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
Vvi17g606 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00095 . . Cme12g01967 . . . . . . . . Sed08g2094 . . . . . . . . Bhi08g01130 Tan05g2411 . Lac10g0124 Hepe07g2485 . . Cla04g01177 Cam04g1234 Cec01g1745 Cco01g1791 Clacu04g1262 Cmu04g1241 Cre01g1535 . . . .
Vvi17g607 . . . . Bpe12g00530 . . . . . . Cma11g00119 . . . . . Bhi02g00283 . . . . . . Cla06g01564 . . . . . . . . . . . . . . . . . . . . . . . . Cmo11g00193 . . . Car18g00007 . . . . . . . . . . . . . . . . Lsi06g01438 Csa01g00268 Chy02g02467 Cme02g01854
Vvi17g608 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa01g00575 . . . . . Bda14g00882 . Bpe15g00590 . . . . . . . . . . . Bhi08g01128 . . Lac10g0125 Hepe07g2484 . . . . . . . . . . . . .
Vvi17g609 Blo04g00784 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00096 . Chy12g01520 Cme12g01966 . . . Bda14g00865 . . Bma03g00842 . Sed08g2095 . . . . . . . . Bhi08g01127 Tan05g2408 Cmetu06g2174 . Hepe07g1737 . . Cla04g01176 Cam04g1233 Cec01g1744 Cco01g1790 Clacu04g1261 Cmu04g1240 Cre01g1534 . . . .
Vvi17g610 . . . . . . Bma06g00258 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g611 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g612 . . Bda06g00529 . . . . Bma12g00973 . . . . Car10g00208 . . . . . . . . . . . . . . . . . . . . Cone13ag0045 Cone19ag0050 . . . . . Blo15g00329 . . Bpe07g00763 . . . . . . . . . . . Cpe18g00769 . . . . . . . . . . . . . . . . . .
Vvi17g613 . Blo16g00175 . . . . . . . . . . Car10g00207 Car11g00174 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe15g00587 . . . . . . . . . . Cpe18g00770 . . . . . . . . . . . . . . . . . .
Vvi17g614 . . Bda06g00530 . . . . Bma12g00974 . . Cma10g00222 . Car10g00206 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe07g00764 . . . . . . . . . . . Cpe18g00771 . . . . . . . . . . . . . . . . . .
Vvi17g615 . . . . . . Bma06g00160 . . . . . . . . Cpe20g00062 . . . . . . . . . . . . . . . Cone2ag0820 . . . . . . . . . Bda11g01714 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 7565688 7567516 + Bda023786.1 Bda06g00529 529
6 7568991 7571357 + Bda023787.1 Bda06g00530 530
11 51573919 51576023 - Bda008611.1 Bda11g01714 1714
14 6676648 6679856 - Bda027640.1 Bda14g00865 865
14 6814763 6815730 + Bda027660.1 Bda14g00882 882
2 5311894 5314131 - XM_039022639.1 Bhi02g00283 283
8 35876212 35879228 + XM_039039192.1 Bhi08g01127 1127
8 35876212 35879228 + XM_039039193.1 Bhi08g01128 1128
8 35879348 35881827 - XM_039038424.1 Bhi08g01130 1130
4 7795788 7798522 - BLOR13696 Blo04g00784 784
15 3854256 3856116 - BLOR06723 Blo15g00329 329
16 3921864 3923276 + BLOR07423 Blo16g00175 175
3 8052058 8055278 - Bma017157.1 Bma03g00842 842
6 2067425 2069610 + Bma022778.1 Bma06g00160 160
6 3565203 3570479 + Bma022889.1 Bma06g00258 258
12 41809759 41811578 + Bma008317.1 Bma12g00973 973
12 41812792 41815331 + Bma008318.1 Bma12g00974 974
7 14159799 14161634 + Bpe021609.1 Bpe07g00763 763
7 14162765 14165353 + Bpe021610.1 Bpe07g00764 764
12 11209051 11210826 - Bpe005796.2 Bpe12g00530 530
15 16823361 16824821 + Bpe001521.1 Bpe15g00587 587
15 16832926 16836177 + Bpe001524.1 Bpe15g00590 590
4 26358995 26362150 + CaPI482276_04g012330.1 Cam04g1233 1233
4 26362802 26365969 - CaPI482276_04g012340.1 Cam04g1234 1234
10 996306 999593 - Carg17937-RA Car10g00206 206
10 1001194 1002693 - Carg17936-RA Car10g00207 207
10 1004673 1007912 - Carg17935-RA Car10g00208 208
11 1006907 1008433 - Carg09215-RA Car11g00174 174
18 27729 32509 + Carg22779-RA Car18g00007 7
1 30613222 30616363 + CcPI632755_01g017900.1 Cco01g1790 1790
1 30617014 30620179 - CcPI632755_01g017910.1 Cco01g1791 1791
1 32035421 32038537 + CePI673135_01g017440.1 Cec01g1744 1744
1 32039189 32041481 - CePI673135_01g017450.1 Cec01g1745 1745
2 28253901 28255616 - Chy2G047340.1 Chy02g02467 2467
12 18979022 18981801 + Chy12G221200.1 Chy12g01520 1520
4 26715113 26718269 + ClG42_04g0126100.10 Clacu04g1261 1261
4 26718921 26722086 - ClG42_04g0126200.10 Clacu04g1262 1262
4 26955935 26959160 + ClCG04G012010.1 Cla04g01176 1176
4 26959544 26963107 - ClCG04G012020.2 Cla04g01177 1177
6 29201148 29202995 - ClCG06G015890.2 Cla06g01564 1564
10 986695 989839 - CmaCh10G002220.1 Cma10g00222 222
11 641425 643272 - CmaCh11G001190.1 Cma11g00119 119
2 25198486 25200174 - MELO3C029755.2.1 Cme02g01854 1854
12 25518334 25521649 + MELO3C002007.2.1 Cme12g01966 1966
12 25521883 25525120 - MELO3C002006.2.1 Cme12g01967 1967
6 28312858 28317212 - PI0025660.1 Cmetu06g2174 2174
11 941656 943371 + CmoCh11G001930.1 Cmo11g00193 193
4 26897037 26900199 + CmPI595203_04g012400.1 Cmu04g1240 1240
4 26900851 26903165 - CmPI595203_04g012410.1 Cmu04g1241 1241
2 34220832 34221817 + Conep02aG0184800.1 Cone2ag0820 820
13 265074 267972 + Conep13aG0004800.1 Cone13ag0045 45
19 325094 328095 + Conep19aG0005400.1 Cone19ag0050 50
18 7334973 7339313 + Cp4.1LG18g07670.1 Cpe18g00769 769
18 7341355 7342857 + Cp4.1LG18g07610.1 Cpe18g00770 770
18 7344186 7347815 + Cp4.1LG18g07600.1 Cpe18g00771 771
20 304168 308533 - Cp4.1LG20g00670.1 Cpe20g00062 62
1 28559471 28562654 + CrPI670011_01g015340.1 Cre01g1534 1534
1 28563287 28566454 - CrPI670011_01g015350.1 Cre01g1535 1535
1 1668697 1670520 + CsaV3_1G002680.1 Csa01g00268 268
1 3696677 3703694 - CsaV3_1G005750.1 Csa01g00575 575
7 59539392 59546383 + Hsped.07g17370.1 Hepe07g1737 1737
7 69171375 69175483 + Hsped.07g24840.1 Hepe07g2484 2484
7 69183881 69185746 - Hsped.07g24850.1 Hepe07g2485 2485
10 941896 945349 + Lag0024169.1 Lac10g0124 124
10 946013 949718 - Lag0024170.1 Lac10g0125 125
2 798991 801600 + Lsi02G000950.1 Lsi02g00095 95
2 801593 805455 - Lsi02G000960.1 Lsi02g00096 96
6 24921817 24923559 - Lsi06G014380.1 Lsi06g01438 1438
8 35064577 35068584 + Sed0025408.1 Sed08g2094 2094
8 35068646 35073712 - Sed0025079.1 Sed08g2095 2095
5 75291636 75295809 + Tan0009466.1 Tan05g2408 2408
5 75295927 75299810 - Tan0018721.3 Tan05g2411 2411
17 7338060 7342277 + Vvi17g606 Vvi17g606 606
17 7343335 7345183 + Vvi17g607 Vvi17g607 607
17 7384485 7411694 - Vvi17g608 Vvi17g608 608
17 7414903 7417081 - Vvi17g609 Vvi17g609 609
17 7424474 7429523 + Vvi17g610 Vvi17g610 610
17 7434850 7435273 - Vvi17g611 Vvi17g611 611
17 7465852 7468766 + Vvi17g612 Vvi17g612 612
17 7475228 7477459 + Vvi17g613 Vvi17g613 613
17 7501795 7507663 + Vvi17g614 Vvi17g614 614
17 7508596 7514311 + Vvi17g615 Vvi17g615 615
       

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