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
Vvi18g250 Blo01g01298 . . . Bpe02g00639 . . Bma01g02074 Cmo04g02483 Cmo15g00679 . Cma09g00787 . . Sed01g3115 Cpe06g00621 . Bhi04g01901 Tan11g1265 Cmetu07g2195 . . . . Cla08g00602 Cam08g1016 Cec08g0606 Cco08g0717 Clacu08g0727 . Cre08g0535 Cone4ag1414 Cone7ag1524 Cone17ag1287 Cone20ag0440 Lsi04g02397 Csa04g01791 . Cme03g00538 Blo17g00175 Blo18g00181 . . Bpe02g01646 Bpe14g00385 Bma01g00810 Bma02g00216 . . Cmo09g00779 . . Car04g02297 Car15g00617 Cpe01g02058 . . . . . . . . Cla11g01541 Cam11g1603 Cec11g1631 Cco11g1633 Clacu11g1759 Cmu11g1576 Cre11g1994 Lsi08g00442 . Chy07g00630 Cme07g00838
Vvi18g251 Blo01g01297 . . . Bpe02g00640 . . Bma01g02073 Cmo04g02481 Cmo15g00681 . . . . Sed01g3118 . . Bhi04g01902 Tan11g1266 Cmetu03g2252 . . . Lcy10g1232 Cla08g00600 Cam08g1013 Cec08g0604 Cco08g0714 Clacu08g0726 . Cre08g0534 . . Cone17ag1286 Cone20ag0441 . Csa04g01951 . Cme03g00540 . . . . . . . . . . . . . Car04g02296 Car15g00618 Cpe01g02057 . . . . . . . . . . . . . . . Lsi08g00441 . Chy03g00788 .
Vvi18g252 . . . Bda03g00013 . Bpe04g00007 Bma04g00012 . Cmo04g02479 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car04g02295 . Cpe01g02056 . . . . . . . . . . . . . . . . . . .
Vvi18g253 . . . . . . . . Cmo04g02477 Cmo15g00685 . . . . Sed01g3120 . . Bhi04g01905 Tan11g1268 Cmetu03g0844 . Hepe02g2259 . Lcy10g1230 Cla08g00599 Cam08g1012 Cec08g0603 Cco08g0713 Clacu08g0724 . Cre08g0533 . . . Cone20ag0442 . . . Cme03g00543 Blo17g00176 . . Bda13g01480 . Bpe14g00384 . Bma02g00217 . . . . . Car04g02294 Car15g00620 Cpe01g02055 . . . . . . . . . . . . . . . Lsi08g00440 . Chy03g00792 .
Vvi18g254 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g255 . . . . . . . . . . . Cma09g00791 . . . Cpe06g00624 . . . . . . . . . . . . . . . Cone4ag1413 Cone7ag1525 . . Lsi04g02394 Csa04g01794 . . . . . Bda01g01441 Bpe02g01645 . . . . . Cmo09g00783 . . . Car09g00704 . . Bhi09g02687 . . . . . . Cla11g01539 Cam11g1600 Cec11g1629 Cco11g1630 Clacu11g1757 Cmu11g1573 Cre11g1991 . . Chy07g00633 Cme07g00847
Vvi18g256 . . . . . . . Bma01g02072 . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag1526 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g257 . . . . . . . . . . Cma01g01395 . . . . . . . . . . . . . . . . . . . . Cone12ag1193 Cone8ag1241 . . . . . . . . Bda08g01232 . . Bpe05g00130 . . . Cmo01g01447 . . . . . . Cpe02g00544 . . . . . . . . . . . . . . . . . .
Vvi18g258 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g259 . . . . . . . . Cmo04g02476 . Cma01g01052 . Car01g00927 . . . . Bhi04g01910 Tan11g1271 . . Hepe02g2263 . . Cla08g00595 . Cec08g0599 Cco08g0709 Clacu08g0719 . Cre08g0529 Cone4ag1411 Cone7ag1527 . . . . . Cme03g00549 . Blo18g00183 . . Bpe02g01644 . Bma01g00813 . Sed07g2802 Cmo01g01092 . . . Car04g02293 . Cpe01g02054 Cpe02g00843 Bhi09g01832 Tan01g3241 Cmetu01g1881 . . Mch11g1322 . . . . . . . . Lsi08g00438 . Chy03g00794 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 50320956 50325683 + Bda003686.1 Bda01g01441 1441
3 334027 338108 - Bda015946.1 Bda03g00013 13
8 50482970 50484393 + Bda030225.1 Bda08g01232 1232
13 37733569 37735896 - Bda000324.1 Bda13g01480 1480
4 47880412 47885877 + XM_039029621.1 Bhi04g01901 1901
4 47946794 47950954 - XM_039028410.1 Bhi04g01902 1902
4 48010574 48017779 - XM_039029285.1 Bhi04g01905 1905
4 48259529 48262022 + XM_039030324.1 Bhi04g01910 1910
9 49753570 49756262 + XM_039042041.1 Bhi09g01832 1832
9 72176927 72185875 - XM_039042952.1 Bhi09g02687 2687
1 49779173 49780342 + BLOR01297 Blo01g01297 1297
1 49781028 49786340 - BLOR01298 Blo01g01298 1298
17 1771070 1773849 + BLOR15996 Blo17g00175 175
17 1799754 1802138 - BLOR15997 Blo17g00176 176
18 1722069 1748855 + BLOR08669 Blo18g00181 181
18 1755207 1758967 + BLOR08671 Blo18g00183 183
1 7594493 7597678 + Bma001028.1 Bma01g00810 810
1 7670267 7672341 + Bma001031.1 Bma01g00813 813
1 76161458 76161916 + Bma002882.1 Bma01g02072 2072
1 76164242 76165446 + Bma002883.1 Bma01g02073 2073
1 76166100 76170942 - Bma002884.1 Bma01g02074 2074
2 2311589 2314874 + Bma014673.1 Bma02g00216 216
2 2324131 2326488 - Bma014674.1 Bma02g00217 217
4 191144 195219 - Bma031076 Bma04g00012 12
2 4182582 4186922 + Bpe008478.1 Bpe02g00639 639
2 4187599 4188759 - Bpe025092 Bpe02g00640 640
2 19205837 19207926 - Bpe009489.1 Bpe02g01644 1644
2 19210161 19214822 - Bpe025160 Bpe02g01645 1645
2 19216960 19219969 - Bpe025161 Bpe02g01646 1646
4 82853 86918 - Bpe014736.1 Bpe04g00007 7
5 2941980 2943384 - Bpe017515.1 Bpe05g00130 130
14 3609020 3611339 + Bpe007037.1 Bpe14g00384 384
14 3619077 3622323 - Bpe007038.1 Bpe14g00385 385
8 16310944 16317804 + CaPI482276_08g010120.1 Cam08g1012 1012
8 16351858 16355900 + CaPI482276_08g010130.1 Cam08g1013 1013
8 16373313 16377148 - CaPI482276_08g010160.1 Cam08g1016 1016
11 28756017 28760118 - CaPI482276_11g016000.1 Cam11g1600 1600
11 28775045 28780832 - CaPI482276_11g016030.1 Cam11g1603 1603
1 8961257 8963646 - Carg23356-RA Car01g00927 927
4 18412154 18415129 - Carg24435-RA Car04g02293 2293
4 18420585 18425184 + Carg24434-RA Car04g02294 2294
4 18425627 18432516 - Carg24433-RA Car04g02295 2295
4 18440015 18442403 + Carg24432-RA Car04g02296 2296
4 18444002 18448613 - Carg24431-RA Car04g02297 2297
9 4172678 4177790 + Carg17023-RA Car09g00704 704
15 3427517 3430354 + Carg01538-RA Car15g00617 617
15 3430886 3433087 - Carg01537-RA Car15g00618 618
15 3443544 3447736 - Carg01535-RA Car15g00620 620
8 18569793 18572184 - CcPI632755_08g007090.1 Cco08g0709 709
8 18666628 18673687 + CcPI632755_08g007130.1 Cco08g0713 713
8 18714733 18718857 + CcPI632755_08g007140.1 Cco08g0714 714
8 18741156 18745022 - CcPI632755_08g007170.1 Cco08g0717 717
11 29132262 29134697 - CcPI632755_11g016300.1 Cco11g1630 1630
11 29152242 29157442 - CcPI632755_11g016330.1 Cco11g1633 1633
8 17402533 17404895 - CePI673135_08g005990.1 Cec08g0599 599
8 17516670 17523526 + CePI673135_08g006030.1 Cec08g0603 603
8 17555276 17559325 + CePI673135_08g006040.1 Cec08g0604 604
8 17579445 17583269 - CePI673135_08g006060.1 Cec08g0606 606
11 30574060 30583961 - CePI673135_11g016290.1 Cec11g1629 1629
11 30595395 30606690 - CePI673135_11g016310.1 Cec11g1631 1631
3 10786315 10789156 - Chy3G057680.1 Chy03g00788 788
3 10815709 10821412 - Chy3G057720.1 Chy03g00792 792
3 10887736 10889985 + Chy3G057740.1 Chy03g00794 794
7 5935314 5943772 + Chy7G134600.1 Chy07g00630 630
7 5977474 5978716 + Chy7G134630.1 Chy07g00633 633
8 16954420 16956775 - ClG42_08g0071900.10 Clacu08g0719 719
8 17054172 17065186 + ClG42_08g0072400.10 Clacu08g0724 724
8 17099608 17100126 + ClG42_08g0072600.10 Clacu08g0726 726
8 17119788 17124671 - ClG42_08g0072700.10 Clacu08g0727 727
11 28744169 28783509 - ClG42_11g0175700.10 Clacu11g1757 1757
11 28794450 28805719 - ClG42_11g0175900.10 Clacu11g1759 1759
8 17766531 17769681 - ClCG08G005730.2 Cla08g00595 595
8 17868183 17875608 + ClCG08G005780.1 Cla08g00599 599
8 17908808 17914418 + ClCG08G005790.2 Cla08g00600 600
8 17933797 17939127 - ClCG08G005800.1 Cla08g00602 602
11 29030178 29070288 - ClCG11G015770.2 Cla11g01539 1539
11 29081073 29094177 - ClCG11G015810.2 Cla11g01541 1541
1 7789110 7791633 - CmaCh01G010520.1 Cma01g01052 1052
1 9879945 9882296 - CmaCh01G013950.1 Cma01g01395 1395
9 3818045 3822330 + CmaCh09G007870.1 Cma09g00787 787
9 3831715 3837020 + CmaCh09G007910.1 Cma09g00791 791
3 8063267 8067425 + MELO3C010625.2.1 Cme03g00538 538
3 8082730 8095591 - MELO3C010624.2.1 Cme03g00540 540
3 8187305 8193869 - MELO3C010623.2.1 Cme03g00543 543
3 8411937 8414537 + MELO3C010619.2.1 Cme03g00549 549
7 8104097 8111040 + MELO3C010490.2.1 Cme07g00838 838
7 8280506 8286035 + MELO3C010482.2.1 Cme07g00847 847
1 8970077 8982421 + PI0023409.1 Cmetu01g1881 1881
3 13878104 13884967 - PI0018952.1 Cmetu03g0844 844
3 13661054 13664402 + PI0022786.1 Cmetu03g2252 2252
7 19795134 19799763 - PI0028691.1 Cmetu07g2195 2195
1 9100615 9103009 - CmoCh01G010920.1 Cmo01g01092 1092
1 11287609 11290185 - CmoCh01G014470.1 Cmo01g01447 1447
4 18271101 18274139 - CmoCh04G024760.1 Cmo04g02476 2476
4 18279987 18285521 + CmoCh04G024770.1 Cmo04g02477 2477
4 18285707 18292273 - CmoCh04G024790.1 Cmo04g02479 2479
4 18300167 18302632 + CmoCh04G024810.1 Cmo04g02481 2481
4 18306236 18310066 - CmoCh04G024830.1 Cmo04g02483 2483
9 3966342 3970638 + CmoCh09G007790.1 Cmo09g00779 779
9 3981717 3986739 + CmoCh09G007830.1 Cmo09g00783 783
15 3330349 3334082 + CmoCh15G006790.1 Cmo15g00679 679
15 3335966 3337293 - CmoCh15G006810.1 Cmo15g00681 681
15 3349906 3354364 - CmoCh15G006850.1 Cmo15g00685 685
11 27997544 28038515 - CmPI595203_11g015730.1 Cmu11g1573 1573
11 28053301 28059090 - CmPI595203_11g015760.1 Cmu11g1576 1576
4 11302179 11304073 - Conep04aG0146100.1 Cone4ag1411 1411
4 11309658 11312579 - Conep04aG0146400.1 Cone4ag1413 1413
4 11313154 11315176 - Conep04aG0146500.1 Cone4ag1414 1414
7 10577119 10580769 + Conep07aG0156800.1 Cone7ag1524 1524
7 10580925 10583475 + Conep07aG0156900.1 Cone7ag1525 1525
7 10583793 10584406 - Conep07aG0157100.1 Cone7ag1526 1526
7 10586547 10588355 + Conep07aG0157200.1 Cone7ag1527 1527
8 10414340 10416112 - Conep08aG0127900.1 Cone8ag1241 1241
12 9395083 9396867 - Conep12aG0123300.1 Cone12ag1193 1193
17 9221135 9223107 + Conep17aG0131800.1 Cone17ag1286 1286
17 9223963 9228729 - Conep17aG0131900.1 Cone17ag1287 1287
20 2221356 2226037 + Conep20aG0045500.1 Cone20ag0440 440
20 2226763 2228613 - Conep20aG0045600.1 Cone20ag0441 441
20 2235493 2239299 - Conep20aG0045700.1 Cone20ag0442 442
1 17408277 17411396 - Cp4.1LG01g20580.1 Cpe01g02054 2054
1 17417169 17421425 + Cp4.1LG01g20560.1 Cpe01g02055 2055
1 17420672 17428940 - Cp4.1LG01g20630.1 Cpe01g02056 2056
1 17435628 17439537 + Cp4.1LG01g20550.1 Cpe01g02057 2057
1 17441057 17445617 - Cp4.1LG01g20610.1 Cpe01g02058 2058
2 3249150 3252214 + Cp4.1LG02g03250.1 Cpe02g00544 544
2 5415469 5418268 + Cp4.1LG02g00370.1 Cpe02g00843 843
6 3844486 3851211 + Cp4.1LG06g06170.1 Cpe06g00621 621
6 3858742 3863739 + Cp4.1LG06g06210.1 Cpe06g00624 624
8 17849624 17852008 - CrPI670011_08g005290.1 Cre08g0529 529
8 17957017 17967984 + CrPI670011_08g005330.1 Cre08g0533 533
8 17995045 17999080 + CrPI670011_08g005340.1 Cre08g0534 534
8 18023837 18027686 - CrPI670011_08g005350.1 Cre08g0535 535
11 31653904 31685027 - CrPI670011_11g019910.1 Cre11g1991 1991
11 31700152 31705940 - CrPI670011_11g019940.1 Cre11g1994 1994
4 17583570 17590505 + CsaV3_4G028170.1 Csa04g01791 1791
4 17614292 17620086 + CsaV3_4G028200.1 Csa04g01794 1794
4 19429525 19432587 + CsaV3_4G029770.1 Csa04g01951 1951
2 64990524 64994765 - Hsped.02g22590.1 Hepe02g2259 2259
2 65433708 65434286 + Hsped.02g22630.1 Hepe02g2263 2263
10 34964379 34968757 + Maker00008754 Lcy10g1230 1230
10 35001365 35004196 + Maker00008553 Lcy10g1232 1232
4 31063877 31105210 - Lsi04G023940.1 Lsi04g02394 2394
4 31118044 31125264 - Lsi04G023970.1 Lsi04g02397 2397
8 11924756 11927292 - Lsi08G004380.1 Lsi08g00438 438
8 11986661 11994271 + Lsi08G004400.1 Lsi08g00440 440
8 12034744 12039794 + Lsi08G004410.1 Lsi08g00441 441
8 12044547 12050660 - Lsi08G004420.1 Lsi08g00442 442
11 9347452 9350170 + MC11g1094 Mch11g1322 1322
1 42867839 42872875 + Sed0016452.2 Sed01g3115 3115
1 42897882 42899066 - Sed0016824.2 Sed01g3118 3118
1 43086771 43088057 - Sed0001258.1 Sed01g3120 3120
7 42884946 42889867 - Sed0004108.1 Sed07g2802 2802
1 87030373 87042945 + Tan0010753.1 Tan01g3241 3241
11 10784753 10790236 + Tan0002896.2 Tan11g1265 1265
11 10792753 10796061 - Tan0022658.1 Tan11g1266 1266
11 10822211 10828356 - Tan0009554.1 Tan11g1268 1268
11 10886528 10889323 + Tan0009362.3 Tan11g1271 1271
18 2791845 2798321 + Vvi18g250 Vvi18g250 250
18 2802827 2805264 - Vvi18g251 Vvi18g251 251
18 2813080 2821818 + Vvi18g252 Vvi18g252 252
18 2822056 2827234 - Vvi18g253 Vvi18g253 253
18 2845414 2847132 + Vvi18g254 Vvi18g254 254
18 2855223 2860662 + Vvi18g255 Vvi18g255 255
18 2861112 2864726 - Vvi18g256 Vvi18g256 256
18 2866300 2870837 - Vvi18g257 Vvi18g257 257
18 2875899 2876019 + Vvi18g258 Vvi18g258 258
18 2877303 2880161 + Vvi18g259 Vvi18g259 259
       

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