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
Vvi4g1172 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1173 Blo04g00867 . . . Bpe15g00494 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma03g00933 . . . . . . . . . . . . . . . . . . . . . . . . Lsi07g01068 . . .
Vvi4g1174 . Blo16g00101 . . . Bpe13g00393 . . . . . Cma07g00390 . Car07g00343 . Cpe19g00892 . . . . . . . . Cla01g02030 Cam01g2136 Cec04g1793 Cco04g1859 Clacu01g2152 Cmu01g2028 Cre04g1703 . . . . Lsi01g00540 . . Cme08g00987 . . Bda11g01815 . . . . Bma06g00079 . . Cmo07g00384 . . . . . . . . . . . . . . . . . . . . . Csa06g03391 Chy02g00514 .
Vvi4g1175 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe06g00332 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1176 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1177 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1178 . . . . . . . . . . Cma03g00628 Cma07g00389 Car03g00583 Car07g00342 . Cpe19g00893 Cpe10g00358 . . . . . . . Cla01g02031 Cam01g2137 Cec04g1794 Cco04g1860 Clacu01g2153 Cmu01g2029 Cre04g1704 . . . . Lsi01g00538 . . Cme08g00988 Blo05g00680 . . . . Bpe06g00156 . . . Cmo03g00656 Cmo07g00383 . Cma20g00719 . . . . . . . . . . . . . . . . . . . Csa06g03392 Chy02g00513 .
Vvi4g1179 . . Bda04g00218 . . . . . . . . Cma07g00388 . Car07g00341 . Cpe19g00894 . . . . . . . . Cla01g02032 Cam01g2138 Cec04g1795 Cco04g1861 Clacu01g2154 Cmu01g2030 Cre04g1705 Cone6ag0020 Cone9ag0019 Cone14ag1210 Cone15ag1229 Lsi01g00537 . . Cme08g00989 Blo05g00679 . . . . Bpe06g00157 . . . . Cmo07g00382 . . . . . . Bhi10g02361 . . . . . . Cla02g00088 Cam02g0095 Cec02g0096 Cco02g0088 Clacu02g0092 Cmu02g0087 Cre02g0426 Lsi10g00685 Csa06g03394 Chy02g00512 Cme11g00099
Vvi4g1180 Blo04g00866 . . . Bpe15g00495 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0888 Cone12ag0858 . . . . . . . . . . . . . . . . . Cma16g01265 . . . . . . . . . . . . . . . . . . . Lsi07g01066 . . .
Vvi4g1181 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01813 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi07g01064 . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 8370775 8373587 - Bda018505.1 Bda04g00218 218
11 53291384 53298600 + Bda008743.2 Bda11g01813 1813
11 53305467 53307698 - Bda008745.1 Bda11g01815 1815
10 62070519 62078567 - XM_039045167.1 Bhi10g02361 2361
4 9527249 9538590 - BLOR13778 Blo04g00866 866
4 9547207 9549115 - BLOR13779 Blo04g00867 867
5 22493481 22500891 - BLOR15641 Blo05g00679 679
5 22622666 22625318 + BLOR15642 Blo05g00680 680
16 2413271 2413807 + BLOR07349 Blo16g00101 101
3 9809391 9878964 - Bma031007 Bma03g00933 933
6 1263976 1272810 - Bma022696.2 Bma06g00079 79
6 2848588 2850934 - Bpe019608.2 Bpe06g00156 156
6 2908058 2910592 + Bpe019609.2 Bpe06g00157 157
6 14728914 14731054 + Bpe019830.1 Bpe06g00332 332
13 11687067 11689827 - Bpe006518.1 Bpe13g00393 393
15 16186599 16193634 + Bpe001427.2 Bpe15g00494 494
15 16200344 16211751 + Bpe001428.1 Bpe15g00495 495
1 34192329 34194433 - CaPI482276_01g021360.1 Cam01g2136 2136
1 34196941 34200587 - CaPI482276_01g021370.1 Cam01g2137 2137
1 34205845 34208313 + CaPI482276_01g021380.1 Cam01g2138 2138
2 2060222 2068303 - CaPI482276_02g000950.1 Cam02g0095 95
3 5529843 5533465 + Carg00543-RA Car03g00583 583
7 1706335 1709914 - Carg07921-RA Car07g00341 341
7 1711954 1715350 + Carg07922-RA Car07g00342 342
7 1716167 1718891 + Carg07923-RA Car07g00343 343
2 964199 968676 - CcPI632755_02g000880.1 Cco02g0088 88
4 33276607 33278711 - CcPI632755_04g018590.1 Cco04g1859 1859
4 33281266 33284953 - CcPI632755_04g018600.1 Cco04g1860 1860
4 33289551 33292020 + CcPI632755_04g018610.1 Cco04g1861 1861
2 947478 949586 - CePI673135_02g000960.1 Cec02g0096 96
4 36762073 36764177 - CePI673135_04g017930.1 Cec04g1793 1793
4 36766666 36770385 - CePI673135_04g017940.1 Cec04g1794 1794
4 36774702 36777025 + CePI673135_04g017950.1 Cec04g1795 1795
2 3111456 3114016 - Chy2G027790.1 Chy02g00512 512
2 3118350 3121385 + Chy2G027800.1 Chy02g00513 513
2 3123461 3125701 + Chy2G027810.1 Chy02g00514 514
1 33043642 33045746 - ClG42_01g0215200.10 Clacu01g2152 2152
1 33048228 33051912 - ClG42_01g0215300.10 Clacu01g2153 2153
1 33057066 33059535 + ClG42_01g0215400.10 Clacu01g2154 2154
2 958186 963696 - ClG42_02g0009200.10 Clacu02g0092 92
1 34855041 34857145 - ClCG01G020810.1 Cla01g02030 2030
1 34859444 34863570 - ClCG01G020820.1 Cla01g02031 2031
1 34868473 34871541 + ClCG01G020830.2 Cla01g02032 2032
2 948538 975509 - ClCG02G000850.1 Cla02g00088 88
3 5438109 5443112 + CmaCh03G006280.1 Cma03g00628 628
7 1666988 1670270 - CmaCh07G003880.1 Cma07g00388 388
7 1672191 1675836 + CmaCh07G003890.1 Cma07g00389 389
7 1676542 1679435 + CmaCh07G003900.1 Cma07g00390 390
16 9654863 9667936 - CmaCh16G012650.1 Cma16g01265 1265
20 3326383 3329388 - CmaCh20G007190.1 Cma20g00719 719
8 6452554 6455301 - MELO3C007967.2.1 Cme08g00987 987
8 6457017 6460889 - MELO3C007968.2.1 Cme08g00988 988
8 6465462 6468432 + MELO3C007969.2.1 Cme08g00989 989
11 848532 849824 - MELO3C023285.2.1 Cme11g00099 99
3 5924066 5928258 + CmoCh03G006560.1 Cmo03g00656 656
7 1757514 1760521 - CmoCh07G003820.1 Cmo07g00382 382
7 1762431 1766141 + CmoCh07G003830.1 Cmo07g00383 383
7 1766868 1769743 + CmoCh07G003840.1 Cmo07g00384 384
1 33381216 33383320 - CmPI595203_01g020280.1 Cmu01g2028 2028
1 33385788 33389462 - CmPI595203_01g020290.1 Cmu01g2029 2029
1 33394601 33397052 + CmPI595203_01g020300.1 Cmu01g2030 2030
2 936955 951461 - CmPI595203_02g000870.1 Cmu02g0087 87
6 121496 122163 + Conep06aG0002000.1 Cone6ag0020 20
8 8676627 8686581 + Conep08aG0091400.1 Cone8ag0888 888
9 99910 100911 + Conep09aG0001900.1 Cone9ag0019 19
12 7701430 7710060 + Conep12aG0088300.1 Cone12ag0858 858
14 9857553 9859112 - Conep14aG0124200.1 Cone14ag1210 1210
15 9748359 9750038 - Conep15aG0125800.1 Cone15ag1229 1229
10 2114592 2121034 + Cp4.1LG10g03330.1 Cpe10g00358 358
19 6511803 6514472 - Cp4.1LG19g08510.1 Cpe19g00892 892
19 6515430 6519097 - Cp4.1LG19g08450.1 Cpe19g00893 893
19 6521519 6525135 + Cp4.1LG19g08580.1 Cpe19g00894 894
2 1444069 1445458 - CrPI670011_02g004260.1 Cre02g0426 426
4 35234569 35236673 - CrPI670011_04g017030.1 Cre04g1703 1703
4 35239218 35242866 - CrPI670011_04g017040.1 Cre04g1704 1704
4 35248272 35250743 + CrPI670011_04g017050.1 Cre04g1705 1705
6 28132320 28134466 - CsaV3_6G047770.1 Csa06g03391 3391
6 28137131 28140421 - CsaV3_6G047780.1 Csa06g03392 3392
6 28144323 28147463 + CsaV3_6G047800.1 Csa06g03394 3394
1 4373188 4377719 - Lsi01G005370.1 Lsi01g00537 537
1 4382511 4387721 + Lsi01G005380.1 Lsi01g00538 538
1 4388848 4391484 + Lsi01G005400.1 Lsi01g00540 540
7 16009303 16012812 + Lsi07G010640.1 Lsi07g01064 1064
7 16017882 16030294 - Lsi07G010660.1 Lsi07g01066 1066
7 16042189 16048003 - Lsi07G010680.1 Lsi07g01068 1068
10 9616876 9620384 + Lsi10G006850.1 Lsi10g00685 685
4 20482533 20500673 + Vvi4g1172 Vvi4g1172 1172
4 20501171 20504073 + Vvi4g1173 Vvi4g1173 1173
4 20507824 20508286 - Vvi4g1174 Vvi4g1174 1174
4 20522828 20529516 - Vvi4g1175 Vvi4g1175 1175
4 20530086 20532381 - Vvi4g1176 Vvi4g1176 1176
4 20536348 20537931 + Vvi4g1177 Vvi4g1177 1177
4 20538223 20543019 - Vvi4g1178 Vvi4g1178 1178
4 20556942 20562291 + Vvi4g1179 Vvi4g1179 1179
4 20563524 20579978 + Vvi4g1180 Vvi4g1180 1180
4 20591508 20599705 - Vvi4g1181 Vvi4g1181 1181
       

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