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
Vvi18g1130 Blo01g01603 Blo12g01115 Bda01g00478 . . . . . Cmo05g00314 Cmo12g00355 Cma01g01018 . Car01g00899 Car12g00381 Sed11g1094 . Cpe07g00360 Bhi04g00141 Tan02g2081 Cmetu03g1137 . Hepe10g0160 . Lcy13g1907 Cla08g01417 Cam08g1895 Cec08g1473 Cco08g1606 Clacu08g1588 . Cre08g1372 Cone4ag1978 . Cone17ag1410 Cone20ag0072 . . Chy04g00409 Cme03g00439 . Blo18g00229 . Bda13g01547 . . . Bma02g00291 . Cmo01g01060 . Cma12g00404 Cma05g00312 Car05g00808 Car09g00086 Cpe11g00260 Cpe02g00066 . . . . . . . . . . . . . . Lsi08g00283 Csa02g02140 Chy03g01379 .
Vvi18g1131 . Blo12g00882 . . . Bpe04g00250 . Bma01g02374 Cmo05g00315 . . Cma09g00098 . . . Cpe06g00061 . Bhi04g00140 Tan02g2082 . . Hepe10g0674 . Lcy13g1906 Cla08g01416 . Cec08g1472 Cco08g1605 Clacu08g1587 . Cre08g1370 . . Cone17ag1411 . Lsi04g01754 Csa03g04288 Chy04g00408 Cme03g01872 . . . . Bpe02g01730 Bpe05g00142 . Bma05g00168 Sed01g2481 . Cmo09g00095 Cma12g00403 Cma05g00313 Car05g00260 . Cpe11g00261 . Bhi09g02077 Tan01g5034 Cmetu04g3133 . Hepe01g1607 Mch11g0107 . Cla05g01863 Cam05g1992 Cec05g2004 Cco05g2062 Clacu05g1984 Cmu05g1865 Cre05g1989 Lsi08g01311 Csa02g02142 Chy03g01376 Cme04g00460
Vvi18g1132 . . . . . . . . Cmo05g00316 Cmo12g00353 . . . Car12g00379 . . Cpe07g00357 Bhi04g02197 . . . . . . . . . . . . . Cone4ag1980 Cone7ag1897 . . . . . . . Blo18g00775 . Bda01g01534 Bpe02g01732 . Bma01g00723 . . . . . Cma05g00315 Car05g00261 . Cpe11g00262 . . . . . . . . . . . . . . . . . . .
Vvi18g1133 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1134 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1135 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1413 Cone20ag0070 . . . . Blo17g00233 . Bda08g01214 . . Bpe05g00145 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1136 Blo01g01604 . Bda01g00477 . Bpe02g00342 . . Bma01g02375 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1137 . Blo12g00881 . . . . Bma04g00250 Bma01g02376 . . Cma01g01979 Cma09g00097 Car01g01551 . . Cpe06g00060 . . . . . . . . . . . . . . . . . Cone17ag1414 Cone20ag0069 Lsi04g01755 Csa03g04289 Chy04g00407 . . . . . . . . . Sed01g2483 Cmo01g02038 Cmo09g00094 . . . Car09g00085 . Cpe02g00065 Bhi09g02076 Tan01g5035 Cmetu04g3193 . Hepe01g1606 Mch11g0106 . Cla05g01862 Cam05g1991 Cec05g2003 Cco05g2061 Clacu05g1983 Cmu05g1864 Cre05g1988 . . . Cme04g00459
Vvi18g1138 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1139 . . . . . . . . . . . . . . . . . Bhi04g00138 . . . Hepe10g0163 . . Cla08g01415 Cam08g1894 Cec08g1471 Cco08g1604 Clacu08g1586 . Cre08g1369 . . . Cone20ag0437 . . . Cme03g01871 Blo17g00740 . Bda08g01213 . . Bpe05g00146 . . . . . Cma12g00402 . . Car15g00615 . . . . . . . . . . . . . . . . Lsi08g01310 Csa02g02143 Chy03g00784 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 31845981 31852497 - Bda002479.1 Bda01g00477 477
1 31853617 31854826 - Bda002480.1 Bda01g00478 478
1 51284244 51290334 - Bda003798.1 Bda01g01534 1534
8 49750466 49757098 + Bda030193.1 Bda08g01213 1213
8 49781623 49782663 - Bda030194.1 Bda08g01214 1214
13 38695021 38696032 - Bda000403.1 Bda13g01547 1547
4 3331196 3345698 + XM_039029599.1 Bhi04g00138 138
4 3357662 3358813 - XM_039029604.1 Bhi04g00140 140
4 3451987 3454209 - XM_039030752.1 Bhi04g00141 141
4 60397890 60401884 + XM_039028408.1 Bhi04g02197 2197
9 59337226 59342599 + XM_039044011.1 Bhi09g02076 2076
9 59344581 59346743 - XM_039044012.1 Bhi09g02077 2077
1 55891279 55897617 + BLOR01603 Blo01g01603 1603
1 55902813 55909037 + BLOR01604 Blo01g01604 1604
12 27015006 27018074 + BLOR04900 Blo12g00881 881
12 27019113 27024787 - BLOR04901 Blo12g00882 882
12 28802490 28805746 + BLOR05134 Blo12g01115 1115
17 2381808 2382770 - BLOR16054 Blo17g00233 233
17 22859182 22873903 + BLOR08286 Blo17g00740 740
18 2257098 2257907 - BLOR08717 Blo18g00229 229
18 21885935 21891972 + BLOR09263 Blo18g00775 775
1 6604716 6610669 + Bma000932.1 Bma01g00723 723
1 81385966 81386736 + Bma003245.1 Bma01g02374 2374
1 81388523 81394865 + Bma003246.1 Bma01g02375 2375
1 81396643 81399693 - Bma003247.2 Bma01g02376 2376
2 3340122 3341274 - Bma014742.1 Bma02g00291 291
4 2134193 2137273 - Bma018702.1 Bma04g00250 250
5 4778220 4779005 + Bma020885.1 Bma05g00168 168
2 2241219 2247668 - Bpe008183.1 Bpe02g00342 342
2 19741008 19741775 + Bpe009561.1 Bpe02g01730 1730
2 19751520 19757957 - Bpe009563.1 Bpe02g01732 1732
4 1672685 1674043 + Bpe014963.1 Bpe04g00250 250
5 3708511 3709281 + Bpe017529.1 Bpe05g00142 142
5 4183943 4184998 + Bpe025793 Bpe05g00145 145
5 4186660 4198646 - Bpe017533.3 Bpe05g00146 146
5 28719509 28724624 + CaPI482276_05g019910.1 Cam05g1991 1991
5 28726514 28728075 - CaPI482276_05g019920.1 Cam05g1992 1992
8 24913342 24922732 + CaPI482276_08g018940.1 Cam08g1894 1894
8 24923322 24927589 - CaPI482276_08g018950.1 Cam08g1895 1895
1 8484120 8490730 - Carg26864-RA Car01g00899 899
1 12965060 12968158 - Carg17206-RA Car01g01551 1551
5 1448604 1449347 + Carg09399-RA Car05g00260 260
5 1451583 1455848 + Carg09398-RA Car05g00261 261
5 7675842 7677727 - Carg26436-RA Car05g00808 808
9 433278 436391 + Carg08669-RA Car09g00085 85
9 437417 438930 - Carg08670-RA Car09g00086 86
12 2414917 2419740 - Carg03986-RA Car12g00379 379
12 2434079 2439259 - Carg03988-RA Car12g00381 381
15 3406490 3418236 + Carg01540-RA Car15g00615 615
5 29655630 29660730 + CcPI632755_05g020610.1 Cco05g2061 2061
5 29662647 29664204 - CcPI632755_05g020620.1 Cco05g2062 2062
8 27578247 27587652 + CcPI632755_08g016040.1 Cco08g1604 1604
8 27588244 27592511 - CcPI632755_08g016050.1 Cco08g1605 1605
8 27606527 27607920 - CcPI632755_08g016060.1 Cco08g1606 1606
5 32020583 32023675 + CePI673135_05g020030.1 Cec05g2003 2003
5 32025568 32027128 - CePI673135_05g020040.1 Cec05g2004 2004
8 26441608 26451706 + CePI673135_08g014710.1 Cec08g1471 1471
8 26453904 26456072 - CePI673135_08g014720.1 Cec08g1472 1472
8 26469886 26471278 - CePI673135_08g014730.1 Cec08g1473 1473
3 10665613 10679047 + Chy3G057640.1 Chy03g00784 784
3 16597191 16598902 - Chy3G063560.1 Chy03g01376 1376
3 16605922 16606784 - Chy3G063590.1 Chy03g01379 1379
4 3648687 3651785 + Chy4G071250.1 Chy04g00407 407
4 3652658 3655338 - Chy4G071260.1 Chy04g00408 408
4 3653561 3655089 - Chy4G071270.1 Chy04g00409 409
5 28923763 28926768 + ClG42_05g0198300.10 Clacu05g1983 1983
5 28928643 28930205 - ClG42_05g0198400.10 Clacu05g1984 1984
8 25659241 25669544 + ClG42_08g0158600.10 Clacu08g1586 1586
8 25671424 25673531 - ClG42_08g0158700.10 Clacu08g1587 1587
8 25687075 25688462 - ClG42_08g0158800.10 Clacu08g1588 1588
5 30504288 30507380 + ClCG05G018200.2 Cla05g01862 1862
5 30508879 30510924 - ClCG05G018210.1 Cla05g01863 1863
8 27016248 27026499 + ClCG08G014220.2 Cla08g01415 1415
8 27028798 27030501 - ClCG08G014230.2 Cla08g01416 1416
8 27043614 27045802 - ClCG08G014240.1 Cla08g01417 1417
1 7469123 7480029 - CmaCh01G010180.1 Cma01g01018 1018
1 12738695 12741808 - CmaCh01G019790.1 Cma01g01979 1979
5 1353680 1355752 + CmaCh05G003120.1 Cma05g00312 312
5 1359232 1361013 + CmaCh05G003130.1 Cma05g00313 313
5 1362501 1367255 + CmaCh05G003150.1 Cma05g00315 315
9 433569 436679 + CmaCh09G000970.1 Cma09g00097 97
9 437138 439259 - CmaCh09G000980.1 Cma09g00098 98
12 2077005 2088878 + CmaCh12G004020.1 Cma12g00402 402
12 2089523 2092185 - CmaCh12G004030.1 Cma12g00403 403
12 2094081 2096025 - CmaCh12G004040.1 Cma12g00404 404
3 6142765 6146232 + MELO3C008434.2.1 Cme03g00439 439
3 26935080 26944596 + MELO3C011020.2.1 Cme03g01871 1871
3 26947101 26948231 - MELO3C030111.2.1 Cme03g01872 1872
4 3664044 3667670 + MELO3C003744.2.1 Cme04g00459 459
4 3668049 3670650 - MELO3C003745.2.1 Cme04g00460 460
3 2419496 2420852 + PI0026009.1 Cmetu03g1137 1137
4 29698874 29701069 + PI0014927.1 Cmetu04g3133 3133
4 29701810 29707290 - PI0004805.1 Cmetu04g3193 3193
1 8511669 8522969 - CmoCh01G010600.1 Cmo01g01060 1060
1 14278906 14282004 - CmoCh01G020380.1 Cmo01g02038 2038
5 1394117 1396782 + CmoCh05G003140.1 Cmo05g00314 314
5 1400618 1402404 + CmoCh05G003150.1 Cmo05g00315 315
5 1403562 1408218 + CmoCh05G003160.1 Cmo05g00316 316
9 453119 456229 + CmoCh09G000940.1 Cmo09g00094 94
9 456782 458832 - CmoCh09G000950.1 Cmo09g00095 95
12 2180257 2185125 - CmoCh12G003530.1 Cmo12g00353 353
12 2200133 2205580 - CmoCh12G003550.1 Cmo12g00355 355
5 28649274 28652279 + CmPI595203_05g018640.1 Cmu05g1864 1864
5 28654154 28655716 - CmPI595203_05g018650.1 Cmu05g1865 1865
4 13879218 13880907 + Conep04aG0204200.1 Cone4ag1978 1978
4 13886786 13891326 - Conep04aG0204400.1 Cone4ag1980 1980
7 12167078 12170587 - Conep07aG0195400.1 Cone7ag1897 1897
17 9689129 9690812 + Conep17aG0144700.1 Cone17ag1410 1410
17 9697385 9698775 + Conep17aG0144800.1 Cone17ag1411 1411
17 9701349 9703167 + Conep17aG0145000.1 Cone17ag1413 1413
17 9704438 9708613 - Conep17aG0145100.1 Cone17ag1414 1414
20 331949 336168 + Conep20aG0007100.1 Cone20ag0069 69
20 337042 339483 - Conep20aG0007200.1 Cone20ag0070 70
20 349185 350747 - Conep20aG0007400.1 Cone20ag0072 72
20 2187900 2198514 + Conep20aG0045200.1 Cone20ag0437 437
2 340311 343409 + Cp4.1LG02g07990.1 Cpe02g00065 65
2 340568 346714 - Cp4.1LG02g07870.1 Cpe02g00066 66
6 310180 313290 + Cp4.1LG06g00560.1 Cpe06g00060 60
6 313847 315913 - Cp4.1LG06g00660.1 Cpe06g00061 61
7 2304753 2309600 - Cp4.1LG07g03570.1 Cpe07g00357 357
7 2326165 2331321 - Cp4.1LG07g03580.1 Cpe07g00360 360
11 1408672 1411321 + Cp4.1LG11g02650.1 Cpe11g00260 260
11 1415211 1416953 + Cp4.1LG11g02660.1 Cpe11g00261 261
11 1418617 1424719 + Cp4.1LG11g02600.1 Cpe11g00262 262
5 31962243 31967357 + CrPI670011_05g019880.1 Cre05g1988 1988
5 31969226 31970784 - CrPI670011_05g019890.1 Cre05g1989 1989
8 26717193 26727434 + CrPI670011_08g013690.1 Cre08g1369 1369
8 26729300 26731526 - CrPI670011_08g013700.1 Cre08g1370 1370
8 26746201 26747594 - CrPI670011_08g013720.1 Cre08g1372 1372
2 19375453 19378328 + CsaV3_2G029590.1 Csa02g02140 2140
2 19383919 19386764 + CsaV3_2G029610.1 Csa02g02142 2142
2 19387760 19397426 - CsaV3_2G029620.1 Csa02g02143 2143
3 37543700 37550504 + CsaV3_3G045940.1 Csa03g04288 4288
3 37546653 37552274 - CsaV3_3G045950.1 Csa03g04289 4289
1 81343024 81346131 + Hsped.01g16060.1 Hepe01g1606 1606
1 81348554 81350103 - Hsped.01g16070.1 Hepe01g1607 1607
10 1635964 1638640 + Hsped.10g01600.1 Hepe10g0160 160
10 1665395 1676804 - Hsped.10g01630.1 Hepe10g0163 163
10 8941636 8942388 - Hsped.10g06740.1 Hepe10g0674 674
13 38004040 38005061 - Maker00033701 Lcy13g1906 1906
13 38017119 38020365 - Maker00033724 Lcy13g1907 1907
4 24798564 24800959 + Lsi04G017540.1 Lsi04g01754 1754
4 24802230 24815106 - Lsi04G017550.1 Lsi04g01755 1755
8 7122120 7127750 - Lsi08G002830.1 Lsi08g00283 283
8 21454397 21463908 + Lsi08G013100.1 Lsi08g01310 1310
8 21466639 21469139 - Lsi08G013110.1 Lsi08g01311 1311
11 712408 712578 + MC11g0095 Mch11g0106 106
11 714752 716949 - MC11g0096 Mch11g0107 107
1 18564854 18567729 + Sed0024955.1 Sed01g2481 2481
1 18568920 18574114 - Sed0012955.1 Sed01g2483 2483
11 26594580 26597291 + Sed0014411.3 Sed11g1094 1094
1 115914840 115917158 + Tan0001904.2 Tan01g5034 5034
1 115917964 115923468 - Tan0016771.1 Tan01g5035 5035
2 90348461 90350869 + Tan0009790.1 Tan02g2081 2081
2 90348461 90350869 + Tan0009790.2 Tan02g2082 2082
18 12468308 12470528 + Vvi18g1130 Vvi18g1130 1130
18 12488624 12490747 + Vvi18g1131 Vvi18g1131 1131
18 12501748 12507830 - Vvi18g1132 Vvi18g1132 1132
18 12509085 12513293 - Vvi18g1133 Vvi18g1133 1133
18 12525880 12526911 + Vvi18g1134 Vvi18g1134 1134
18 12533120 12534693 + Vvi18g1135 Vvi18g1135 1135
18 12545222 12566131 + Vvi18g1136 Vvi18g1136 1136
18 12579079 12591899 - Vvi18g1137 Vvi18g1137 1137
18 12608248 12608970 - Vvi18g1138 Vvi18g1138 1138
18 12620618 12628019 - Vvi18g1139 Vvi18g1139 1139
       

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