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
Vvi5g929 . Blo12g00104 Bda03g01139 . Bpe04g01082 . Bma04g01163 . . . . . . . . . . . . . . . . . Cla06g00775 Cam06g0826 Cec06g0842 Cco06g0848 Clacu06g0829 Cmu06g0801 Cre06g1582 . Cone15ag0263 . . . . Chy05g00577 . . . . . . . . . Sed04g2086 . . . . . . . . Bhi12g01477 Tan06g2283 Cmetu05g0705 Lac12g2014 Hepe03g0377 . . . . . . . . . Lsi09g01123 . . Cme05g00735
Vvi5g930 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy05g00175 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g931 . . . . . . . . . Cmo17g00091 . Cma14g01907 Car06g01052 Car14g01708 Sed02g1527 Cpe08g00413 Cpe03g01608 Bhi01g00197 Tan10g0493 Cmetu06g2051 Lac12g2015 Hepe05g1777 . Lcy11g1792 . . . . . . . Cone14ag0245 Cone15ag0262 Cone7ag0410 . Lsi05g01860 . . Cme06g00366 . . Bda11g00324 Bda13g00476 . Bpe13g00869 Bma02g01194 Bma06g01272 Sed09g0169 Cmo06g01237 Cmo14g01962 . Cma17g00085 . Car17g00080 Cpe12g00078 . Bhi12g01476 Tan06g2282 Cmetu05g1668 . Hepe03g0378 . . Cla05g00330 Cam05g0360 Cec05g0364 Cco05g0366 Clacu05g0357 Cmu05g0342 Cre05g0405 Lsi09g01122 Csa03g01076 Chy06g00346 Cme05g00736
Vvi5g932 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g933 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g934 . . Bda03g01138 . Bpe04g01081 . Bma04g01164 . . . . . . . . . . . . . . . . . Cla06g00778 Cam06g0832 Cec06g0846 Cco06g0856 Clacu06g0835 Cmu06g0806 Cre06g1587 . . . . . . Chy05g00581 . . . . . . . . . Sed09g0168 . . . . . . . . Bhi12g01475 Tan06g2279 Cmetu05g0652 . Hepe03g0379 . . . . . . . . . Lsi09g01121 . . Cme05g00737
Vvi5g935 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g936 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g937 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g938 . . . . . . . . Cmo08g00990 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma08g01020 . Car08g00897 . . Cpe17g00256 . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 11984269 12009521 - Bda017186.1 Bda03g01138 1138
3 12011939 12013546 - Bda017187.1 Bda03g01139 1139
11 3574434 3575504 - Bda005050.1 Bda11g00324 324
13 5672308 5673405 + Bda001381.1 Bda13g00476 476
1 3819505 3821167 - XM_039037294.1 Bhi01g00197 197
12 47598649 47642862 - XM_039018829.1 Bhi12g01475 1475
12 47737556 47739538 + XM_039019944.1 Bhi12g01476 1476
12 47790738 47796848 + XM_039019430.1 Bhi12g01477 1477
12 7479403 7481006 + BLOR04123 Blo12g00104 104
2 54040648 54041749 + Bma016036.1 Bma02g01194 1194
4 30046488 30048155 + Bma019898.1 Bma04g01163 1163
4 30091321 30103346 + Bma019900.1 Bma04g01164 1164
6 49809112 49811028 - Bma024380.1 Bma06g01272 1272
4 8309303 8328879 - Bpe015753.1 Bpe04g01081 1081
4 8344143 8345750 - Bpe015755.1 Bpe04g01082 1082
13 14859776 14860858 + Bpe010556.1 Bpe13g00869 869
5 3341955 3343269 - CaPI482276_05g003600.1 Cam05g0360 360
6 11496052 11501524 - CaPI482276_06g008260.1 Cam06g0826 826
6 11713253 11740847 + CaPI482276_06g008320.1 Cam06g0832 832
6 7904500 7906289 - Carg06307-RA Car06g01052 1052
8 6022802 6026055 - Carg11027-RA Car08g00897 897
14 13566903 13568330 + Carg24775-RA Car14g01708 1708
17 456268 457952 + Carg10152-RA Car17g00080 80
5 2973880 2975194 - CcPI632755_05g003660.1 Cco05g0366 366
6 10298811 10303644 - CcPI632755_06g008480.1 Cco06g0848 848
6 10532719 10552540 + CcPI632755_06g008560.1 Cco06g0856 856
5 2983937 2987132 - CePI673135_05g003640.1 Cec05g0364 364
6 10452816 10457724 - CePI673135_06g008420.1 Cec06g0842 842
6 10602528 10628426 + CePI673135_06g008460.1 Cec06g0846 846
5 1378489 1380528 - Chy5G092210.1 Chy05g00175 175
5 6526393 6531019 - Chy5G096230.1 Chy05g00577 577
5 6569023 6595764 + Chy5G096270.1 Chy05g00581 581
6 2299458 2300732 - Chy6G108740.1 Chy06g00346 346
5 3055839 3057153 - ClG42_05g0035700.10 Clacu05g0357 357
6 10178800 10184291 - ClG42_06g0082900.10 Clacu06g0829 829
6 10352271 10372104 + ClG42_06g0083500.10 Clacu06g0835 835
5 2998549 2999348 - ClCG05G003140.2 Cla05g00330 330
6 10480312 10486108 - ClCG06G007980.2 Cla06g00775 775
6 10660024 10686437 + ClCG06G007990.1 Cla06g00778 778
8 6385493 6388969 - CmaCh08G010200.1 Cma08g01020 1020
14 13482500 13483869 + CmaCh14G019070.1 Cma14g01907 1907
17 425346 426985 + CmaCh17G000850.1 Cma17g00085 85
5 8853839 8858350 - MELO3C020426.2.1 Cme05g00735 735
5 8880624 8882449 - MELO3C020425.2.1 Cme05g00736 736
5 8896689 8918410 + MELO3C020422.2.1 Cme05g00737 737
6 2263669 2265270 - MELO3C006295.2.1 Cme06g00366 366
5 15838093 15866134 - PI0009010.1 Cmetu05g0652 652
5 15947810 15953037 + PI0011806.1 Cmetu05g0705 705
5 15930873 15933448 + PI0006234.1 Cmetu05g1668 1668
6 2473068 2474976 - PI0024906.1 Cmetu06g2051 2051
6 9346659 9348207 - CmoCh06G012370.1 Cmo06g01237 1237
8 6439513 6442949 - CmoCh08G009900.1 Cmo08g00990 990
14 14482895 14484293 + CmoCh14G019620.1 Cmo14g01962 1962
17 491334 493198 + CmoCh17G000910.1 Cmo17g00091 91
5 2894318 2895632 - CmPI595203_05g003420.1 Cmu05g0342 342
6 9995362 10000850 - CmPI595203_06g008010.1 Cmu06g0801 801
6 10170941 10188631 + CmPI595203_06g008060.1 Cmu06g0806 806
7 1824178 1825639 + Conep07aG0042000.1 Cone7ag0410 410
14 1132276 1133963 + Conep14aG0025000.1 Cone14ag0245 245
15 1234418 1235937 + Conep15aG0026800.1 Cone15ag0262 262
15 1237860 1239816 - Conep15aG0026900.1 Cone15ag0263 263
3 12381703 12382955 + Cp4.1LG03g18080.1 Cpe03g01608 1608
8 2655583 2657410 + Cp4.1LG08g02660.1 Cpe08g00413 413
12 469056 471142 + Cp4.1LG12g00650.1 Cpe12g00078 78
17 1683912 1688603 + Cp4.1LG17g03300.1 Cpe17g00256 256
5 3673595 3674985 - CrPI670011_05g004050.1 Cre05g0405 405
6 11143095 11148475 - CrPI670011_06g015820.1 Cre06g1582 1582
6 11253062 11278943 + CrPI670011_06g015870.1 Cre06g1587 1587
3 8549097 8550926 - CsaV3_3G010760.1 Csa03g01076 1076
3 5405568 5412613 - Hsped.03g03770.1 Hepe03g0377 377
3 5431821 5433662 - Hsped.03g03780.1 Hepe03g0378 378
3 5455366 5484700 + Hsped.03g03790.1 Hepe03g0379 379
5 68077309 68078655 + Hsped.05g17770.1 Hepe05g1777 1777
12 37063023 37068920 - Lag0016386.1 Lac12g2014 2014
12 37090160 37091621 - Lag0016387.1 Lac12g2015 2015
11 41716449 41718167 + Maker00031534 Lcy11g1792 1792
5 25829776 25831793 + Lsi05G018600.1 Lsi05g01860 1860
9 17921389 17949043 - Lsi09G011210.1 Lsi09g01121 1121
9 18005613 18008010 - Lsi09G011220.1 Lsi09g01122 1122
9 18035250 18041610 + Lsi09G011230.1 Lsi09g01123 1123
2 51017264 51018370 + Sed0002206.1 Sed02g1527 1527
4 35167509 35173537 - Sed0009765.1 Sed04g2086 2086
9 1337291 1360042 - Sed0014363.1 Sed09g0168 168
9 1365956 1368365 + Sed0001043.1 Sed09g0169 169
6 73710382 73745758 - Tan0017314.2 Tan06g2279 2279
6 73801405 73803346 + Tan0020189.1 Tan06g2282 2282
6 73838245 73843862 + Tan0002630.1 Tan06g2283 2283
10 3978875 3980342 - Tan0020651.1 Tan10g0493 493
5 15242015 15245854 + Vvi5g929 Vvi5g929 929
5 15291832 15293125 - Vvi5g930 Vvi5g930 930
5 15301391 15303247 - Vvi5g931 Vvi5g931 931
5 15337617 15339863 + Vvi5g932 Vvi5g932 932
5 15339881 15340519 + Vvi5g933 Vvi5g933 933
5 15363271 15434023 + Vvi5g934 Vvi5g934 934
5 15437398 15444641 + Vvi5g935 Vvi5g935 935
5 15463870 15464144 + Vvi5g936 Vvi5g936 936
5 15501339 15501980 + Vvi5g937 Vvi5g937 937
5 15512471 15515241 + Vvi5g938 Vvi5g938 938
       

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