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
Vvi18g150 . Blo12g00870 . Bda03g00303 . Bpe04g00265 Bma04g00267 . . . . Cma09g00080 . . . Cpe06g00044 . . . . . . . . . . . . . . . . . . . Lsi04g01783 Csa04g02673 . . . . . . . . . . Sed01g2460 . Cmo09g00079 . . . . . . Bhi09g02942 Tan01g5062 Cmetu07g1712 . Hepe01g2310 Mch11g0084 . Cla05g01593 Cam05g1701 Cec05g1701 Cco05g1751 Clacu05g1688 Cmu05g1577 Cre05g1694 . . Chy07g00365 Cme07g00084
Vvi18g151 . . . . . . . . . . . . . . . . . Bhi04g00084 . . . . . . Cla08g01393 Cam08g1867 Cec08g1446 Cco08g1579 Clacu08g1561 . Cre08g1345 . . . Cone20ag0053 . . . Cme03g01542 . . Bda08g01187 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi08g01285 . Chy03g01050 .
Vvi18g152 . . . Bda03g00302 . Bpe04g00264 Bma04g00266 . . . . Cma09g00081 . . . Cpe06g00045 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed10g2110 . Cmo09g00080 . . . Car09g00070 . . Bhi09g01887 Tan01g3346 Cmetu01g0289 . . . . . . . . . . . . . . .
Vvi18g153 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g154 Blo01g01614 . . . Bpe02g00332 . . Bma01g02388 Cmo04g02557 . Cma01g01992 . Car01g01564 . . . . . . . . . . . . . . . . . . . Cone7ag1915 Cone17ag0791 Cone20ag0386 Lsi04g01782 . Chy04g00388 . . . . . . . . . . . . . . Car04g02350 Car15g00559 Cpe01g02111 Cpe02g00053 . . . . . . . Cla05g01594 . . . . . . Lsi08g00545 . . .
Vvi18g155 . . . . . . . . . . . . . . . . . . . . . . . . Cla08g01395 Cam08g1870 Cec08g1448 Cco08g1582 Clacu08g1563 . Cre08g1348 . . . . . . . Cme03g01541 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi08g01288 . Chy03g01049 .
Vvi18g156 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g157 Blo01g01613 . . . Bpe02g00333 Bpe04g00263 Bma04g00264 Bma01g02387 . . . Cma09g00082 . . . Cpe06g00046 . . . . . . . . . . . . . . . . . . . Lsi04g01781 . Chy04g00389 . . . . . . . . . . . Cmo09g00081 . . . Car09g00071 . . . . . . . . . Cla05g01595 Cam05g1706 Cec05g1706 Cco05g1762 Clacu05g1693 Cmu05g1582 Cre05g1699 . . . .
Vvi18g158 . . . . . . . . Cmo05g00331 . . . . . . . . . . . . . . . Cla08g01396 Cam08g1871 Cec08g1449 Cco08g1583 Clacu08g1564 . Cre08g1349 . . Cone17ag1431 . . . . Cme03g01540 Blo17g00727 . . . . . . . . . . . Cma05g00328 Car05g00275 . . . . . . . . . . . . . . . . . Lsi08g01289 . Chy03g01048 .
Vvi18g159 . . . . . . . . Cmo05g00330 . . . . . . . . . . . . . . . Cla08g01397 Cam08g1874 Cec08g1451 Cco08g1585 Clacu08g1567 . Cre08g1351 . . . . . . . Cme03g01539 Blo17g00734 . Bda08g01188 . . Bpe05g00163 . . . . . . Cma05g00327 Car05g00274 . . . . . . . . . . . . . . . . . Lsi08g01291 . Chy03g01047 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 2654706 2656962 + Bda016261.1 Bda03g00302 302
3 2658621 2659573 + Bda016262.1 Bda03g00303 303
8 47879835 47880689 - Bda030139.1 Bda08g01187 1187
8 47902603 47905854 - Bda030140.1 Bda08g01188 1188
4 2244756 2245862 + XM_039029518.1 Bhi04g00084 84
9 52273132 52278061 - XM_039043748.1 Bhi09g01887 1887
9 76672184 76673881 - XM_039043032.1 Bhi09g02942 2942
1 56030184 56030522 - BLOR01613 Blo01g01613 1613
1 56034216 56045571 + BLOR01614 Blo01g01614 1614
12 26911158 26912094 - BLOR04889 Blo12g00870 870
17 22093559 22098013 + BLOR08273 Blo17g00727 727
17 22373720 22385623 + BLOR08280 Blo17g00734 734
1 81455950 81456453 - Bma003258.1 Bma01g02387 2387
1 81458040 81464353 + Bma003259.1 Bma01g02388 2388
4 2184193 2184693 - Bma018716.1 Bma04g00264 264
4 2202056 2204337 + Bma018718.1 Bma04g00266 266
4 2206182 2207134 + Bma018719.1 Bma04g00267 267
2 2165494 2171618 - Bpe008173.1 Bpe02g00332 332
2 2172952 2173455 + Bpe008174.1 Bpe02g00333 333
4 1725273 1725773 - Bpe014973.1 Bpe04g00263 263
4 1727619 1729842 + Bpe014974.1 Bpe04g00264 264
4 1734941 1735888 + Bpe014975.1 Bpe04g00265 265
5 4813159 4816187 + Bpe017551.2 Bpe05g00163 163
5 25320437 25321302 - CaPI482276_05g017010.1 Cam05g1701 1701
5 25420974 25421477 + CaPI482276_05g017060.1 Cam05g1706 1706
8 24700163 24701011 - CaPI482276_08g018670.1 Cam08g1867 1867
8 24721636 24722919 + CaPI482276_08g018700.1 Cam08g1870 1870
8 24724885 24730175 - CaPI482276_08g018710.1 Cam08g1871 1871
8 24750524 24760916 - CaPI482276_08g018740.1 Cam08g1874 1874
1 13026120 13028587 + Carg21391-RA Car01g01564 1564
4 18906157 18912201 - Carg15784-RA Car04g02350 2350
5 1501788 1506486 + Carg09385-RA Car05g00274 274
5 1508172 1513288 + Carg09384-RA Car05g00275 275
9 347667 353882 - Carg08653-RA Car09g00070 70
9 355272 355775 + Carg08654-RA Car09g00071 71
15 3078254 3088487 + Carg01596-RA Car15g00559 559
5 25894352 25895262 - CcPI632755_05g017510.1 Cco05g1751 1751
5 26076847 26077350 + CcPI632755_05g017620.1 Cco05g1762 1762
8 27368058 27368906 - CcPI632755_08g015790.1 Cco08g1579 1579
8 27389959 27391242 + CcPI632755_08g015820.1 Cco08g1582 1582
8 27393193 27398485 - CcPI632755_08g015830.1 Cco08g1583 1583
8 27419160 27427351 - CcPI632755_08g015850.1 Cco08g1585 1585
5 28278801 28281816 - CePI673135_05g017010.1 Cec05g1701 1701
5 28377516 28378025 + CePI673135_05g017060.1 Cec05g1706 1706
8 26226494 26227318 - CePI673135_08g014460.1 Cec08g1446 1446
8 26247084 26248367 + CePI673135_08g014480.1 Cec08g1448 1448
8 26250352 26255645 - CePI673135_08g014490.1 Cec08g1449 1449
8 26275886 26284410 - CePI673135_08g014510.1 Cec08g1451 1451
3 13957690 13964403 + Chy3G060270.1 Chy03g01047 1047
3 13966886 13972420 + Chy3G060280.1 Chy03g01048 1048
3 13974117 13975400 + Chy3G060290.1 Chy03g01049 1049
3 13980546 13981393 + Chy3G060300.1 Chy03g01050 1050
4 3429929 3437770 - Chy4G071060.1 Chy04g00388 388
4 3452929 3453588 + Chy4G071070.1 Chy04g00389 389
7 2959623 2960312 + Chy7G131950.1 Chy07g00365 365
5 25498876 25499741 - ClG42_05g0168800.10 Clacu05g1688 1688
5 25615919 25616422 + ClG42_05g0169300.10 Clacu05g1693 1693
8 25444325 25445173 - ClG42_08g0156100.10 Clacu08g1561 1561
8 25474173 25475456 + ClG42_08g0156300.10 Clacu08g1563 1563
8 25477023 25482311 - ClG42_08g0156400.10 Clacu08g1564 1564
8 25502246 25510574 - ClG42_08g0156700.10 Clacu08g1567 1567
5 26940513 26942173 - ClCG05G015370.1 Cla05g01593 1593
5 27021993 27028198 - ClCG05G015380.2 Cla05g01594 1594
5 27065303 27065806 + ClCG05G015390.1 Cla05g01595 1595
8 26798196 26799772 - ClCG08G013970.2 Cla08g01393 1393
8 26828171 26829454 + ClCG08G013990.1 Cla08g01395 1395
8 26830441 26836635 - ClCG08G014000.1 Cla08g01396 1396
8 26842136 26875573 - ClCG08G014010.1 Cla08g01397 1397
1 12796667 12804432 + CmaCh01G019920.1 Cma01g01992 1992
5 1416924 1421835 + CmaCh05G003270.1 Cma05g00327 327
5 1422755 1428501 + CmaCh05G003280.1 Cma05g00328 328
9 352548 355129 - CmaCh09G000800.1 Cma09g00080 80
9 355518 360388 - CmaCh09G000810.1 Cma09g00081 81
9 361527 362030 + CmaCh09G000820.1 Cma09g00082 82
3 24516948 24524040 + MELO3C011337.2.1 Cme03g01539 1539
3 24525324 24531433 + MELO3C011336.2.1 Cme03g01540 1540
3 24533249 24534734 + MELO3C011335.2.1 Cme03g01541 1541
3 24540781 24541756 + MELO3C011334.2.1 Cme03g01542 1542
7 524436 526046 - MELO3C016998.2.1 Cme07g00084 84
1 18327816 18332152 - PI0001195.1 Cmetu01g0289 289
7 24268053 24269594 + PI0018378.1 Cmetu07g1712 1712
4 18735020 18748470 - CmoCh04G025570.1 Cmo04g02557 2557
5 1457170 1462094 + CmoCh05G003300.1 Cmo05g00330 330
5 1463539 1468911 + CmoCh05G003310.1 Cmo05g00331 331
9 368664 369652 - CmoCh09G000790.1 Cmo09g00079 79
9 370101 374784 - CmoCh09G000800.1 Cmo09g00080 80
9 375946 376449 + CmoCh09G000810.1 Cmo09g00081 81
5 25220495 25221360 - CmPI595203_05g015770.1 Cmu05g1577 1577
5 25337158 25337661 + CmPI595203_05g015820.1 Cmu05g1582 1582
7 12257561 12263603 + Conep07aG0197200.1 Cone7ag1915 1915
17 6136205 6156763 + Conep17aG0080900.1 Cone17ag0791 791
17 9772248 9776053 + Conep17aG0146900.1 Cone17ag1431 1431
20 254347 256763 - Conep20aG0005400.1 Cone20ag0053 53
20 1812146 1822981 + Conep20aG0040000.1 Cone20ag0386 386
1 17859216 17873622 - Cp4.1LG01g21170.1 Cpe01g02111 2111
2 277513 286509 - Cp4.1LG02g08160.1 Cpe02g00053 53
6 229091 232078 - Cp4.1LG06g00550.1 Cpe06g00044 44
6 232841 237024 - Cp4.1LG06g00500.1 Cpe06g00045 45
6 238144 238647 + Cp4.1LG06g00360.1 Cpe06g00046 46
5 28437826 28438690 - CrPI670011_05g016940.1 Cre05g1694 1694
5 28518099 28518602 + CrPI670011_05g016990.1 Cre05g1699 1699
8 26506075 26506923 - CrPI670011_08g013450.1 Cre08g1345 1345
8 26527770 26529053 + CrPI670011_08g013480.1 Cre08g1348 1348
8 26532655 26537947 - CrPI670011_08g013490.1 Cre08g1349 1349
8 26558126 26566667 - CrPI670011_08g013510.1 Cre08g1351 1351
4 25978911 25980534 + CsaV3_4G036990.1 Csa04g02673 2673
1 87711233 87712158 + Hsped.01g23100.1 Hepe01g2310 2310
4 25008239 25008742 - Lsi04G017810.1 Lsi04g01781 1781
4 25024973 25031302 + Lsi04G017820.1 Lsi04g01782 1782
4 25051704 25053307 + Lsi04G017830.1 Lsi04g01783 1783
8 13577550 13590978 - Lsi08G005450.1 Lsi08g00545 545
8 21216527 21217729 - Lsi08G012850.1 Lsi08g01285 1285
8 21241264 21242547 + Lsi08G012880.1 Lsi08g01288 1288
8 21243604 21261317 - Lsi08G012890.1 Lsi08g01289 1289
8 21287349 21296107 - Lsi08G012910.1 Lsi08g01291 1291
11 541373 542714 - MC11g0076 Mch11g0084 84
1 18341035 18343342 - Sed0004106.1 Sed01g2460 2460
10 37578772 37583689 + Sed0017116.1 Sed10g2110 2110
1 91846353 91850782 + Tan0010391.1 Tan01g3346 3346
1 116174748 116175603 + Tan0016516.1 Tan01g5062 5062
18 1457638 1459963 - Vvi18g150 Vvi18g150 150
18 1461040 1462318 - Vvi18g151 Vvi18g151 151
18 1464151 1468615 - Vvi18g152 Vvi18g152 152
18 1474563 1474728 + Vvi18g153 Vvi18g153 153
18 1477097 1491666 - Vvi18g154 Vvi18g154 154
18 1522792 1524300 + Vvi18g155 Vvi18g155 155
18 1529487 1530816 + Vvi18g156 Vvi18g156 156
18 1535487 1536276 + Vvi18g157 Vvi18g157 157
18 1536670 1544403 - Vvi18g158 Vvi18g158 158
18 1550511 1554616 - Vvi18g159 Vvi18g159 159
       

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