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
Vvi2g552 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy06g02097 .
Vvi2g553 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g554 . . . . . . . . . . . . . . Sed04g1648 . . Bhi11g00086 Tan01g2110 Cmetu06g0162 . . Mch10g1602 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g555 . . . . . . . . . Cmo16g01152 . . . . . Cpe14g00912 . . . . . . . . . . . . . . . . . . . . . . Cme06g02521 . . . . . . . . . . . . Cma16g01102 . Car16g01043 . . . . . . . . . . . . . . . . . Csa03g00224 . .
Vvi2g556 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g557 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g558 Blo02g01010 . . Bda08g00611 Bpe05g00545 . . . Cmo06g00845 Cmo16g01150 . . . . . Cpe14g00910 . Bhi11g00087 . . . . Mch10g1603 . Cla10g00206 Cam10g0212 Cec10g0217 Cco10g0218 Clacu10g0215 Cmu10g1058 Cre10g0466 . . . . Lsi07g01247 . . Cme06g02518 . . . . . . Bma05g00737 . . . . Cma06g00823 Cma16g01101 . Car16g01042 . . Bhi05g00574 Tan07g1902 . Lac11g2344 Hepe06g1246 . . . . . . . . . . Csa03g00222 Chy06g02099 .
Vvi2g559 . . Bda06g01306 . . . . . . Cmo16g01149 . . . . . Cpe14g00909 Cpe05g00215 Bhi11g00089 Tan01g2113 . . . Mch10g1604 . Cla10g00205 Cam10g0211 Cec10g0216 Cco10g0217 Clacu10g0214 Cmu10g1057 Cre10g0465 . . Cone6ag0630 Cone9ag0634 Lsi07g01246 . . Cme06g02517 . . . . . . . . . . Cmo19g00398 . Cma16g01100 . Car16g01041 . . Bhi05g00574 Tan07g1902 . Lac11g2344 Hepe06g1246 . . Cla09g01206 Cam09g1272 Cec09g1286 Cco09g1320 . . Cre09g1232 . . . .
Vvi2g560 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g561 Blo02g01009 . . . . Bpe07g00200 . . Cmo06g00846 . Cma02g01575 . Car02g01339 . Sed07g1306 . . Bhi11g00090 Tan01g2114 Cmetu06g0159 . . . . . . . . . . . . . . . . . Chy04g00030 . . . . . . . . Bma12g00194 Sed01g4056 Cmo02g01617 . Cma06g00824 . . . . . Bhi05g00573 Tan07g1903 Cmetu04g2483 . . . Lcy12g1880 . . . . . . . . Csa03g04671 Chy06g02100 Cme04g00040
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 43732618 43734870 - Bda023160.1 Bda06g01306 1306
8 6234716 6236427 - Bda029073.1 Bda08g00611 611
5 14184172 14187629 - XM_039031441.1 Bhi05g00573 573
5 14184172 14187628 - XM_039031440.1 Bhi05g00574 574
11 2034175 2036454 - XM_039049865.1 Bhi11g00086 86
11 2117187 2121192 - XM_039047111.1 Bhi11g00087 87
11 2174400 2178760 + XM_039050197.1 Bhi11g00089 89
11 2174400 2178760 + XM_039050196.1 Bhi11g00090 90
2 39212255 39219736 - BLOR10739 Blo02g01009 1009
2 39240813 39243185 + BLOR10740 Blo02g01010 1010
5 43386444 43390047 - Bma021832.1 Bma05g00737 737
12 2615138 2617353 + Bma007080.1 Bma12g00194 194
5 19644259 19646369 + Bpe017962.1 Bpe05g00545 545
7 1370973 1372626 + Bpe021010.1 Bpe07g00200 200
9 15001805 15004050 - CaPI482276_09g012720.1 Cam09g1272 1272
10 3809388 3813244 - CaPI482276_10g002110.1 Cam10g0211 211
10 3829663 3833049 + CaPI482276_10g002120.1 Cam10g0212 212
2 8860641 8862958 + Carg08806-RA Car02g01339 1339
16 8923156 8926466 - Carg23245-RA Car16g01041 1041
16 8937339 8941578 + Carg23246-RA Car16g01042 1042
16 8945093 8952868 + Carg23247-RA Car16g01043 1043
9 15032538 15034785 - CcPI632755_09g013200.1 Cco09g1320 1320
10 2255916 2259947 - CcPI632755_10g002170.1 Cco10g0217 217
10 2280847 2284250 + CcPI632755_10g002180.1 Cco10g0218 218
9 15198844 15201089 - CePI673135_09g012860.1 Cec09g1286 1286
10 2358372 2361267 - CePI673135_10g002160.1 Cec10g0216 216
10 2393721 2397131 + CePI673135_10g002170.1 Cec10g0217 217
4 308172 310343 + Chy4G067480.1 Chy04g00030 30
6 25158006 25159044 - Chy6G126250.1 Chy06g02097 2097
6 25172000 25175369 - Chy6G126270.1 Chy06g02099 2099
6 25185277 25188218 + Chy6G126280.1 Chy06g02100 2100
10 2555145 2558158 - ClG42_10g0021400.10 Clacu10g0214 214
10 2575469 2578855 + ClG42_10g0021500.10 Clacu10g0215 215
9 15036673 15038921 - ClCG09G012645.1 Cla09g01206 1206
10 2378144 2382320 - ClCG10G002110.1 Cla10g00205 205
10 2398380 2402729 + ClCG10G002120.1 Cla10g00206 206
2 8949003 8951415 + CmaCh02G015750.1 Cma02g01575 1575
6 4433702 4437548 - CmaCh06G008230.1 Cma06g00823 823
6 4467804 4471652 + CmaCh06G008240.1 Cma06g00824 824
16 8462514 8465987 - CmaCh16G011000.1 Cma16g01100 1100
16 8475054 8479126 + CmaCh16G011010.1 Cma16g01101 1101
16 8481921 8482262 + CmaCh16G011020.1 Cma16g01102 1102
4 264034 266221 + MELO3C003339.2.1 Cme04g00040 40
6 32209642 32213917 - MELO3C013892.2.1 Cme06g02517 2517
6 32223503 32227414 + MELO3C013893.2.1 Cme06g02518 2518
6 32265095 32266570 + MELO3C013895.2.1 Cme06g02521 2521
4 33189421 33191605 - PI0027531.1 Cmetu04g2483 2483
6 29192819 29197135 + PI0007688.1 Cmetu06g0159 159
6 26583778 26585405 - PI0010170.1 Cmetu06g0162 162
2 9321069 9324426 + CmoCh02G016170.1 Cmo02g01617 1617
6 4713364 4717288 - CmoCh06G008450.1 Cmo06g00845 845
6 4743890 4747740 + CmoCh06G008460.1 Cmo06g00846 846
16 8196897 8200345 - CmoCh16G011490.1 Cmo16g01149 1149
16 8209106 8213868 + CmoCh16G011500.1 Cmo16g01150 1150
16 8223666 8224597 + CmoCh16G011520.1 Cmo16g01152 1152
19 4619085 4621662 - CmoCh19G003980.1 Cmo19g00398 398
10 2706134 2709006 - CmPI595203_10g010570.1 Cmu10g1057 1057
10 2726444 2729830 + CmPI595203_10g010580.1 Cmu10g1058 1058
6 3185492 3188427 - Conep06aG0064900.1 Cone6ag0630 630
9 3016907 3020512 - Conep09aG0065000.1 Cone9ag0634 634
5 1192385 1196466 - Cp4.1LG05g01920.1 Cpe05g00215 215
14 7648303 7651881 - Cp4.1LG14g09150.1 Cpe14g00909 909
14 7661921 7666994 + Cp4.1LG14g09100.1 Cpe14g00910 910
14 7677193 7677525 + Cp4.1LG14g09120.1 Cpe14g00912 912
9 15151126 15153366 - CrPI670011_09g012320.1 Cre09g1232 1232
10 3671055 3675074 - CrPI670011_10g004650.1 Cre10g0465 465
10 3694379 3697785 + CrPI670011_10g004660.1 Cre10g0466 466
3 1788904 1793145 + CsaV3_3G002220.1 Csa03g00222 222
3 1798516 1800576 + CsaV3_3G002240.1 Csa03g00224 224
3 40632430 40634556 - CsaV3_3G049770.1 Csa03g04671 4671
6 62240388 62242664 + Hsped.06g12460.1 Hepe06g1246 1246
11 39511742 39514327 + Lag0032982.1 Lac11g2344 2344
12 39988295 39996736 + Maker00038139 Lcy12g1880 1880
7 18193235 18197754 - Lsi07G012460.1 Lsi07g01246 1246
7 18215035 18218985 + Lsi07G012470.1 Lsi07g01247 1247
10 16112898 16113203 - MC10g1269 Mch10g1602 1602
10 16117857 16121662 - MC10g1270 Mch10g1603 1603
10 16136246 16140933 + MC10g1271 Mch10g1604 1604
1 69540303 69543721 + Sed0001674.2 Sed01g4056 4056
4 31150773 31152387 + Sed0027041.1 Sed04g1648 1648
7 9822977 9825844 + Sed0007078.1 Sed07g1306 1306
1 24279474 24281909 - Tan0003251.1 Tan01g2110 2110
1 24340314 24344624 + Tan0020262.1 Tan01g2113 2113
1 24340314 24344624 + Tan0020262.2 Tan01g2114 2114
7 70591016 70595244 + Tan0021318.1 Tan07g1902 1902
7 70591016 70595244 + Tan0021318.2 Tan07g1903 1903
2 5507979 5508728 - Vvi2g552 Vvi2g552 552
2 5514037 5514631 + Vvi2g553 Vvi2g553 553
2 5523272 5523828 - Vvi2g554 Vvi2g554 554
2 5533774 5534520 - Vvi2g555 Vvi2g555 555
2 5537680 5537878 + Vvi2g556 Vvi2g556 556
2 5555759 5556550 - Vvi2g557 Vvi2g557 557
2 5557549 5562196 - Vvi2g558 Vvi2g558 558
2 5573343 5579529 + Vvi2g559 Vvi2g559 559
2 5582142 5591653 + Vvi2g560 Vvi2g560 560
2 5592159 5598339 + Vvi2g561 Vvi2g561 561
       

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