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
Vvi18g260 Blo01g01296 Blo12g01127 Bda01g00654 Bda03g00012 Bpe02g00642 Bpe04g00006 Bma04g00011 Bma01g02071 Cmo04g02472 Cmo15g00690 . . . . . . . Bhi04g01914 . . . Hepe02g2268 . . Cla08g00590 Cam08g1005 Cec08g0595 Cco08g0704 Clacu08g0714 . Cre08g0525 Cone4ag1410 Cone7ag1528 . . . . . Cme03g00556 . . . . . . . . . . . . . Car04g02290 Car15g00623 Cpe01g02051 . . . . . . . . . . . . . . . Lsi08g00436 . Chy03g00799 .
Vvi18g261 . . . . . . . . . Cmo15g00691 . . . . Sed01g3125 . . Bhi04g01915 Tan11g1277 Cmetu03g1464 . Hepe02g2272 . Lcy10g1225 Cla08g00589 Cam08g1004 Cec08g0594 Cco08g0703 Clacu08g0713 . Cre08g0524 . Cone7ag1529 . . . . . Cme03g00559 . . . Bda01g01428 Bpe02g01642 . . . . . . . . . Car15g00624 . . . . . . . . . . . . . . . . Lsi08g00435 . Chy03g00800 .
Vvi18g262 . Blo12g00890 . Bda03g00283 . . Bma04g00240 . Cmo04g02471 . . . . . . Cpe06g00076 . . . . . . . . Cla08g00588 Cam08g1003 Cec08g0593 Cco08g0702 Clacu08g0712 . Cre08g0523 . Cone7ag1530 Cone17ag1283 Cone20ag0443 Lsi04g01729 . . . . Blo18g00184 . . . . . . . . . . . Car04g02288 Car09g00102 Cpe01g02050 . . . . . . . . . . . . . . . Lsi08g00434 . . .
Vvi18g263 . . . . . . . . . Cmo15g00692 . . . . Sed01g3126 . . Bhi04g01916 Tan11g1279 Cmetu03g0859 . Hepe02g2273 . Lcy10g1224 . . . . . . . . . . . . . . Cme03g00560 . . . Bda01g01427 Bpe02g01641 . Bma01g00819 . . . . . . . . . . . . . . . . . . . . . . . . . . Chy03g00801 .
Vvi18g264 Blo01g01295 . . . Bpe02g00643 . . Bma01g02070 Cmo04g02470 Cmo15g00693 . . . . Sed01g3127 . . Bhi04g01917 Tan11g1281 Cmetu03g0812 . Hepe02g2274 . Lcy10g1223 Cla08g00587 Cam08g1002 Cec08g0591 Cco08g0701 Clacu08g0711 . Cre08g0522 Cone4ag1409 Cone7ag1531 . . . . . Cme03g00563 . . . . . . . . . . . . . Car04g02287 Car15g00626 Cpe01g02049 . . . . . . . . . . . . . . . Lsi08g00433 . Chy03g00803 .
Vvi18g265 . . . . Bpe02g00644 . . Bma01g02069 . . Cma01g01396 . . . . . . . . . . . . . . . . . . . . . Cone7ag1532 . . Lsi04g02392 Csa04g01800 . . . . . . . . . . . Cmo01g01448 Cmo09g00787 . . . Car09g00708 . . . . . . . . . Cla11g01537 Cam11g1597 Cec11g1626 Cco11g1627 Clacu11g1755 Cmu11g1571 Cre11g1988 . . Chy07g00643 Cme07g00852
Vvi18g266 . . . . . . . . . . . . . . . . Cpe07g00148 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g267 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1408 Cone7ag1533 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g268 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g269 Blo01g01294 . . Bda03g00011 Bpe02g00645 . Bma04g00010 Bma01g02068 Cmo04g02469 Cmo15g00694 . . . . Sed03g0789 . . Bhi04g01918 Tan11g1283 Cmetu03g1887 . Hepe02g2275 . . Cla08g00586 Cam08g1001 Cec08g0590 Cco08g0700 Clacu08g0710 . Cre08g0521 . . . . . . . Cme03g00566 Blo17g00177 . . Bda13g01481 Bpe02g01640 Bpe14g00383 Bma01g00820 . . . . . . Car04g02286 Car15g00627 Cpe01g02048 . . . . . . . . . . . . . . . . . Chy03g00806 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 33528371 33530244 + Bda002681.1 Bda01g00654 654
1 50184361 50186842 + Bda003672.1 Bda01g01427 1427
1 50187547 50189221 - Bda003673.1 Bda01g01428 1428
3 322985 323727 + Bda015943.1 Bda03g00011 11
3 330573 332996 + Bda015945.2 Bda03g00012 12
3 2480830 2484627 + Bda016241.1 Bda03g00283 283
13 37747052 37748118 - Bda000325.1 Bda13g01481 1481
4 48282161 48286183 - XM_039028653.1 Bhi04g01914 1914
4 48288325 48292377 + XM_039028655.1 Bhi04g01915 1915
4 48341045 48346531 - XM_039029126.1 Bhi04g01916 1916
4 48367889 48371780 + XM_039029215.1 Bhi04g01917 1917
4 48381506 48383119 - XM_039028368.1 Bhi04g01918 1918
1 49689239 49690096 + BLOR01294 Blo01g01294 1294
1 49770053 49771155 - BLOR01295 Blo01g01295 1295
1 49771687 49774758 + BLOR01296 Blo01g01296 1296
12 27077103 27083284 - BLOR04909 Blo12g00890 890
12 28896379 28900640 - BLOR05146 Blo12g01127 1127
17 1828379 1830046 - BLOR15998 Blo17g00177 177
18 1759525 1769076 - BLOR08672 Blo18g00184 184
1 7735307 7737756 - Bma001038.1 Bma01g00819 819
1 7743008 7744186 - Bma001039.1 Bma01g00820 820
1 76151812 76152740 + Bma002878.1 Bma01g02068 2068
1 76154002 76155060 - Bma002879.1 Bma01g02069 2069
1 76156357 76157577 - Bma002880.1 Bma01g02070 2070
1 76158313 76160864 + Bma002881.1 Bma01g02071 2071
4 183248 184354 + Bma018460.1 Bma04g00010 10
4 187509 190116 + Bma018461.1 Bma04g00011 11
4 2070644 2074445 + Bma018692.1 Bma04g00240 240
2 4192533 4195237 - Bpe008479.1 Bpe02g00642 642
2 4195995 4197180 + Bpe025094 Bpe02g00643 643
2 4203410 4204972 + Bpe008480.1 Bpe02g00644 644
2 4206300 4207162 - Bpe008481.1 Bpe02g00645 645
2 19190643 19191803 + Bpe009485.1 Bpe02g01640 1640
2 19195947 19199427 + Bpe009486.1 Bpe02g01641 1641
2 19201584 19203263 - Bpe009487.1 Bpe02g01642 1642
4 79513 81880 + Bpe025559 Bpe04g00006 6
14 3598528 3599614 + Bpe007036.1 Bpe14g00383 383
8 16142077 16143348 + CaPI482276_08g010010.1 Cam08g1001 1001
8 16152689 16154545 - CaPI482276_08g010020.1 Cam08g1002 1002
8 16175614 16179520 + CaPI482276_08g010030.1 Cam08g1003 1003
8 16181787 16187074 - CaPI482276_08g010040.1 Cam08g1004 1004
8 16187120 16190063 + CaPI482276_08g010050.1 Cam08g1005 1005
11 28702699 28704751 + CaPI482276_11g015970.1 Cam11g1597 1597
4 18382052 18383674 + Carg24442-RA Car04g02286 2286
4 18388536 18390560 - Carg24441-RA Car04g02287 2287
4 18396983 18400731 + Carg24440-RA Car04g02288 2288
4 18404341 18405747 + Carg24437-RA Car04g02290 2290
9 498541 502565 - Carg08686-RA Car09g00102 102
9 4213699 4215552 - Carg17027-RA Car09g00708 708
15 3460652 3463409 - Carg01532-RA Car15g00623 623
15 3464018 3467510 + Carg01531-RA Car15g00624 624
15 3477823 3479013 + Carg01529-RA Car15g00626 626
15 3484129 3487917 - Carg01528-RA Car15g00627 627
8 18483413 18484681 + CcPI632755_08g007000.1 Cco08g0700 700
8 18500738 18502516 - CcPI632755_08g007010.1 Cco08g0701 701
8 18522289 18526163 + CcPI632755_08g007020.1 Cco08g0702 702
8 18528292 18533704 - CcPI632755_08g007030.1 Cco08g0703 703
8 18533750 18536700 + CcPI632755_08g007040.1 Cco08g0704 704
11 29078025 29080098 + CcPI632755_11g016270.1 Cco11g1627 1627
8 17315461 17316711 + CePI673135_08g005900.1 Cec08g0590 590
8 17337841 17339614 - CePI673135_08g005910.1 Cec08g0591 591
8 17365345 17369243 + CePI673135_08g005930.1 Cec08g0593 593
8 17371615 17376891 - CePI673135_08g005940.1 Cec08g0594 594
8 17376938 17379884 + CePI673135_08g005950.1 Cec08g0595 595
11 30527838 30529881 + CePI673135_11g016260.1 Cec11g1626 1626
3 10962145 10965542 - Chy3G057790.1 Chy03g00799 799
3 10966904 10970521 + Chy3G057800.1 Chy03g00800 800
3 10972482 10976441 - Chy3G057810.1 Chy03g00801 801
3 11022679 11024353 + Chy3G057830.1 Chy03g00803 803
3 11091341 11092736 - Chy3G057860.1 Chy03g00806 806
7 6092199 6094171 - Chy7G134730.1 Chy07g00643 643
8 16868982 16870261 + ClG42_08g0071000.10 Clacu08g0710 710
8 16897006 16898798 - ClG42_08g0071100.10 Clacu08g0711 711
8 16917378 16921287 + ClG42_08g0071200.10 Clacu08g0712 712
8 16923618 16928945 - ClG42_08g0071300.10 Clacu08g0713 713
8 16928991 16931940 + ClG42_08g0071400.10 Clacu08g0714 714
11 28727923 28729964 + ClG42_11g0175500.10 Clacu11g1755 1755
8 17676736 17678997 + ClCG08G005630.2 Cla08g00586 586
8 17708433 17710488 - ClCG08G005640.1 Cla08g00587 587
8 17728886 17733124 + ClCG08G005650.1 Cla08g00588 588
8 17735187 17738983 - ClCG08G005670.2 Cla08g00589 589
8 17740332 17743509 + ClCG08G005680.2 Cla08g00590 590
11 29013903 29016449 + ClCG11G015750.1 Cla11g01537 1537
1 9884123 9886541 + CmaCh01G013960.1 Cma01g01396 1396
3 8599248 8603842 - MELO3C010614.2.1 Cme03g00556 556
3 8627971 8631851 + MELO3C010612.2.1 Cme03g00559 559
3 8633154 8637954 - MELO3C010611.2.1 Cme03g00560 560
3 8711437 8713977 + MELO3C010608.2.1 Cme03g00563 563
3 8757380 8759591 - MELO3C010605.2.1 Cme03g00566 566
7 8381256 8383968 - MELO3C010478.2.1 Cme07g00852 852
3 14161644 14163525 + PI0026373.1 Cmetu03g0812 812
3 14127959 14133216 - PI0012673.1 Cmetu03g0859 859
3 14115959 14120144 + PI0006964.1 Cmetu03g1464 1464
3 13286470 13288234 - PI0012172.1 Cmetu03g1887 1887
1 11291708 11294096 + CmoCh01G014480.1 Cmo01g01448 1448
4 18241204 18242829 + CmoCh04G024690.1 Cmo04g02469 2469
4 18247639 18249613 - CmoCh04G024700.1 Cmo04g02470 2470
4 18255211 18260048 + CmoCh04G024710.1 Cmo04g02471 2471
4 18260815 18264056 + CmoCh04G024720.1 Cmo04g02472 2472
9 4024756 4027265 - CmoCh09G007870.1 Cmo09g00787 787
15 3366944 3369605 - CmoCh15G006900.1 Cmo15g00690 690
15 3370321 3373773 + CmoCh15G006910.1 Cmo15g00691 691
15 3375209 3380334 - CmoCh15G006920.1 Cmo15g00692 692
15 3384093 3385642 + CmoCh15G006930.1 Cmo15g00693 693
15 3390670 3392873 - CmoCh15G006940.1 Cmo15g00694 694
11 27981262 27983303 + CmPI595203_11g015710.1 Cmu11g1571 1571
4 11288740 11290730 - Conep04aG0145700.1 Cone4ag1408 1408
4 11291482 11293367 - Conep04aG0145800.1 Cone4ag1409 1409
4 11299050 11301704 + Conep04aG0146000.1 Cone4ag1410 1410
7 10588615 10591815 - Conep07aG0157300.1 Cone7ag1528 1528
7 10592228 10593992 + Conep07aG0157400.1 Cone7ag1529 1529
7 10594933 10597444 - Conep07aG0157600.1 Cone7ag1530 1530
7 10599552 10601185 + Conep07aG0157700.1 Cone7ag1531 1531
7 10601749 10603227 + Conep07aG0157800.1 Cone7ag1532 1532
7 10604058 10605800 + Conep07aG0157900.1 Cone7ag1533 1533
17 9212551 9215865 + Conep17aG0131400.1 Cone17ag1283 1283
20 2251960 2255889 - Conep20aG0045800.1 Cone20ag0443 443
1 17378680 17380274 + Cp4.1LG01g20350.1 Cpe01g02048 2048
1 17385058 17387341 - Cp4.1LG01g20490.1 Cpe01g02049 2049
1 17392355 17397050 + Cp4.1LG01g20390.1 Cpe01g02050 2050
1 17397954 17402243 + Cp4.1LG01g20380.1 Cpe01g02051 2051
6 373175 379306 - Cp4.1LG06g00650.1 Cpe06g00076 76
7 837726 843491 - Cp4.1LG07g01520.1 Cpe07g00148 148
8 17771851 17773139 + CrPI670011_08g005210.1 Cre08g0521 521
8 17794019 17795813 - CrPI670011_08g005220.1 Cre08g0522 522
8 17813806 17817711 + CrPI670011_08g005230.1 Cre08g0523 523
8 17820115 17825363 - CrPI670011_08g005240.1 Cre08g0524 524
8 17825409 17828361 + CrPI670011_08g005250.1 Cre08g0525 525
11 31627090 31629129 + CrPI670011_11g019880.1 Cre11g1988 1988
4 17668278 17670903 - CsaV3_4G028260.1 Csa04g01800 1800
2 65606659 65610117 - Hsped.02g22680.1 Hepe02g2268 2268
2 65678791 65683251 + Hsped.02g22720.1 Hepe02g2272 2272
2 65684783 65689562 - Hsped.02g22730.1 Hepe02g2273 2273
2 65712355 65715750 + Hsped.02g22740.1 Hepe02g2274 2274
2 65742196 65743983 - Hsped.02g22750.1 Hepe02g2275 2275
10 34878147 34880964 - Maker00008649 Lcy10g1223 1223
10 34889332 34894394 + Maker00008453 Lcy10g1224 1224
10 34897979 34902617 - Maker00008596 Lcy10g1225 1225
4 24643241 24648775 + Lsi04G017290.1 Lsi04g01729 1729
4 31049768 31052712 + Lsi04G023920.1 Lsi04g02392 2392
8 11852289 11856152 - Lsi08G004330.1 Lsi08g00433 433
8 11879529 11885006 + Lsi08G004340.1 Lsi08g00434 434
8 11887209 11891421 - Lsi08G004350.1 Lsi08g00435 435
8 11893341 11897442 + Lsi08G004360.1 Lsi08g00436 436
1 43240929 43268118 + Sed0026599.1 Sed01g3125 3125
1 43270556 43275347 - Sed0013030.1 Sed01g3126 3126
1 43336435 43339699 + Sed0008649.1 Sed01g3127 3127
3 4769560 4771144 - Sed0014468.1 Sed03g0789 789
11 10906017 10912781 + Tan0017023.2 Tan11g1277 1277
11 10914462 10918721 - Tan0015905.2 Tan11g1279 1279
11 10937343 10940565 + Tan0016868.1 Tan11g1281 1281
11 10958684 10959919 - Tan0015694.1 Tan11g1283 1283
18 2881692 2885346 - Vvi18g260 Vvi18g260 260
18 2885809 2894159 + Vvi18g261 Vvi18g261 261
18 2899089 2903995 + Vvi18g262 Vvi18g262 262
18 2904022 2905267 + Vvi18g263 Vvi18g263 263
18 2905699 2907507 + Vvi18g264 Vvi18g264 264
18 2909149 2910931 + Vvi18g265 Vvi18g265 265
18 2911981 2914912 + Vvi18g266 Vvi18g266 266
18 2914954 2920741 + Vvi18g267 Vvi18g267 267
18 2921244 2922590 + Vvi18g268 Vvi18g268 268
18 2924979 2926780 - Vvi18g269 Vvi18g269 269
       

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