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
Vvi4g462 Blo01g01381 . Bda01g00739 Bda03g00066 . . . . Cmo05g00387 . . Cma05g00388 . . Sed01g1369 . . Bhi04g00975 Tan02g2713 Cmetu03g1797 . Hepe10g0261 . Lcy13g1780 . . . . . . . . . . . . . . Cme03g01622 . . . . . . . . . . . . . . Car05g00329 Cpe11g00332 . . . . . . . . Cla08g01325 Cam08g1787 Cec08g1365 Cco08g1493 Clacu08g1481 . Cre08g1270 . . Chy03g01129 .
Vvi4g463 . . . . . . . . . Cmo12g00281 . . . Car12g00313 . Cpe07g00290 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma12g00332 . . . . . . . . . . . . . . . . . . Lsi08g01195 . . .
Vvi4g464 . Blo12g01080 . Bda03g00067 . . Bma04g00064 . . . . . Car09g00408 . . . . . . . . . . . Cla05g01746 Cam05g1859 Cec05g1871 Cco05g1934 Clacu05g1850 Cmu05g1731 Cre05g1863 . . . . Lsi04g02139 Csa03g04343 Chy04g00359 . . . . . . Bpe04g00052 . . Sed05g1692 . Cmo09g00473 Cma09g00466 . . . . . Bhi09g02257 Tan01g3659 Cmetu04g0660 . . . . . . . . . . . . . . Cme04g00401
Vvi4g465 . . . . . . . . . Cmo12g00282 . . . Car12g00314 . . . Bhi04g00972 . . . . . . . . . . . . . . . . . . . . . . . . Bda13g01266 Bpe14g00577 . . . . . . . Cma12g00333 . . . . . . . . . . . . . . . . . . Lsi08g01196 . . .
Vvi4g466 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g467 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g468 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g469 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g470 Blo01g01383 Blo12g01079 Bda01g00741 Bda03g00068 Bpe02g01244 Bpe02g00566 . . Cmo05g00386 Cmo12g00285 . Cma05g00386 . Car12g00317 . Cpe07g00294 . Bhi04g00968 Tan02g2718 . . Hepe10g0257 . Lcy13g1788 . . . . . . . . . . . . . . Cme03g01618 Blo17g00022 Blo18g00029 Bda01g00999 Bda13g01265 Bpe14g00578 Bpe04g00053 Bma01g01279 Bma02g00027 . . . . Cma12g00336 . Car05g00327 Cpe11g00330 . . . . . . . . Cla08g01330 Cam08g1792 Cec08g1370 Cco08g1501 Clacu08g1486 . Cre08g1275 Lsi08g01201 . Chy03g01124 .
Vvi4g471 . . . . . . . . . . . . . . . . . . . . . . . . Cla05g01744 Cam05g1857 Cec05g1869 Cco05g1932 Clacu05g1848 Cmu05g1729 Cre05g1861 . . . . . Csa03g04341 Chy04g00361 . . . . . . . . . Sed05g1697 . . . . . . . . Bhi09g02252 Tan01g3656 Cmetu04g0153 . Hepe01g2029 Mch11g0563 . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 34676832 34677418 + Bda002778.1 Bda01g00739 739
1 34683729 34687007 - Bda002780.1 Bda01g00741 741
1 43582058 43585437 - Bda003158.3 Bda01g00999 999
3 723981 724559 + Bda016002.1 Bda03g00066 66
3 726623 732722 - Bda016003.1 Bda03g00067 67
3 735133 738323 - Bda016004.1 Bda03g00068 68
13 35043466 35046924 + Bda032808 Bda13g01265 1265
13 35047379 35048833 - Bda000071.5 Bda13g01266 1266
4 24190885 24196091 + XM_039029333.1 Bhi04g00968 968
4 24238368 24241163 - XM_039028273.1 Bhi04g00972 972
4 24422702 24423198 - XM_039028447.1 Bhi04g00975 975
9 63247049 63248777 - XM_039043100.1 Bhi09g02252 2252
9 63355113 63364842 + XM_039044121.1 Bhi09g02257 2257
1 52071896 52079717 + BLOR01381 Blo01g01381 1381
1 52119211 52121883 - BLOR01383 Blo01g01383 1383
12 28496511 28500608 + BLOR05098 Blo12g01079 1079
12 28501998 28508584 + BLOR05099 Blo12g01080 1080
17 127366 130871 + BLOR15843 Blo17g00022 22
18 213883 215130 + BLOR08517 Blo18g00029 29
1 17310403 17312886 + Bma001594.1 Bma01g01279 1279
2 313407 316877 + Bma014483.2 Bma02g00027 27
4 570446 582407 - Bma018515.1 Bma04g00064 64
2 3649909 3652703 + Bpe008408.1 Bpe02g00566 566
2 15989367 15992775 - Bpe009100.2 Bpe02g01244 1244
4 455961 462043 - Bpe014775.1 Bpe04g00052 52
4 464387 467608 - Bpe014776.1 Bpe04g00053 53
14 4887249 4889075 + Bpe007226.1 Bpe14g00577 577
14 4889532 4892998 - Bpe007227.1 Bpe14g00578 578
5 27524808 27526106 - CaPI482276_05g018570.1 Cam05g1857 1857
5 27547684 27556870 + CaPI482276_05g018590.1 Cam05g1859 1859
8 24056934 24057624 + CaPI482276_08g017870.1 Cam08g1787 1787
8 24092942 24097332 - CaPI482276_08g017920.1 Cam08g1792 1792
5 1782422 1787579 + Carg09332-RA Car05g00327 327
5 1793839 1794403 - Carg09330-RA Car05g00329 329
9 2256583 2264338 + Carg02889-RA Car09g00408 408
12 2027342 2027874 + Carg03920-RA Car12g00313 313
12 2029349 2032261 + Carg03921-RA Car12g00314 314
12 2038936 2043890 - Carg03924-RA Car12g00317 317
5 28415695 28417023 - CcPI632755_05g019320.1 Cco05g1932 1932
5 28440971 28450038 + CcPI632755_05g019340.1 Cco05g1934 1934
8 26710109 26710755 + CcPI632755_08g014930.1 Cco08g1493 1493
8 26752415 26756810 - CcPI632755_08g015010.1 Cco08g1501 1501
5 30769409 30770724 - CePI673135_05g018690.1 Cec05g1869 1869
5 30792281 30801658 + CePI673135_05g018710.1 Cec05g1871 1871
8 25572012 25572666 + CePI673135_08g013650.1 Cec08g1365 1365
8 25606474 25612711 - CePI673135_08g013700.1 Cec08g1370 1370
3 14529662 14534535 + Chy3G061040.1 Chy03g01124 1124
3 14554366 14554965 - Chy3G061090.1 Chy03g01129 1129
4 3173573 3182085 - Chy4G070770.1 Chy04g00359 359
4 3197133 3199298 + Chy4G070790.1 Chy04g00361 361
5 27727941 27729244 - ClG42_05g0184800.10 Clacu05g1848 1848
5 27750412 27759875 + ClG42_05g0185000.10 Clacu05g1850 1850
8 24804688 24805315 + ClG42_08g0148100.10 Clacu08g1481 1481
8 24838638 24844841 - ClG42_08g0148600.10 Clacu08g1486 1486
5 29276105 29277414 - ClCG05G016980.1 Cla05g01744 1744
5 29298880 29308729 + ClCG05G017010.1 Cla05g01746 1746
8 26132058 26133455 + ClCG08G013250.2 Cla08g01325 1325
8 26169949 26175167 - ClCG08G013310.2 Cla08g01330 1330
5 1695936 1702730 + CmaCh05G003860.1 Cma05g00386 386
5 1709018 1709635 - CmaCh05G003880.1 Cma05g00388 388
9 2041550 2048578 + CmaCh09G004660.1 Cma09g00466 466
12 1693681 1694292 + CmaCh12G003320.1 Cma12g00332 332
12 1695684 1697492 + CmaCh12G003330.1 Cma12g00333 333
12 1704730 1709438 - CmaCh12G003360.1 Cma12g00336 336
3 25079953 25085206 + MELO3C011256.2.1 Cme03g01618 1618
3 25103351 25104414 - MELO3C011252.2.1 Cme03g01622 1622
4 3176750 3185696 - MELO3C003691.2.1 Cme04g00401 401
3 4287355 4289538 + PI0003411.1 Cmetu03g1797 1797
4 30152799 30154645 - PI0010363.1 Cmetu04g0153 153
4 30169384 30178449 + PI0003398.1 Cmetu04g0660 660
5 1738046 1744309 + CmoCh05G003860.1 Cmo05g00386 386
5 1751622 1752308 - CmoCh05G003870.1 Cmo05g00387 387
9 2124069 2131256 + CmoCh09G004730.1 Cmo09g00473 473
12 1797442 1798193 + CmoCh12G002810.1 Cmo12g00281 281
12 1799563 1802400 + CmoCh12G002820.1 Cmo12g00282 282
12 1809619 1814058 - CmoCh12G002850.1 Cmo12g00285 285
5 27445871 27447175 - CmPI595203_05g017290.1 Cmu05g1729 1729
5 27468623 27477812 + CmPI595203_05g017310.1 Cmu05g1731 1731
7 1905544 1906079 + Cp4.1LG07g02880.1 Cpe07g00290 290
7 1917391 1922262 - Cp4.1LG07g02940.1 Cpe07g00294 294
11 1758701 1763953 + Cp4.1LG11g03160.1 Cpe11g00330 330
11 1771497 1772043 - Cp4.1LG11g03260.1 Cpe11g00332 332
5 30765809 30767140 - CrPI670011_05g018610.1 Cre05g1861 1861
5 30788530 30797769 + CrPI670011_05g018630.1 Cre05g1863 1863
8 25854504 25855046 + CrPI670011_08g012700.1 Cre08g1270 1270
8 25889458 25895533 - CrPI670011_08g012750.1 Cre08g1275 1275
3 37936372 37938511 - CsaV3_3G046470.1 Csa03g04341 4341
3 37950613 37959619 + CsaV3_3G046490.1 Csa03g04343 4343
1 84999866 85004389 - Hsped.01g20290.1 Hepe01g2029 2029
10 2666528 2671747 + Hsped.10g02570.1 Hepe10g0257 257
10 2701229 2701727 - Hsped.10g02610.1 Hepe10g0261 261
13 36723215 36726733 + Maker00033832 Lcy13g1780 1780
13 36859274 36864653 - Maker00033809 Lcy13g1788 1788
4 28509009 28522418 + Lsi04G021390.1 Lsi04g02139 2139
8 20525264 20525810 + Lsi08G011950.1 Lsi08g01195 1195
8 20533459 20535276 + Lsi08G011960.1 Lsi08g01196 1196
8 20561158 20564827 - Lsi08G012010.1 Lsi08g01201 1201
11 3607722 3608657 - MC11g0462 Mch11g0563 563
1 10187489 10188065 + Sed0000578.1 Sed01g1369 1369
5 30769356 30786599 - Sed0015882.3 Sed05g1692 1692
5 30815451 30818133 + Sed0007274.4 Sed05g1697 1697
1 101428875 101429790 - Tan0006457.1 Tan01g3656 3656
1 101462661 101474342 + Tan0006267.2 Tan01g3659 3659
2 95434026 95434624 + Tan0014564.1 Tan02g2713 2713
2 95478353 95483785 - Tan0012106.2 Tan02g2718 2718
4 4758786 4759438 + Vvi4g462 Vvi4g462 462
4 4760939 4761762 + Vvi4g463 Vvi4g463 463
4 4762275 4774766 - Vvi4g464 Vvi4g464 464
4 4774936 4776688 + Vvi4g465 Vvi4g465 465
4 4778509 4779248 - Vvi4g466 Vvi4g466 466
4 4786681 4788669 + Vvi4g467 Vvi4g467 467
4 4793094 4794952 - Vvi4g468 Vvi4g468 468
4 4797332 4800203 - Vvi4g469 Vvi4g469 469
4 4803495 4813915 - Vvi4g470 Vvi4g470 470
4 4816135 4818232 + Vvi4g471 Vvi4g471 471
       

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