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
Vvi18g690 . . . . . . . . . . . . . . . . Cpe07g00506 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma12g00578 . Car05g00136 . . . . . . . . . . . . . . . . . Lsi08g01506 Csa02g01915 Chy03g01570 .
Vvi18g691 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g692 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g693 . Blo12g00976 Bda01g00581 Bda03g00194 Bpe02g00444 Bpe04g00165 Bma04g00147 Bma01g02257 Cmo05g00159 Cmo12g00518 Cma01g01803 Cma09g00270 Car01g01408 Car12g00532 Sed10g1978 Cpe06g00185 Cpe07g00503 Bhi04g00390 Tan02g0995 Cmetu01g1482 . Hepe08g1310 . Lcy13g2114 Cla08g01600 Cam08g2100 Cec08g1681 Cco08g1812 Clacu08g1785 . Cre08g1567 . . Cone17ag0869 Cone20ag0217 Lsi04g01508 Csa04g02456 . Cme03g02080 . . . Bda01g01560 . Bpe05g00036 . Bma05g00047 . Cmo01g01859 Cmo09g00266 Cma12g00577 Cma05g00158 Car05g00137 Car09g00224 Cpe11g00133 Cpe02g00206 Bhi09g03262 . . . Hepe01g1808 . . Cla05g02086 Cam05g2238 Cec05g2258 Cco05g2298 Clacu05g2234 Cmu05g2098 Cre05g2223 Lsi08g01505 Csa02g01916 Chy07g00171 .
Vvi18g694 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe05g00489 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g695 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g696 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g697 Blo01g01506 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car09g00223 . . Bhi09g03264 . . . . . . Cla05g02084 . . . . . . . . Chy07g00168 .
Vvi18g698 Blo01g01509 . . . . . . . . . Cma01g01805 Cma09g00267 . . . . . . . . . . . . . . . . . . . . . . . Lsi04g01511 Csa04g02453 . . . . . . . . . . . Cmo01g01862 . . . . . . Cpe02g00204 . . . . . . . . . . . . . . . . . .
Vvi18g699 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 32830373 32832261 - Bda002600.1 Bda01g00581 581
1 51495590 51497796 - Bda003829.1 Bda01g01560 1560
3 1558109 1560119 + Bda016139.1 Bda03g00194 194
4 10133246 10135576 - XM_039029720.1 Bhi04g00390 390
9 83471184 83476686 + XM_039043204.1 Bhi09g03262 3262
9 83605735 83608854 + XM_039040758.1 Bhi09g03264 3264
1 54631776 54632683 - BLOR01506 Blo01g01506 1506
1 54642834 54644387 - BLOR01509 Blo01g01509 1509
12 27814784 27820291 - BLOR04995 Blo12g00976 976
1 79747472 79748625 + Bma003112.1 Bma01g02257 2257
4 1283818 1285824 + Bma018592.2 Bma04g00147 147
5 2323966 2324908 - Bma020736.1 Bma05g00047 47
2 2906099 2907915 - Bpe008285.1 Bpe02g00444 444
4 1081293 1083317 + Bpe014885.1 Bpe04g00165 165
5 702446 704351 - Bpe017423.2 Bpe05g00036 36
5 19122893 19123462 - Bpe017909.1 Bpe05g00489 489
5 30609286 30617128 - CaPI482276_05g022380.1 Cam05g2238 2238
8 26488282 26490095 - CaPI482276_08g021000.1 Cam08g2100 2100
1 12228308 12232486 + Carg10629-RA Car01g01408 1408
5 679259 680814 + Carg11868-RA Car05g00136 136
5 681997 683873 + Carg11867-RA Car05g00137 137
9 1265768 1267845 - Carg21798-RA Car09g00223 223
9 1270216 1272631 - Carg21797-RA Car09g00224 224
12 3524768 3526895 - Carg27307-RA Car12g00532 532
5 31630106 31636003 - CcPI632755_05g022980.1 Cco05g2298 2298
8 29187366 29189177 - CcPI632755_08g018120.1 Cco08g1812 1812
5 33998344 33999496 - CePI673135_05g022580.1 Cec05g2258 2258
8 28093077 28094890 - CePI673135_08g016810.1 Cec08g1681 1681
3 17817866 17821526 - Chy3G065500.1 Chy03g01570 1570
7 1404983 1407809 - Chy7G129980.1 Chy07g00168 168
7 1422202 1424360 - Chy7G130010.1 Chy07g00171 171
5 30812053 30817839 - ClG42_05g0223400.10 Clacu05g2234 2234
8 27240746 27242563 - ClG42_08g0178500.10 Clacu08g1785 1785
5 32494952 32497069 - ClCG05G020310.2 Cla05g02084 2084
5 32502845 32508359 - ClCG05G020325.1 Cla05g02086 2086
8 28660635 28662737 - ClCG08G016260.1 Cla08g01600 1600
1 12023071 12025280 + CmaCh01G018030.1 Cma01g01803 1803
1 12029068 12031631 + CmaCh01G018050.1 Cma01g01805 1805
5 686175 688470 + CmaCh05G001580.1 Cma05g00158 158
9 1109388 1111813 - CmaCh09G002670.1 Cma09g00267 267
9 1114199 1116416 - CmaCh09G002700.1 Cma09g00270 270
12 3019501 3021743 - CmaCh12G005770.1 Cma12g00577 577
12 3023990 3028038 - CmaCh12G005780.1 Cma12g00578 578
3 28205221 28207380 - MELO3C010828.2.1 Cme03g02080 2080
1 843638 846592 - PI0016386.1 Cmetu01g1482 1482
1 13520996 13525502 + CmoCh01G018590.1 Cmo01g01859 1859
1 13529829 13532319 + CmoCh01G018620.1 Cmo01g01862 1862
5 686871 689130 + CmoCh05G001590.1 Cmo05g00159 159
9 1172689 1178848 - CmoCh09G002660.1 Cmo09g00266 266
12 3185191 3187419 - CmoCh12G005180.1 Cmo12g00518 518
5 30546512 30552279 - CmPI595203_05g020980.1 Cmu05g2098 2098
17 6892006 6893882 - Conep17aG0088900.1 Cone17ag0869 869
20 931327 933139 - Conep20aG0022700.1 Cone20ag0217 217
2 1052436 1056431 - Cp4.1LG02g06600.1 Cpe02g00204 204
2 1058884 1064470 - Cp4.1LG02g06570.1 Cpe02g00206 206
6 995417 999399 - Cp4.1LG06g01980.1 Cpe06g00185 185
7 3300135 3302639 - Cp4.1LG07g04950.1 Cpe07g00503 503
7 3323608 3326734 - Cp4.1LG07g04960.1 Cpe07g00506 506
11 725289 727486 + Cp4.1LG11g01350.1 Cpe11g00133 133
5 33887321 33888452 - CrPI670011_05g022230.1 Cre05g2223 2223
8 28289464 28291277 - CrPI670011_08g015670.1 Cre08g1567 1567
2 18048006 18052185 + CsaV3_2G026350.1 Csa02g01915 1915
2 18053116 18056491 + CsaV3_2G026360.1 Csa02g01916 1916
4 24601161 24604034 - CsaV3_4G034790.1 Csa04g02453 2453
4 24614388 24616562 - CsaV3_4G034820.1 Csa04g02456 2456
1 83084556 83090842 - Hsped.01g18080.1 Hepe01g1808 1808
8 14851347 14854128 - Hsped.08g13100.1 Hepe08g1310 1310
13 40077248 40079536 - Maker00025168 Lcy13g2114 2114
4 22713118 22720058 + Lsi04G015080.1 Lsi04g01508 1508
4 22748193 22750916 + Lsi04G015110.1 Lsi04g01511 1511
8 23165205 23167558 - Lsi08G015050.1 Lsi08g01505 1505
8 23170049 23174187 - Lsi08G015060.1 Lsi08g01506 1506
10 36424674 36429638 + Sed0001979.1 Sed10g1978 1978
2 13927453 13931137 - Tan0002640.1 Tan02g0995 995
18 7977193 7980354 + Vvi18g690 Vvi18g690 690
18 7981191 7983386 - Vvi18g691 Vvi18g691 691
18 7983437 7986889 - Vvi18g692 Vvi18g692 692
18 7996241 7998773 + Vvi18g693 Vvi18g693 693
18 8000359 8000941 - Vvi18g694 Vvi18g694 694
18 8002638 8020766 - Vvi18g695 Vvi18g695 695
18 8020848 8029561 - Vvi18g696 Vvi18g696 696
18 8045603 8049549 + Vvi18g697 Vvi18g697 697
18 8050119 8054991 + Vvi18g698 Vvi18g698 698
18 8069330 8072096 + Vvi18g699 Vvi18g699 699
       

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