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
Vvi4g472 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe02g00336 . . . . . . . . . . . . . . . . . .
Vvi4g473 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g474 . . . . . . . . . . . . Car09g00406 . . . . . . . . . . . Cla05g01743 Cam05g1856 Cec05g1868 Cco05g1931 Clacu05g1847 Cmu05g1728 Cre05g1860 . . . . Lsi04g02135 . . . . . . . . . . . Sed13g2029 . Cmo09g00472 Cma09g00463 . . . . . Bhi09g02251 Tan01g3655 . . Hepe01g2028 Mch11g0562 . . . . . . . . . . . .
Vvi4g475 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda13g01264 . . . Bma02g00026 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g476 Blo01g01384 . Bda01g00742 . . Bpe02g00565 . . . . Cma01g01500 . . . . . . . . . . . . . Cla05g01742 Cam05g1855 Cec05g1867 Cco05g1930 Clacu05g1846 Cmu05g1727 Cre05g1859 . . . . Lsi04g02134 Csa03g04340 Chy04g00362 . . . . . . . . . Sed13g2028 Cmo01g01556 . . . . . . Cpe02g00455 Bhi09g02250 Tan01g3654 Cmetu04g0930 . Hepe01g2027 Mch11g0561 . . . . . . . . . . . Cme04g00404
Vvi4g477 . . . . Bpe02g01245 . . . Cmo05g00385 . . Cma05g00384 . . . . . Bhi04g00961 . . . Hepe10g0255 . . . . . . . . . Cone4ag1794 . . . . . . . . Blo18g00027 Bda01g01000 . . . Bma01g01277 . . . . . . . . Cpe11g00329 . . . . . . . . Cla08g01331 Cam08g1793 Cec08g1372 . Clacu08g1487 . . Lsi08g01203 . Chy03g01123 .
Vvi4g478 Blo01g01386 Blo12g01078 Bda01g00744 Bda03g00069 . Bpe02g00563 Bma04g00066 . . . Cma01g01479 . Car09g00404 . . . Cpe06g00343 . . . . . . . Cla05g01741 Cam05g1854 Cec05g1866 Cco05g1928 Clacu05g1844 Cmu05g1725 Cre05g1858 Cone4ag1792 Cone7ag1701 . . Lsi04g02133 Csa03g04338 Chy04g00364 . . . . . . Bpe04g00054 . . . Cmo01g01535 Cmo09g00470 Cma09g00461 . . . . . Bhi09g02248 . . . . . . . . . . . . . . . . Cme04g00406
Vvi4g479 . . . . Bpe02g01247 . . . Cmo05g00384 . . Cma05g00383 . . . . . Bhi04g00959 . . . Hepe10g0254 . . . . . . . . . . . Cone17ag1023 Cone20ag0669 . . . Cme03g01617 . Blo18g00026 . . . . . . . . . . . . Car05g00326 Cpe11g00328 . . . . . . . . Cla08g01332 Cam08g1794 Cec08g1373 Cco08g1502 Clacu08g1488 . Cre08g1276 Lsi08g01204 . Chy03g01122 .
Vvi4g480 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g481 . . . . . . . . . Cmo12g00286 . . . Car12g00318 . Cpe07g00295 . Bhi04g00955 . . . Hepe10g0252 . . . . . . . . . . . Cone17ag1022 . . . . . . . . . . . . . . . . . Cma12g00337 . . . . . . . . . . . Cla08g01333 Cam08g1795 Cec08g1374 . Clacu08g1489 . . . . Chy03g01121 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 34688790 34690147 - Bda002781.3 Bda01g00742 742
1 34698262 34699075 - Bda002783.1 Bda01g00744 744
1 43591622 43594706 + Bda003159.1 Bda01g01000 1000
3 741933 742669 - Bda016005.1 Bda03g00069 69
13 35042082 35043023 + Bda000070.1 Bda13g01264 1264
4 24171984 24175691 - XM_039029415.1 Bhi04g00955 955
4 24175834 24180590 - XM_039029413.1 Bhi04g00959 959
4 24181312 24188002 - XM_039029411.1 Bhi04g00961 961
9 63152733 63154781 + XM_039044004.1 Bhi09g02248 2248
9 63234846 63238619 + XM_039043636.1 Bhi09g02250 2250
9 63244194 63245627 + XM_039040658.1 Bhi09g02251 2251
1 52122289 52126043 - BLOR01384 Blo01g01384 1384
1 52152465 52153836 - BLOR01386 Blo01g01386 1386
12 28493030 28494358 + BLOR05097 Blo12g01078 1078
18 198175 202234 - BLOR08514 Blo18g00026 26
18 204415 208704 - BLOR08515 Blo18g00027 27
1 17300207 17304719 - Bma001593.1 Bma01g01277 1277
2 305506 306519 + Bma014482.1 Bma02g00026 26
4 589462 590195 - Bma031080 Bma04g00066 66
2 3632254 3633048 + Bpe008404.4 Bpe02g00563 563
2 3641955 3643301 + Bpe008406.1 Bpe02g00565 565
2 15995523 16000055 + Bpe009101.1 Bpe02g01245 1245
2 16001717 16004108 + Bpe009103.1 Bpe02g01247 1247
4 470637 471372 - Bpe014777.2 Bpe04g00054 54
5 27494329 27495495 + CaPI482276_05g018540.1 Cam05g1854 1854
5 27512005 27521214 + CaPI482276_05g018550.1 Cam05g1855 1855
5 27523248 27524186 + CaPI482276_05g018560.1 Cam05g1856 1856
8 24102475 24106351 + CaPI482276_08g017930.1 Cam08g1793 1793
8 24109040 24111457 + CaPI482276_08g017940.1 Cam08g1794 1794
8 24111802 24115171 + CaPI482276_08g017950.1 Cam08g1795 1795
5 1771728 1779633 - Carg09333-RA Car05g00326 326
9 2243837 2244957 + Carg02885-RA Car09g00404 404
9 2251647 2252594 + Carg02887-RA Car09g00406 406
12 2045166 2049026 + Carg03925-RA Car12g00318 318
5 28390230 28391396 + CcPI632755_05g019280.1 Cco05g1928 1928
5 28408247 28412209 + CcPI632755_05g019300.1 Cco05g1930 1930
5 28414132 28415070 + CcPI632755_05g019310.1 Cco05g1931 1931
8 26761848 26774511 + CcPI632755_08g015020.1 Cco08g1502 1502
5 30743518 30744684 + CePI673135_05g018660.1 Cec05g1866 1866
5 30755707 30765480 + CePI673135_05g018670.1 Cec05g1867 1867
5 30767849 30768787 + CePI673135_05g018680.1 Cec05g1868 1868
8 25618033 25621824 + CePI673135_08g013720.1 Cec08g1372 1372
8 25622781 25626937 + CePI673135_08g013730.1 Cec08g1373 1373
8 25628095 25630645 + CePI673135_08g013740.1 Cec08g1374 1374
3 14511299 14513821 - Chy3G061010.1 Chy03g01121 1121
3 14515013 14519443 - Chy3G061020.1 Chy03g01122 1122
3 14520105 14523970 - Chy3G061030.1 Chy03g01123 1123
4 3199989 3202063 - Chy4G070800.1 Chy04g00362 362
4 3212256 3213361 - Chy4G070820.1 Chy04g00364 364
5 27697131 27698297 + ClG42_05g0184400.10 Clacu05g1844 1844
5 27720235 27724330 + ClG42_05g0184600.10 Clacu05g1846 1846
5 27726384 27727322 + ClG42_05g0184700.10 Clacu05g1847 1847
8 24849881 24853748 + ClG42_08g0148700.10 Clacu08g1487 1487
8 24856431 24858848 + ClG42_08g0148800.10 Clacu08g1488 1488
8 24859246 24862566 + ClG42_08g0148900.10 Clacu08g1489 1489
5 29243958 29245428 + ClCG05G016920.2 Cla05g01741 1741
5 29262603 29272494 + ClCG05G016940.2 Cla05g01742 1742
5 29274548 29275486 + ClCG05G016970.1 Cla05g01743 1743
8 26178033 26183999 + ClCG08G013320.1 Cla08g01331 1331
8 26184202 26193944 + ClCG08G013330.2 Cla08g01332 1332
8 26190286 26193604 + ClCG08G013340.2 Cla08g01333 1333
1 10416824 10417624 - CmaCh01G014790.1 Cma01g01479 1479
1 10538615 10542251 - CmaCh01G015000.1 Cma01g01500 1500
5 1686515 1689703 - CmaCh05G003830.1 Cma05g00383 383
5 1690664 1694548 - CmaCh05G003840.1 Cma05g00384 384
9 2028621 2030524 + CmaCh09G004610.1 Cma09g00461 461
9 2036700 2037647 + CmaCh09G004630.1 Cma09g00463 463
12 1710698 1714446 + CmaCh12G003370.1 Cma12g00337 337
3 25062581 25077368 - MELO3C011257.2.1 Cme03g01617 1617
4 3209047 3211319 - MELO3C003693.2.1 Cme04g00404 404
4 3219740 3221709 - MELO3C003695.2.1 Cme04g00406 406
4 30148753 30149028 + PI0019012.1 Cmetu04g0930 930
1 11839451 11840104 - CmoCh01G015350.1 Cmo01g01535 1535
1 11978061 11981281 - CmoCh01G015560.1 Cmo01g01556 1556
5 1728849 1732121 - CmoCh05G003840.1 Cmo05g00384 384
5 1732535 1738278 - CmoCh05G003850.1 Cmo05g00385 385
9 2110532 2112508 + CmoCh09G004700.1 Cmo09g00470 470
9 2118801 2122233 + CmoCh09G004720.1 Cmo09g00472 472
12 1814981 1819264 + CmoCh12G002860.1 Cmo12g00286 286
5 27415672 27416838 + CmPI595203_05g017250.1 Cmu05g1725 1725
5 27437477 27442241 + CmPI595203_05g017270.1 Cmu05g1727 1727
5 27444314 27445252 + CmPI595203_05g017280.1 Cmu05g1728 1728
4 13040697 13041570 + Conep04aG0185000.1 Cone4ag1792 1792
4 13044755 13048442 - Conep04aG0185200.1 Cone4ag1794 1794
7 11339494 11340800 + Conep07aG0175200.1 Cone7ag1701 1701
17 7788517 7791993 - Conep17aG0105000.1 Cone17ag1022 1022
17 7795482 7798033 - Conep17aG0105100.1 Cone17ag1023 1023
20 4089484 4095003 + Conep20aG0069000.1 Cone20ag0669 669
2 1805259 1813673 - Cp4.1LG02g05360.1 Cpe02g00336 336
2 2573474 2576476 + Cp4.1LG02g04200.1 Cpe02g00455 455
6 1904800 1905918 + Cp4.1LG06g03420.1 Cpe06g00343 343
7 1923542 1927707 + Cp4.1LG07g02860.1 Cpe07g00295 295
11 1747964 1751199 - Cp4.1LG11g03250.1 Cpe11g00328 328
11 1751719 1757606 - Cp4.1LG11g03220.1 Cpe11g00329 329
5 30739769 30740933 + CrPI670011_05g018580.1 Cre05g1858 1858
5 30752198 30762056 + CrPI670011_05g018590.1 Cre05g1859 1859
5 30764246 30765184 + CrPI670011_05g018600.1 Cre05g1860 1860
8 25900790 25913464 + CrPI670011_08g012760.1 Cre08g1276 1276
3 37921638 37923626 + CsaV3_3G046440.1 Csa03g04338 4338
3 37933215 37937774 + CsaV3_3G046460.1 Csa03g04340 4340
1 84994323 84997179 + Hsped.01g20270.1 Hepe01g2027 2027
1 84998551 84999483 + Hsped.01g20280.1 Hepe01g2028 2028
10 2646933 2648503 - Hsped.10g02520.1 Hepe10g0252 252
10 2651338 2655683 - Hsped.10g02540.1 Hepe10g0254 254
10 2657287 2661164 - Hsped.10g02550.1 Hepe10g0255 255
4 28467155 28469276 + Lsi04G021330.1 Lsi04g02133 2133
4 28474688 28483574 + Lsi04G021340.1 Lsi04g02134 2134
4 28485431 28486369 + Lsi04G021350.1 Lsi04g02135 2135
8 20570323 20574194 + Lsi08G012030.1 Lsi08g01203 1203
8 20575171 20579320 + Lsi08G012040.1 Lsi08g01204 1204
11 3598265 3605286 + MC11g0460 Mch11g0561 561
11 3606467 3607372 + MC11g0461 Mch11g0562 562
13 25180912 25185183 + Sed0007501.1 Sed13g2028 2028
13 25195944 25197045 + Sed0001739.1 Sed13g2029 2029
1 101419051 101422423 + Tan0016750.1 Tan01g3654 3654
1 101427528 101428460 + Tan0018850.1 Tan01g3655 3655
4 4818333 4838381 - Vvi4g472 Vvi4g472 472
4 4838887 4840624 + Vvi4g473 Vvi4g473 473
4 4842065 4842998 - Vvi4g474 Vvi4g474 474
4 4843999 4845216 - Vvi4g475 Vvi4g475 475
4 4847962 4851533 - Vvi4g476 Vvi4g476 476
4 4881182 4886034 + Vvi4g477 Vvi4g477 477
4 4888329 4892373 - Vvi4g478 Vvi4g478 478
4 4893676 4897069 + Vvi4g479 Vvi4g479 479
4 4898928 4902166 + Vvi4g480 Vvi4g480 480
4 4902230 4906088 + Vvi4g481 Vvi4g481 481
       

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