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
Vvi19g714 Blo03g00497 . Bda07g00422 . . . . Bma13g01130 . . Cma01g01063 Cma09g01026 Car01g00937 Car09g00929 Sed07g2752 Cpe06g00833 Cpe02g00834 Bhi09g01797 Tan01g3212 Cmetu01g0145 . . Mch11g1300 . . . . . . . . . . . . Lsi02g01811 . . . . . . Bda12g00980 Bpe11g00597 . . Bma14g00672 . Cmo01g01104 Cmo09g01028 . . . Car16g00969 . . . . . . . . . Cla09g02094 Cam09g2180 Cec09g2247 . . . . . . Chy01g01124 Cme01g00873
Vvi19g715 . . . . Bpe09g00111 . Bma10g00600 Bma13g01131 . . Cma01g01062 . Car01g00936 . Sed11g1171 . Cpe02g00835 Bhi09g01801 Tan01g3213 Cmetu03g0372 . . Mch11g1302 . . . . . . . . . . . . . . . . . . Bda05g00674 Bda12g00981 . Bpe03g00747 . . . Cmo01g01103 . . . . . . . . . . . . . . Cla09g02095 Cam09g2181 Cec09g2248 . . . . . . Chy01g01122 Cme01g00870
Vvi19g716 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g717 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g718 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g719 . . Bda07g00423 Bda09g00442 . . . . . . Cma01g01060 Cma09g01029 Car01g00934 Car09g00932 Sed04g3626 Cpe06g00836 Cpe02g00836 Bhi09g01804 Tan01g3218 Cmetu01g2692 . . Mch11g1304 . . . . . . . . . . . . Lsi02g01808 . . . . . . . Bpe11g00598 . . Bma14g00671 . Cmo01g01101 Cmo09g01031 . . . . . . . . . . . . . Cla09g02097 Cam09g2183 Cec09g2250 . . . . . . Chy01g01120 Cme01g00868
Vvi19g720 . . . . Bpe09g00110 . Bma10g00601 Bma13g01133 . . . . . . . . . . . . . . . . Cla10g00365 Cam10g0377 Cec10g0397 Cco10g0390 Clacu10g0383 Cmu10g1218 Cre10g0632 . . . . . . . . . Blo10g00879 Bda05g00672 Bda12g00983 . Bpe03g00746 . . . . . . Cma16g00992 . . . . . . . . . . . . . . . . . . . . . .
Vvi19g721 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g722 . . . . Bpe09g00109 Bpe08g01086 . . Cmo16g01031 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo10g00880 Bda05g00671 Bda12g00984 . Bpe03g00745 Bma07g01240 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g723 Blo03g00496 . Bda07g00424 . . . . . . . . Cma09g01030 . . Sed04g3622 Cpe06g00837 . Bhi09g01806 Tan01g3222 Cmetu01g1457 . . Mch11g1305 . . . . . . . . . . . . Lsi02g01807 . . . . . . . Bpe11g00599 . . Bma14g00669 . . Cmo09g01032 . . . . . . . . . . . . . Cla09g02098 Cam09g2184 Cec09g2251 . . . . . . Chy01g01119 Cme01g00861
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 55026059 55028975 + Bda021803.1 Bda05g00671 671
5 55030296 55032524 - Bda021804.1 Bda05g00672 672
5 55038996 55052721 - Bda033652 Bda05g00674 674
7 5413694 5415324 + Bda025517.1 Bda07g00422 422
7 5418031 5424028 - Bda025518.3 Bda07g00423 423
7 5428151 5428908 + Bda025519.1 Bda07g00424 424
9 5839036 5844245 - Bda031032.1 Bda09g00442 442
12 40942561 40944064 + Bda009526.1 Bda12g00980 980
12 40948971 40952825 + Bda009527.1 Bda12g00981 981
12 40968645 40970714 + Bda009530.1 Bda12g00983 983
12 40972661 40975386 - Bda009531.1 Bda12g00984 984
9 48905467 48907998 + XM_039041321.1 Bhi09g01797 1797
9 48949569 48954479 + XM_039044197.1 Bhi09g01801 1801
9 49020777 49030100 - XM_039041841.1 Bhi09g01804 1804
9 49056182 49061881 + XM_039040849.1 Bhi09g01806 1806
3 17946562 17947297 - BLOR11677 Blo03g00496 496
3 18086362 18087998 - BLOR11678 Blo03g00497 497
10 27574828 27598127 + BLOR02669 Blo10g00879 879
10 27599840 27602737 - BLOR02670 Blo10g00880 880
7 47345593 47348444 + Bma026492.1 Bma07g01240 1240
10 7320045 7322353 + Bma004307.1 Bma10g00600 600
10 7329891 7332116 + Bma004308.1 Bma10g00601 601
13 44393231 44394738 + Bma010259.1 Bma13g01130 1130
13 44409032 44413148 + Bma010260.1 Bma13g01131 1131
13 44423041 44425109 + Bma010263.1 Bma13g01133 1133
14 7257992 7260535 - Bma011118.1 Bma14g00669 669
14 7279356 7285396 + Bma011122.1 Bma14g00671 671
14 7287258 7288806 - Bma011123.1 Bma14g00672 672
3 27533125 27536052 + Bpe012654.1 Bpe03g00745 745
3 27539330 27541496 - Bpe012655.1 Bpe03g00746 746
3 27548833 27557069 - Bpe012656.3 Bpe03g00747 747
8 12965762 12968773 + Bpe023209.1 Bpe08g01086 1086
9 738247 741062 + Bpe023787.1 Bpe09g00109 109
9 742148 744178 - Bpe023788.2 Bpe09g00110 110
9 753000 757281 - Bpe023789.2 Bpe09g00111 111
11 4542952 4544523 + Bpe003962.2 Bpe11g00597 597
11 4549401 4555433 - Bpe003963.1 Bpe11g00598 598
11 4561943 4563354 + Bpe003964.1 Bpe11g00599 599
9 36313536 36319753 + CaPI482276_09g021800.1 Cam09g2180 2180
9 36324421 36328245 + CaPI482276_09g021810.1 Cam09g2181 2181
9 36333600 36340432 - CaPI482276_09g021830.1 Cam09g2183 2183
9 36344634 36364522 + CaPI482276_09g021840.1 Cam09g2184 2184
10 6051991 6054092 - CaPI482276_10g003770.1 Cam10g0377 377
1 9030428 9037557 + Carg23346-RA Car01g00934 934
1 9039378 9044515 - Carg23344-RA Car01g00936 936
1 9049200 9052258 - Carg23343-RA Car01g00937 937
9 5723236 5729796 + Carg24745-RA Car09g00929 929
9 5734034 5742242 - Carg24742-RA Car09g00932 932
16 8084760 8091807 - Carg25214-RA Car16g00969 969
10 4572826 4574925 - CcPI632755_10g003900.1 Cco10g0390 390
9 39341623 39349158 + CePI673135_09g022470.1 Cec09g2247 2247
9 39353559 39357417 + CePI673135_09g022480.1 Cec09g2248 2248
9 39362555 39369567 - CePI673135_09g022500.1 Cec09g2250 2250
9 39373900 39379669 + CePI673135_09g022510.1 Cec09g2251 2251
10 4769583 4774351 - CePI673135_10g003970.1 Cec10g0397 397
1 12797873 12815606 - Chy1G011190.1 Chy01g01119 1119
1 12815654 12823047 + Chy1G011200.1 Chy01g01120 1120
1 12840760 12844633 - Chy1G011220.1 Chy01g01122 1122
1 12873412 12874949 - Chy1G011240.1 Chy01g01124 1124
10 4841765 4843866 - ClG42_10g0038300.10 Clacu10g0383 383
9 38472958 38480724 + ClCG09G021510.2 Cla09g02094 2094
9 38485234 38489535 + ClCG09G021520.2 Cla09g02095 2095
9 38494346 38501952 - ClCG09G021540.1 Cla09g02097 2097
9 38506140 38511793 + ClCG09G021550.1 Cla09g02098 2098
10 4876225 4881303 - ClCG10G003890.1 Cla10g00365 365
1 7844159 7851138 + CmaCh01G010600.1 Cma01g01060 1060
1 7853061 7858001 - CmaCh01G010620.1 Cma01g01062 1062
1 7869119 7872561 - CmaCh01G010630.1 Cma01g01063 1063
9 5270586 5273381 + CmaCh09G010260.1 Cma09g01026 1026
9 5277219 5285408 - CmaCh09G010290.1 Cma09g01029 1029
9 5286192 5292720 + CmaCh09G010300.1 Cma09g01030 1030
16 7634180 7641640 + CmaCh16G009920.1 Cma16g00992 992
1 9786702 9791942 - MELO3C028909.2.1 Cme01g00861 861
1 9891492 9899239 + MELO3C024969.2.1 Cme01g00868 868
1 9911893 9916215 - MELO3C024967.2.1 Cme01g00870 870
1 9955188 9958149 - MELO3C024964.2.1 Cme01g00873 873
1 14190393 14191994 + PI0029176.1 Cmetu01g0145 145
1 14259984 14271801 + PI0028226.3 Cmetu01g1457 1457
1 14239186 14247196 - PI0012165.1 Cmetu01g2692 2692
3 22799635 22803627 + PI0020353.1 Cmetu03g0372 372
1 9167289 9174375 + CmoCh01G011010.1 Cmo01g01101 1101
1 9176070 9180978 - CmoCh01G011030.1 Cmo01g01103 1103
1 9185983 9189603 - CmoCh01G011040.1 Cmo01g01104 1104
9 5496998 5500165 + CmoCh09G010280.1 Cmo09g01028 1028
9 5503860 5512438 - CmoCh09G010310.1 Cmo09g01031 1031
9 5512265 5520098 + CmoCh09G010320.1 Cmo09g01032 1032
16 7195032 7198329 + CmoCh16G010310.1 Cmo16g01031 1031
10 4982685 4984786 - CmPI595203_10g012180.1 Cmu10g1218 1218
2 5337877 5341608 + Cp4.1LG02g00360.1 Cpe02g00834 834
2 5346636 5352763 + Cp4.1LG02g00390.1 Cpe02g00835 835
2 5353421 5360371 - Cp4.1LG02g00290.1 Cpe02g00836 836
6 5355990 5358324 + Cp4.1LG06g08280.1 Cpe06g00833 833
6 5362372 5371065 - Cp4.1LG06g08150.1 Cpe06g00836 836
6 5371429 5378152 + Cp4.1LG06g08290.1 Cpe06g00837 837
10 5894149 5898733 - CrPI670011_10g006320.1 Cre10g0632 632
2 23856222 23860051 - Lsi02G018070.1 Lsi02g01807 1807
2 23875347 23882702 + Lsi02G018080.1 Lsi02g01808 1808
2 23889611 23904650 - Lsi02G018110.1 Lsi02g01811 1811
11 9189657 9193066 + MC11g1076 Mch11g1300 1300
11 9204225 9209123 + MC11g1078 Mch11g1302 1302
11 9212963 9221241 - MC11g1080 Mch11g1304 1304
11 9222917 9227961 + MC11g1081 Mch11g1305 1305
4 45446486 45451883 - Sed0017011.1 Sed04g3622 3622
4 45455254 45462396 + Sed0019267.3 Sed04g3626 3626
7 42582017 42585162 - Sed0004744.2 Sed07g2752 2752
11 27617365 27623184 + Sed0008203.1 Sed11g1171 1171
1 86364109 86383404 + Tan0005123.1 Tan01g3212 3212
1 86437881 86442078 + Tan0009844.1 Tan01g3213 3213
1 86458400 86466535 - Tan0015593.2 Tan01g3218 3218
1 86517566 86524079 + Tan0015776.2 Tan01g3222 3222
19 9082907 9084983 + Vvi19g714 Vvi19g714 714
19 9094387 9098703 + Vvi19g715 Vvi19g715 715
19 9101590 9103718 - Vvi19g716 Vvi19g716 716
19 9113582 9114711 + Vvi19g717 Vvi19g717 717
19 9116146 9126416 + Vvi19g718 Vvi19g718 718
19 9136130 9146070 + Vvi19g719 Vvi19g719 719
19 9146519 9157750 + Vvi19g720 Vvi19g720 720
19 9157795 9158177 + Vvi19g721 Vvi19g721 721
19 9160944 9162797 - Vvi19g722 Vvi19g722 722
19 9168928 9178255 + Vvi19g723 Vvi19g723 723
       

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