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
Vvi18g510 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma02g00113 . . . Cma12g00198 . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g511 . . . . . . . . . Cmo12g00152 . . . Car12g00180 . . Cpe07g00168 . . . . . . . . . . . . . . . . . . . . . . . . . Bda13g01358 Bpe02g01149 . . Bma02g00113 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g512 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma02g00114 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g513 . . . . . . . . . Cmo12g00153 . . . . . . Cpe07g00169 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma12g00199 . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g514 . . Bda01g00910 . . . . . . . . . . Car12g00181 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma02g00115 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g515 . . . . Bpe02g00139 . . . . . Cma01g01646 . . . Sed05g1562 . Cpe07g00170 Bhi04g01382 Tan02g2480 Cmetu04g1739 . Hepe10g0431 . Lcy13g1480 . . . . . . . Cone4ag1297 Cone7ag0858 . . Lsi04g02279 Csa03g04492 . . . . Bda11g00799 . . . . . . Cmo01g01696 . . . . . . . . . . . . . . Cla11g01423 Cam11g1479 Cec11g1509 Cco11g1505 Clacu11g1640 Cmu11g1458 Cre11g1876 . . . .
Vvi18g516 . . . . . . . Bma01g02586 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy04g00208 . . . . . . . . . . . . . . . . . . Bhi09g02497 . . . . Mch11g0708 . . . . . . . . . . . Cme04g00238
Vvi18g517 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g518 . Blo12g00732 . Bda03g00456 . . Bma04g00431 Bma01g02585 . Cmo12g00155 . . . Car12g00183 Sed01g4279 . Cpe07g00171 Bhi04g01383 Tan02g2479 Cmetu03g0752 . Hepe10g0432 . Lcy13g1481 . . . . . . . . . . . Lsi04g02280 Csa03g04493 Chy04g00207 . . . Bda11g00800 . . . . . Sed05g1560 . . Cma12g00201 . . . . . Bhi09g02498 Tan01g3852 Cmetu04g3041 . Hepe01g2170 Mch11g0709 . Cla11g01425 Cam11g1480 Cec11g1510 Cco11g1506 Clacu11g1641 Cmu11g1459 Cre11g1877 . . . Cme04g00237
Vvi18g519 . . . . Bpe02g00140 . . Bma01g02584 . Cmo12g00156 . . . Car12g00184 . . Cpe07g00172 Bhi04g01385 . . . Hepe10g0433 . Lcy13g1482 . . . . . . . . . . . . . . . . . Bda11g00801 . . . . . . . . Cma12g00202 . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 42107916 42119092 + Bda003051.1 Bda01g00910 910
3 3948476 3953266 + Bda016424.1 Bda03g00456 456
11 7943854 7952321 + Bda005549.1 Bda11g00799 799
11 7952796 7956349 - Bda033061 Bda11g00800 800
11 7958726 7959205 + Bda005550.1 Bda11g00801 801
13 35982392 35992678 + Bda000175.1 Bda13g01358 1358
4 34849700 34861771 + XM_039028522.1 Bhi04g01382 1382
4 34872266 34877706 - XM_039030163.1 Bhi04g01383 1383
4 34987751 34991370 + XM_039030515.1 Bhi04g01385 1385
9 67548246 67557791 + XM_039040890.1 Bhi09g02497 2497
9 67558036 67562897 - XM_039044316.1 Bhi09g02498 2498
12 25650191 25654980 - BLOR04751 Blo12g00732 732
1 83468839 83469318 - Bma003470.1 Bma01g02584 2584
1 83471085 83482995 + Bma003471.1 Bma01g02585 2585
1 83488341 83496771 - Bma003472.1 Bma01g02586 2586
2 1035076 1046954 + Bma014569.1 Bma02g00113 113
2 1048204 1053731 + Bma030855 Bma02g00114 114
2 1054805 1065668 - Bma014570.2 Bma02g00115 115
4 3544928 3548603 + Bma018899.1 Bma04g00431 431
2 956453 964818 + Bpe007989.1 Bpe02g00139 139
2 971127 971594 + Bpe007990.1 Bpe02g00140 140
2 15080815 15093362 - Bpe009009.1 Bpe02g01149 1149
11 27527347 27537301 + CaPI482276_11g014790.1 Cam11g1479 1479
11 27538591 27544488 - CaPI482276_11g014800.1 Cam11g1480 1480
12 1110312 1118841 + Carg22514-RA Car12g00180 180
12 1119626 1124922 - Carg22513-RA Car12g00181 181
12 1132799 1136719 - Carg22511-RA Car12g00183 183
12 1142324 1142836 + Carg22510-RA Car12g00184 184
11 27867288 27881810 + CcPI632755_11g015050.1 Cco11g1505 1505
11 27883102 27887371 - CcPI632755_11g015060.1 Cco11g1506 1506
11 29298655 29312882 + CePI673135_11g015090.1 Cec11g1509 1509
11 29314211 29320146 - CePI673135_11g015100.1 Cec11g1510 1510
4 1897303 1901159 + Chy4G069250.1 Chy04g00207 207
4 1902345 1910808 - Chy4G069260.1 Chy04g00208 208
11 27551546 27566548 + ClG42_11g0164000.10 Clacu11g1640 1640
11 27567847 27573667 - ClG42_11g0164100.10 Clacu11g1641 1641
11 27788210 27798022 + ClCG11G014560.1 Cla11g01423 1423
11 27799205 27805025 - ClCG11G014580.2 Cla11g01425 1425
1 11267130 11277230 + CmaCh01G016460.1 Cma01g01646 1646
12 922037 935804 + CmaCh12G001980.1 Cma12g00198 198
12 935507 942820 - CmaCh12G001990.1 Cma12g00199 199
12 950680 954038 - CmaCh12G002010.1 Cma12g00201 201
12 955584 959011 + CmaCh12G002020.1 Cma12g00202 202
4 1863572 1868512 + MELO3C003523.2.1 Cme04g00237 237
4 1868965 1877843 - MELO3C003524.2.1 Cme04g00238 238
3 2948708 2953401 + PI0000145.1 Cmetu03g0752 752
4 31483483 31490086 + PI0016922.1 Cmetu04g1739 1739
4 31492876 31497135 - PI0003452.1 Cmetu04g3041 3041
1 12744206 12752837 + CmoCh01G016960.1 Cmo01g01696 1696
12 986368 995113 + CmoCh12G001520.1 Cmo12g00152 152
12 995821 1001555 - CmoCh12G001530.1 Cmo12g00153 153
12 1008884 1012965 - CmoCh12G001550.1 Cmo12g00155 155
12 1016996 1020368 + CmoCh12G001560.1 Cmo12g00156 156
11 26804201 26818323 + CmPI595203_11g014580.1 Cmu11g1458 1458
11 26819600 26825361 - CmPI595203_11g014590.1 Cmu11g1459 1459
4 10705010 10713151 - Conep04aG0134300.1 Cone4ag1297 1297
7 6570791 6580538 + Conep07aG0088700.1 Cone7ag0858 858
7 996922 1005844 + Cp4.1LG07g01690.1 Cpe07g00168 168
7 1006208 1012140 - Cp4.1LG07g01780.1 Cpe07g00169 169
7 1013174 1018691 + Cp4.1LG07g01670.1 Cpe07g00170 170
7 1019219 1023409 - Cp4.1LG07g01750.1 Cpe07g00171 171
7 1033627 1034139 + Cp4.1LG07g01720.1 Cpe07g00172 172
11 30426099 30437569 + CrPI670011_11g018760.1 Cre11g1876 1876
11 30438875 30444772 - CrPI670011_11g018770.1 Cre11g1877 1877
3 39128226 39137149 + CsaV3_3G047980.1 Csa03g04492 4492
3 39137686 39142225 - CsaV3_3G047990.1 Csa03g04493 4493
1 86343353 86349187 - Hsped.01g21700.1 Hepe01g2170 2170
10 4832778 4838965 + Hsped.10g04310.1 Hepe10g0431 431
10 4842214 4847527 - Hsped.10g04320.1 Hepe10g0432 432
10 4872995 4876781 + Hsped.10g04330.1 Hepe10g0433 433
13 33418329 33425471 + Maker00033965 Lcy13g1480 1480
13 33424942 33430722 - Maker00034156 Lcy13g1481 1481
13 33449505 33453353 + Maker00033778 Lcy13g1482 1482
4 29819329 29828868 + Lsi04G022790.1 Lsi04g02279 2279
4 29829839 29834651 - Lsi04G022800.1 Lsi04g02280 2280
11 4666785 4675934 + MC11g0597 Mch11g0708 708
11 4676116 4680181 - MC11g0598 Mch11g0709 709
1 71028531 71030921 - Sed0027437.1 Sed01g4279 4279
5 29368646 29374123 + Sed0019515.1 Sed05g1560 1560
5 29375330 29386311 - Sed0004579.1 Sed05g1562 1562
1 103271853 103275907 - Tan0000868.1 Tan01g3852 3852
2 93335502 93339804 + Tan0016069.1 Tan02g2479 2479
2 93342240 93347076 - Tan0000393.1 Tan02g2480 2480
18 5715454 5718850 + Vvi18g510 Vvi18g510 510
18 5730102 5742364 + Vvi18g511 Vvi18g511 511
18 5743182 5751624 + Vvi18g512 Vvi18g512 512
18 5751662 5762206 - Vvi18g513 Vvi18g513 513
18 5765988 5795580 - Vvi18g514 Vvi18g514 514
18 5807851 5821053 + Vvi18g515 Vvi18g515 515
18 5822105 5822793 + Vvi18g516 Vvi18g516 516
18 5831366 5832854 + Vvi18g517 Vvi18g517 517
18 5833779 5844784 - Vvi18g518 Vvi18g518 518
18 5846803 5850896 + Vvi18g519 Vvi18g519 519
       

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