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
Vvi17g116 . Blo16g00265 . . Bpe12g00483 Bpe13g00204 Bma06g00256 . Cmo13g00835 . Cma10g00065 Cma11g00035 Car10g00053 Car11g00032 . Cpe20g00308 Cpe04g01614 . . . . . . . . . . . . . . . . . Cone19ag0206 . . Chy12g01170 Cme12g01592 . . Bda11g01602 Bda14g01366 . Bpe15g00216 Bma03g01256 . Sed08g2438 Cmo10g00061 Cmo11g00037 Cma13g00803 Cma18g00319 Car13g00651 Car18g00228 Cpe09g00962 . Bhi08g01486 Tan05g2961 Cmetu04g0927 Lac10g0582 Hepe07g2107 . . Cla03g00352 Cam03g0370 Cec03g0358 Cco03g0373 Clacu03g0370 Cmu03g0976 Cre03g0668 . . . .
Vvi17g117 . . Bda06g00730 . Bpe12g00484 . . . . . Cma10g00066 Cma11g00036 Car10g00054 Car11g00033 . . Cpe04g01613 Bhi02g00681 . . . . . . Cla06g01738 Cam06g1928 . Cco06g1982 Clacu06g1884 . Cre06g2641 . . Cone13ag0216 Cone19ag0205 . . . . . Blo15g00210 . . . . . . . Cmo10g00062 Cmo11g00038 . . . . . . . . . . . . . . . . . . . . Lsi06g01638 Csa01g00060 Chy02g02659 Cme02g02061
Vvi17g118 . . . . . . . . . . . Cma11g00037 . Car11g00034 . . Cpe04g01612 . . . . . . . Cla06g01737 Cam06g1927 Cec06g1978 Cco06g1981 Clacu06g1883 Cmu06g1826 Cre06g2640 Cone2ag0971 Cone16ag0019 . . . . . . . . . . Bpe07g00888 . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi06g01637 Csa01g00062 Chy02g02657 Cme02g02060
Vvi17g119 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g120 . . . . . . . . . . Cma10g00068 Cma11g00038 Car10g00055 . . . Cpe04g01611 . . . . . . . Cla06g01736 Cam06g1926 Cec06g1977 Cco06g1980 Clacu06g1882 Cmu06g1825 Cre06g2639 . . . . . . . . . . . . . . . . . Cmo10g00063 Cmo11g00039 . . . . . . . . . . . . . . . . . . . . . Csa01g00063 Chy02g02656 Cme02g02059
Vvi17g121 . . . . . . . Bma12g01080 . . . Cma11g00039 . Car11g00035 . . Cpe04g01610 . . . . . . . . . . . . . . . . . Cone19ag0204 . . . . . . . . . . . . . . Cmo11g00040 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g122 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g123 . . Bda06g00732 . Bpe12g00486 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe07g00885 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g124 . . . . . . . . Cmo13g00834 Cmo18g00216 . . . . . Cpe20g00309 . . . . . . . . . . . . . . . . . . . Lsi02g00500 Csa01g00961 Chy12g01172 Cme12g01594 . . . Bda14g01367 . Bpe15g00215 Bma03g01257 . Sed01g1566 . . Cma13g00802 Cma18g00321 Car13g00650 Car18g00226 Cpe09g00964 . Bhi08g01483 Tan05g2958 . . Hepe07g2103 . . Cla03g00351 Cam03g0368 Cec03g0356 Cco03g0371 Clacu03g0368 Cmu03g0974 Cre03g0666 . . . .
Vvi17g125 . . . . . . . . Cmo13g00833 Cmo18g00213 . . . . . . . . . . . . . . . . . . . . . Cone2ag0969 Cone16ag0021 . . . . Chy12g01174 Cme12g01596 . . . Bda14g01368 . Bpe15g00214 Bma03g01258 . . . . . Cma18g00322 . . Cpe09g00966 . . . . . . . . Cla03g00350 Cam03g0367 Cec03g0355 Cco03g0370 Clacu03g0367 Cmu03g0973 Cre03g0665 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 9964866 9967505 + Bda024033.1 Bda06g00730 730
6 9971175 9972452 + Bda024035.1 Bda06g00732 732
11 49652969 49654918 + Bda008483.1 Bda11g01602 1602
14 16027255 16029210 + Bda011066.1 Bda14g01366 1366
14 16037758 16040876 - Bda011067.1 Bda14g01367 1367
14 16042437 16044376 - Bda011068.1 Bda14g01368 1368
2 13342173 13345098 + XM_039024369.1 Bhi02g00681 681
8 43179279 43183089 + XM_039039577.1 Bhi08g01483 1483
8 43188853 43192253 - XM_039038690.1 Bhi08g01486 1486
15 2150914 2153588 + BLOR06604 Blo15g00210 210
16 6254324 6256273 - BLOR07513 Blo16g00265 265
3 21081145 21083100 + Bma017718.1 Bma03g01256 1256
3 21183160 21186259 - Bma017720.1 Bma03g01257 1257
3 21187580 21189518 - Bma017721.1 Bma03g01258 1258
6 3506836 3508785 - Bma022887.1 Bma06g00256 256
12 43111541 43113028 - Bma008427.1 Bma12g01080 1080
7 14948495 14949632 - Bpe026084 Bpe07g00885 885
7 14958136 14960294 + Bpe021729.1 Bpe07g00888 888
12 10646726 10648678 + Bpe005746.1 Bpe12g00483 483
12 10649253 10651571 - Bpe005747.1 Bpe12g00484 484
12 10670294 10671602 + Bpe005749.1 Bpe12g00486 486
13 10055728 10057677 + Bpe006326.1 Bpe13g00204 204
15 13276035 13277969 + Bpe001151.1 Bpe15g00214 214
15 13282389 13285574 + Bpe024549 Bpe15g00215 215
15 13291361 13293322 - Bpe001152.1 Bpe15g00216 216
3 4798803 4816113 - CaPI482276_03g003670.1 Cam03g0367 367
3 4822387 4826107 + CaPI482276_03g003680.1 Cam03g0368 368
3 4829495 4834264 - CaPI482276_03g003700.1 Cam03g0370 370
6 30215043 30228116 - CaPI482276_06g019260.1 Cam06g1926 1926
6 30233680 30238203 - CaPI482276_06g019270.1 Cam06g1927 1927
6 30242218 30245013 + CaPI482276_06g019280.1 Cam06g1928 1928
10 236582 238540 + Carg10285-RA Car10g00053 53
10 239792 241409 - Carg10286-RA Car10g00054 54
10 245281 247041 + Carg10287-RA Car10g00055 55
11 171293 173242 + Carg20170-RA Car11g00032 32
11 173545 176515 - Carg20171-RA Car11g00033 33
11 177740 181179 + Carg20172-RA Car11g00034 34
11 185328 187779 - Carg20173-RA Car11g00035 35
13 8061337 8065204 + Carg07600-RA Car13g00650 650
13 8066683 8068662 - Carg07601-RA Car13g00651 651
18 1292428 1296608 + Carg06793-RA Car18g00226 226
18 1303178 1305169 - Carg06795-RA Car18g00228 228
3 4023665 4036047 - CcPI632755_03g003700.1 Cco03g0370 370
3 4047465 4051165 + CcPI632755_03g003710.1 Cco03g0371 371
3 4055962 4058863 - CcPI632755_03g003730.1 Cco03g0373 373
6 29952874 29966844 - CcPI632755_06g019800.1 Cco06g1980 1980
6 29973866 29977302 - CcPI632755_06g019810.1 Cco06g1981 1981
6 29981289 29984093 + CcPI632755_06g019820.1 Cco06g1982 1982
3 3967429 3984389 - CePI673135_03g003550.1 Cec03g0355 355
3 3990740 3994434 + CePI673135_03g003560.1 Cec03g0356 356
3 3997738 4002474 - CePI673135_03g003580.1 Cec03g0358 358
6 33042510 33044535 - CePI673135_06g019770.1 Cec06g1977 1977
6 33051052 33054806 - CePI673135_06g019780.1 Cec06g1978 1978
2 29595310 29597326 - Chy2G049230.1 Chy02g02656 2656
2 29602472 29605241 - Chy2G049240.1 Chy02g02657 2657
2 29607228 29609552 + Chy2G049260.1 Chy02g02659 2659
12 16583153 16585129 + Chy12G217700.1 Chy12g01170 1170
12 16591292 16594265 - Chy12G217720.1 Chy12g01172 1172
12 16613446 16614921 + Chy12G217740.1 Chy12g01174 1174
3 4115064 4132130 - ClG42_03g0036700.10 Clacu03g0367 367
3 4138200 4141915 + ClG42_03g0036800.10 Clacu03g0368 368
3 4145283 4150054 - ClG42_03g0037000.10 Clacu03g0370 370
6 29264809 29278880 - ClG42_06g0188200.10 Clacu06g1882 1882
6 29285438 29288970 - ClG42_06g0188300.10 Clacu06g1883 1883
6 29292985 29295780 + ClG42_06g0188400.10 Clacu06g1884 1884
3 4058352 4075815 - ClCG03G003700.2 Cla03g00350 350
3 4081708 4085794 + ClCG03G003720.2 Cla03g00351 351
3 4086848 4093673 - ClCG03G003730.2 Cla03g00352 352
6 30917302 30922674 - ClCG06G017820.2 Cla06g01736 1736
6 30928133 30932774 - ClCG06G017840.2 Cla06g01737 1737
6 30936535 30939725 + ClCG06G017850.1 Cla06g01738 1738
10 249523 251481 + CmaCh10G000650.1 Cma10g00065 65
10 252314 254466 - CmaCh10G000660.1 Cma10g00066 66
10 262587 266990 + CmaCh10G000680.1 Cma10g00068 68
11 162015 163964 + CmaCh11G000350.1 Cma11g00035 35
11 164586 167178 - CmaCh11G000360.1 Cma11g00036 36
11 167509 171990 + CmaCh11G000370.1 Cma11g00037 37
11 173319 174910 + CmaCh11G000380.1 Cma11g00038 38
11 175633 178841 - CmaCh11G000390.1 Cma11g00039 39
13 6815950 6822066 + CmaCh13G008020.1 Cma13g00802 802
13 6823642 6825615 - CmaCh13G008030.1 Cma13g00803 803
18 1702191 1704173 + CmaCh18G003190.1 Cma18g00319 319
18 1710644 1714734 - CmaCh18G003210.1 Cma18g00321 321
18 1716278 1733426 + CmaCh18G003220.1 Cma18g00322 322
2 26588824 26591458 - MELO3C026212.2.1 Cme02g02059 2059
2 26596346 26599707 - MELO3C026211.2.1 Cme02g02060 2060
2 26601658 26604630 + MELO3C026210.2.1 Cme02g02061 2061
12 23218332 23220537 + MELO3C002359.2.1 Cme12g01592 1592
12 23225750 23230974 - MELO3C002357.2.1 Cme12g01594 1594
12 23248218 23250512 + MELO3C002355.2.1 Cme12g01596 1596
4 15738148 15739979 + PI0028573.1 Cmetu04g0927 927
10 282379 284337 + CmoCh10G000610.1 Cmo10g00061 61
10 285217 287259 - CmoCh10G000620.1 Cmo10g00062 62
10 287927 294608 + CmoCh10G000630.1 Cmo10g00063 63
11 157117 159066 + CmoCh11G000370.1 Cmo11g00037 37
11 159719 162276 - CmoCh11G000380.1 Cmo11g00038 38
11 163670 170045 + CmoCh11G000390.1 Cmo11g00039 39
11 170944 174086 - CmoCh11G000400.1 Cmo11g00040 40
13 7745294 7747562 + CmoCh13G008330.1 Cmo13g00833 833
13 7747948 7752690 + CmoCh13G008340.1 Cmo13g00834 834
13 7754168 7756147 - CmoCh13G008350.1 Cmo13g00835 835
18 1389641 1407791 - CmoCh18G002130.1 Cmo18g00213 213
18 1409223 1413533 + CmoCh18G002160.1 Cmo18g00216 216
3 4328823 4345891 - CmPI595203_03g009730.1 Cmu03g0973 973
3 4351980 4355695 + CmPI595203_03g009740.1 Cmu03g0974 974
3 4359063 4363834 - CmPI595203_03g009760.1 Cmu03g0976 976
6 29180453 29182511 - CmPI595203_06g018250.1 Cmu06g1825 1825
6 29188764 29192527 - CmPI595203_06g018260.1 Cmu06g1826 1826
2 35222828 35223322 + Conep02aG0200300.1 Cone2ag0969 969
2 35231733 35233139 - Conep02aG0200500.1 Cone2ag0971 971
13 1399045 1402679 - Conep13aG0022100.1 Cone13ag0216 216
16 140867 143175 + Conep16aG0001900.1 Cone16ag0019 19
16 150691 152433 - Conep16aG0002100.1 Cone16ag0021 21
19 1294983 1297900 + Conep19aG0021000.1 Cone19ag0204 204
19 1298670 1301204 + Conep19aG0021100.1 Cone19ag0205 205
19 1303296 1305468 - Conep19aG0021200.1 Cone19ag0206 206
4 12523202 12526802 + Cp4.1LG04g16020.1 Cpe04g01610 1610
4 12527159 12528735 - Cp4.1LG04g16130.1 Cpe04g01611 1611
4 12530282 12533637 - Cp4.1LG04g16140.1 Cpe04g01612 1612
4 12534635 12540105 + Cp4.1LG04g16050.1 Cpe04g01613 1613
4 12537686 12539635 - Cp4.1LG04g16110.1 Cpe04g01614 1614
9 8594080 8596050 + Cp4.1LG09g09560.1 Cpe09g00962 962
9 8603047 8607272 - Cp4.1LG09g09680.1 Cpe09g00964 964
9 8622220 8627862 + Cp4.1LG09g09650.1 Cpe09g00966 966
20 1732404 1735154 + Cp4.1LG20g03080.1 Cpe20g00308 308
20 1735866 1742591 - Cp4.1LG20g03130.1 Cpe20g00309 309
3 5538163 5555222 - CrPI670011_03g006650.1 Cre03g0665 665
3 5562088 5565796 + CrPI670011_03g006660.1 Cre03g0666 666
3 5569019 5573784 - CrPI670011_03g006680.1 Cre03g0668 668
6 33995642 34009445 - CrPI670011_06g026390.1 Cre06g2639 2639
6 34016336 34020075 - CrPI670011_06g026400.1 Cre06g2640 2640
6 34025809 34028609 + CrPI670011_06g026410.1 Cre06g2641 2641
1 349622 353054 - CsaV3_1G000600.1 Csa01g00060 60
1 354128 357620 + CsaV3_1G000620.1 Csa01g00062 62
1 362093 364751 + CsaV3_1G000630.1 Csa01g00063 63
1 5959457 5962379 + CsaV3_1G009610.1 Csa01g00961 961
7 65347479 65358964 + Hsped.07g21030.1 Hepe07g2103 2103
7 65393664 65396208 - Hsped.07g21070.1 Hepe07g2107 2107
10 4476452 4478431 - Lag0024627.1 Lac10g0582 582
2 4247264 4250966 + Lsi02G005000.1 Lsi02g00500 500
6 26666402 26677908 - Lsi06G016370.1 Lsi06g01637 1637
6 26679724 26689023 + Lsi06G016380.1 Lsi06g01638 1638
1 11374541 11378541 - Sed0016483.2 Sed01g1566 1566
8 37407388 37410034 + Sed0002707.1 Sed08g2438 2438
5 81679623 81683679 + Tan0011587.2 Tan05g2958 2958
5 81690153 81693514 - Tan0005542.1 Tan05g2961 2961
17 1030105 1032033 + Vvi17g116 Vvi17g116 116
17 1033933 1037516 - Vvi17g117 Vvi17g117 117
17 1043079 1048331 + Vvi17g118 Vvi17g118 118
17 1048897 1056090 + Vvi17g119 Vvi17g119 119
17 1060848 1062387 + Vvi17g120 Vvi17g120 120
17 1071680 1074904 - Vvi17g121 Vvi17g121 121
17 1078640 1079500 - Vvi17g122 Vvi17g122 122
17 1081236 1084315 + Vvi17g123 Vvi17g123 123
17 1085034 1089874 - Vvi17g124 Vvi17g124 124
17 1091338 1094293 - Vvi17g125 Vvi17g125 125
       

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