cmo02g01471 Cmo15g01305 . . . . . Cpe13g00145 Bhi12g00287 . . Lac11g2070 Hepe06g1527 . Lcy12g1632 Cla01g00248 Cam01g0252 Cec01g0245 Cco01g0258 Clacu01g0250 Cmu01g0240 Cre09g2268 Lsi09g00238 . . Cme09g01779
Vvi2g19 . . . . . . . Bma14g00606 . . . Cma15g01241 . Car15g01118 . . . . . . . . . . . . . . . . . Cone8ag0288 Cone12ag0294 . . . Csa05g00262 Chy09g01245 . . . . . . Bpe11g00661 . . . . Cmo15g01306 . . . . . Cpe13g00144 Bhi12g00288 . . Lac11g2069 Hepe06g1526 . Lcy12g1631 Cla01g00247 Cam01g0251 Cec01g0244 Cco01g0257 Clacu01g0249 Cmu01g0239 Cre09g2269 Lsi09g00237 . . Cme09g01780
Vvi2g20 . . . . . . . Bma14g00605 . . Cma02g01435 Cma15g01242 Car02g01204 Car15g01119 . . Cpe05g00352 . . . . . . . . . . . . . . Cone8ag0287 Cone12ag0293 Cone6ag0795 . . Csa05g00261 Chy09g01246 . . . . . . Bpe11g00662 . . . Cmo02g01470 Cmo15g01307 . . . . . Cpe13g00143 Bhi12g00289 . . Lac11g2068 Hepe06g1525 . Lcy12g1629 Cla01g00246 Cam01g0250 Cec01g0243 Cco01g0256 Clacu01g0248 Cmu01g0238 Cre09g2270 Lsi09g00236 . . Cme09g01781
Vvi2g21 Blo02g01114 Blo03g00219 . Bda08g00512 Bpe05g00650 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0292 Cone6ag0796 . . . . . . . . . . . Bma05g00823 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 1838932 1840575 - Bda023309.1 Bda06g00114 114
6 1847783 1849391 - Bda023311.1 Bda06g00116 116
7 6067217 6068560 - Bda025585.1 Bda07g00483 483
8 5182295 5184335 - Bda024967.1 Bda08g00512 512
8 5191602 5193250 + Bda024968.2 Bda08g00513 513
8 5194621 5196347 + Bda024969.1 Bda08g00514 514
9 480857 482881 + Bda030553.1 Bda09g00033 33
12 8202167 8206322 - XM_039020185.1 Bhi12g00284 284
12 8210048 8223584 - XM_039018576.1 Bhi12g00287 287
12 8238401 8246590 + XM_039018497.1 Bhi12g00288 288
12 8327684 8402380 - XM_039018947.1 Bhi12g00289 289
2 42178803 42182458 - BLOR10842 Blo02g01112 1112
2 42265109 42266743 - BLOR10843 Blo02g01113 1113
2 42271559 42279561 + BLOR10844 Blo02g01114 1114
3 4954457 4960847 - BLOR11399 Blo03g00218 218
3 4968387 4970196 + BLOR11400 Blo03g00219 219
19 21899238 21907714 + BLOR09673 Blo19g00330 330
5 45575330 45577106 - Bma021931.1 Bma05g00821 821
5 45578562 45582135 - Bma021932.1 Bma05g00822 822
5 45584304 45586368 + Bma031210 Bma05g00823 823
7 52220433 52222580 + Bma026960.1 Bma07g01663 1663
7 52224666 52225826 + Bma026961.1 Bma07g01664 1664
12 1271464 1272249 + Bma006941.1 Bma12g00071 71
12 1278083 1279893 + Bma006942.1 Bma12g00072 72
14 6581718 6583006 + Bma011044.1 Bma14g00605 605
14 6586450 6591438 - Bma011045.1 Bma14g00606 606
14 6595365 6596740 + Bma011046.1 Bma14g00607 607
5 20287609 20289360 - Bpe018063.1 Bpe05g00648 648
5 20290958 20292338 - Bpe018064.1 Bpe05g00649 649
5 20295745 20297795 + Bpe018065.1 Bpe05g00650 650
7 737953 739579 + Bpe020916.1 Bpe07g00102 102
7 741421 742672 + Bpe020917.1 Bpe07g00103 103
11 5072254 5073508 - Bpe004017.1 Bpe11g00660 660
11 5077561 5082605 + Bpe004018.2 Bpe11g00661 661
11 5086761 5088042 - Bpe004019.1 Bpe11g00662 662
1 2812638 2814680 + CaPI482276_01g002500.1 Cam01g0250 250
1 2830943 2839586 - CaPI482276_01g002510.1 Cam01g0251 251
1 2841420 2850669 + CaPI482276_01g002520.1 Cam01g0252 252
1 2856386 2858013 + CaPI482276_01g002540.1 Cam01g0254 254
7 21162646 21167149 - CaPI482276_07g008450.1 Cam07g0845 845
2 8172685 8173926 + Carg02544-RA Car02g01204 1204
2 8177415 8183729 + Carg02543-RA Car02g01205 1205
2 8189301 8191116 + Carg02541-RA Car02g01207 1207
6 7036743 7041396 - Carg24655-RA Car06g00910 910
15 8804557 8806945 - Carg16626-RA Car15g01116 1116
15 8809738 8821133 - Carg16625-RA Car15g01117 1117
15 8821993 8830182 + Carg16624-RA Car15g01118 1118
15 8838069 8839657 - Carg16623-RA Car15g01119 1119
1 2441688 2443716 + CcPI632755_01g002560.1 Cco01g0256 256
1 2460073 2468632 - CcPI632755_01g002570.1 Cco01g0257 257
1 2470472 2479880 + CcPI632755_01g002580.1 Cco01g0258 258
1 2485461 2487090 + CcPI632755_01g002600.1 Cco01g0260 260
7 20494914 20500056 - CcPI632755_07g008800.1 Cco07g0880 880
1 2416515 2418557 + CePI673135_01g002430.1 Cec01g0243 243
1 2436805 2445271 - CePI673135_01g002440.1 Cec01g0244 244
1 2445406 2454679 + CePI673135_01g002450.1 Cec01g0245 245
1 2460413 2462039 + CePI673135_01g002460.1 Cec01g0246 246
7 22282106 22286805 - CePI673135_07g008970.1 Cec07g0897 897
7 17035687 17040250 - Chy7G140540.1 Chy07g01224 1224
9 14482230 14487739 - Chy9G169590.1 Chy09g01243 1243
9 14487792 14496006 - Chy9G169600.1 Chy09g01244 1244
9 14497849 14504477 + Chy9G169610.1 Chy09g01245 1245
9 14518057 14520078 - Chy9G169620.1 Chy09g01246 1246
1 2431310 2433327 + ClG42_01g0024800.10 Clacu01g0248 248
1 2449344 2459694 - ClG42_01g0024900.10 Clacu01g0249 249
1 2459757 2469030 + ClG42_01g0025000.10 Clacu01g0250 250
1 2474712 2476339 + ClG42_01g0025200.10 Clacu01g0252 252
7 20871049 20875748 - ClG42_07g0082000.10 Clacu07g0820 820
1 2478455 2480716 + ClCG01G002510.1 Cla01g00246 246
1 2502331 2509143 - ClCG01G002520.2 Cla01g00247 247
1 2511127 2522414 + ClCG01G002530.2 Cla01g00248 248
1 2527795 2529422 + ClCG01G002540.2 Cla01g00249 249
7 22001348 22006866 - ClCG07G008230.2 Cla07g00785 785
2 5963564 5966209 - CmaCh02G010030.1 Cma02g01003 1003
2 8264427 8265643 + CmaCh02G014350.1 Cma02g01435 1435
2 8269234 8276534 + CmaCh02G014370.1 Cma02g01437 1437
15 7852624 7855654 - CmaCh15G012390.1 Cma15g01239 1239
15 7856949 7868815 - CmaCh15G012400.1 Cma15g01240 1240
15 7869818 7877626 + CmaCh15G012410.1 Cma15g01241 1241
15 7884926 7886384 - CmaCh15G012420.1 Cma15g01242 1242
16 3103867 3107126 - CmaCh16G006010.1 Cma16g00601 601
7 22131824 22137112 - MELO3C016363.2.1 Cme07g01639 1639
9 22224576 22227642 - MELO3C005692.2.1 Cme09g01778 1778
9 22230065 22239005 - MELO3C005693.2.1 Cme09g01779 1779
9 22239839 22246907 + MELO3C005694.2.1 Cme09g01780 1780
9 22260740 22262382 - MELO3C005695.2.1 Cme09g01781 1781
2 8625409 8626623 + CmoCh02G014700.1 Cmo02g01470 1470
2 8630208 8637386 + CmoCh02G014710.1 Cmo02g01471 1471
2 8638743 8643687 + CmoCh02G014720.1 Cmo02g01472 1472
6 8461578 8466736 - CmoCh06G010990.1 Cmo06g01099 1099
15 8944516 8946309 - CmoCh15G013030.1 Cmo15g01303 1303
15 8949684 8960989 - CmoCh15G013050.1 Cmo15g01305 1305
15 8961854 8970781 + CmoCh15G013060.1 Cmo15g01306 1306
15 8978851 8980653 - CmoCh15G013070.1 Cmo15g01307 1307
16 3238168 3243114 - CmoCh16G006560.1 Cmo16g00656 656
1 2384239 2386259 + CmPI595203_01g002380.1 Cmu01g0238 238
1 2402263 2412589 - CmPI595203_01g002390.1 Cmu01g0239 239
1 2412652 2421921 + CmPI595203_01g002400.1 Cmu01g0240 240
1 2427604 2429231 + CmPI595203_01g002420.1 Cmu01g0242 242
7 21084863 21089562 - CmPI595203_07g008240.1 Cmu07g0824 824
6 4014721 4016922 - Conep06aG0081300.1 Cone6ag0789 789
6 4025813 4029396 - Conep06aG0081500.1 Cone6ag0791 791
6 4035589 4037760 - Conep06aG0081800.1 Cone6ag0794 794
6 4041890 4043241 - Conep06aG0081900.1 Cone6ag0795 795
6 4047446 4049732 + Conep06aG0082000.1 Cone6ag0796 796
8 1657373 1658565 + Conep08aG0030200.1 Cone8ag0287 287
8 1660045 1665199 - Conep08aG0030300.1 Cone8ag0288 288
8 1665217 1676330 + Conep08aG0030400.1 Cone8ag0289 289
9 3797182 3800140 - Conep09aG0080900.1 Cone9ag0791 791
9 3805128 3808801 - Conep09aG0081100.1 Cone9ag0793 793
12 1583041 1586042 - Conep12aG0030400.1 Cone12ag0292 292
12 1593068 1593889 + Conep12aG0030500.1 Cone12ag0293 293
12 1596705 1602543 - Conep12aG0030600.1 Cone12ag0294 294
12 1602814 1608909 + Conep12aG0030700.1 Cone12ag0295 295
12 1612615 1614737 + Conep12aG0030800.1 Cone12ag0296 296
5 1953671 1956838 - Cp4.1LG05g03230.1 Cpe05g00349 349
5 1957686 1964476 - Cp4.1LG05g03270.1 Cpe05g00350 350
5 1967766 1969247 - Cp4.1LG05g03240.1 Cpe05g00352 352
13 1032339 1033411 + Cp4.1LG13g01430.1 Cpe13g00143 143
13 1043943 1051851 - Cp4.1LG13g01480.1 Cpe13g00144 144
13 1057094 1064464 + Cp4.1LG13g01410.1 Cpe13g00145 145
13 1065851 1069602 + Cp4.1LG13g01370.1 Cpe13g00146 146
14 3232995 3237945 - Cp4.1LG14g02060.1 Cpe14g00511 511
7 24573304 24577992 - CrPI670011_07g011810.1 Cre07g1181 1181
9 41855601 41857229 - CrPI670011_09g022670.1 Cre09g2267 2267
9 41862906 41872164 - CrPI670011_09g022680.1 Cre09g2268 2268
9 41872299 41880785 + CrPI670011_09g022690.1 Cre09g2269 2269
9 41899381 41901179 - CrPI670011_09g022700.1 Cre09g2270 2270
4 3856617 3860730 + CsaV3_4G005860.1 Csa04g00586 586
5 1587303 1590056 + CsaV3_5G002610.1 Csa05g00261 261
5 1601017 1608964 - CsaV3_5G002620.1 Csa05g00262 262
5 1610588 1618606 + CsaV3_5G002640.1 Csa05g00264 264
5 1620832 1624667 + CsaV3_5G002650.1 Csa05g00265 265
6 65934231 65936424 + Hsped.06g15250.1 Hepe06g1525 1525
6 65965597 65975218 - Hsped.06g15260.1 Hepe06g1526 1526
6 65976364 65991419 + Hsped.06g15270.1 Hepe06g1527 1527
11 36514627 36516301 + Lag0032706.1 Lac11g2068 2068
11 36550793 36562540 - Lag0032707.1 Lac11g2069 2069
11 36562602 36570886 + Lag0032708.1 Lac11g2070 2070
12 36608515 36610272 + Maker00029327 Lcy12g1629 1629
12 36641260 36649169 - Maker00029445 Lcy12g1631 1631
12 36655953 36663703 + Maker00029415 Lcy12g1632 1632
9 2482220 2484730 + Lsi09G002360.1 Lsi09g00236 236
9 2505345 2512917 - Lsi09G002370.1 Lsi09g00237 237
9 2512831 2523158 + Lsi09G002380.1 Lsi09g00238 238
9 2529297 2530326 + Lsi09G002400.1 Lsi09g00240 240
2 209925 211742 + Vvi2g12 Vvi2g12 12
2 213714 224334 + Vvi2g13 Vvi2g13 13
2 236397 241211 + Vvi2g14 Vvi2g14 14
2 243558 247500 - Vvi2g15 Vvi2g15 15
2 249699 251327 - Vvi2g16 Vvi2g16 16
2 251331 253144 - Vvi2g17 Vvi2g17 17
2 254141 263652 - Vvi2g18 Vvi2g18 18
2 264632 274383 + Vvi2g19 Vvi2g19 19
2 279461 280511 - Vvi2g20 Vvi2g20 20
2 281174 287055 + Vvi2g21 Vvi2g21 21
       

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