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
Vvi5g1319 . . . . . Bpe14g00787 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda13g00541 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1320 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1321 . Blo12g00272 Bda03g00963 . Bpe04g00891 Bpe14g00789 Bma04g00857 . . . . Cma14g01438 Car06g01427 . . . . Bhi01g03682 . . . . . . . . . . . . . Cone14ag0621 Cone15ag0629 . . . . . . . . . Bda13g00540 . . . . . Cmo06g01675 Cmo14g01474 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1322 Blo01g00181 Blo12g00273 Bda03g00962 Bda08g00169 Bpe04g00890 . . Bma05g01153 Cmo08g00190 Cmo17g00602 . . . . . . . . . . . . . . Cla06g00102 Cam06g0113 Cec06g0114 Cco06g0113 Clacu06g0115 Cmu06g0113 Cre06g0883 Cone14ag0619 Cone15ag0627 . . . . . . . . . . Bpe05g00963 . . . Sed09g0394 . . . Cma17g00618 Car08g00169 Car17g00583 . Cpe17g01079 Bhi12g02468 Tan06g1530 Cmetu11g1399 . Hepe03g1100 . . . . . . . . . . . . Cme11g02436
Vvi5g1323 . . . . . Bpe14g00790 . . . . . . Car06g01428 Car14g01266 . . . Bhi01g03681 . . . . . . . . . . . . . Cone14ag0618 Cone15ag0625 . Cone11ag0673 . . . . . . . Bda13g00539 . . . . . Cmo06g01677 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1324 . . . . . Bpe14g00791 . . . . Cma06g01693 . Car06g01434 . . . . . . . . . . . . . . . . . . . . . . . . . Cme07g01946 . . . Bda13g00538 . . . . . Cmo06g01684 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1325 . Blo12g00274 Bda03g00961 . Bpe04g00889 . . . Cmo08g00189 . . . . . . . . . . . . . . . Cla06g00103 Cam06g0112 Cec06g0115 Cco06g0114 Clacu06g0116 Cmu06g0114 Cre06g0884 Cone14ag0617 Cone15ag0624 . . . . . . . . . . . . . . Sed09g0393 . . . . . . . Cpe17g01078 Bhi12g02467 Tan06g1529 Cmetu11g0399 . Hepe03g1101 . . . . . . . . . . . . .
Vvi5g1326 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1327 . Blo12g00275 Bda03g00960 . Bpe04g00888 Bpe14g00792 Bma04g00856 . Cmo08g00188 . Cma06g01692 . . . . . . Bhi01g03674 Tan10g1432 . . . . . Cla06g00104 Cam06g0111 Cec06g0116 Cco06g0115 Clacu06g0117 Cmu06g0115 Cre06g0885 Cone14ag0616 Cone15ag0623 . Cone11ag0674 . . . Cme07g01945 . . . Bda13g00537 . . . . Sed07g0076 . . . . Car08g00167 . . Cpe17g01077 Bhi12g02466 Tan06g1528 Cmetu11g0606 . . . . . . . . . . . . . . Cme11g02434
Vvi5g1328 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 8702090 8704125 - Bda016969.1 Bda03g00960 960
3 8708402 8708966 - Bda016970.1 Bda03g00961 961
3 8713036 8714549 + Bda016971.1 Bda03g00962 962
3 8714799 8715580 - Bda016972.1 Bda03g00963 963
8 1560755 1561998 - Bda024580.1 Bda08g00169 169
13 6385372 6386900 - Bda001448.1 Bda13g00537 537
13 6390365 6392362 - Bda001449.1 Bda13g00538 538
13 6394522 6406591 + Bda001450.1 Bda13g00539 539
13 6409167 6412220 - Bda001451.1 Bda13g00540 540
13 6418178 6421941 + Bda001452.2 Bda13g00541 541
1 93818984 93823124 + XM_039039676.1 Bhi01g03674 3674
1 94118453 94142806 + XM_039038030.1 Bhi01g03681 3681
1 94169810 94174844 + XM_039050507.1 Bhi01g03682 3682
12 77584277 77590539 - XM_039051073.1 Bhi12g02466 2466
12 77604155 77606579 - XM_039019424.1 Bhi12g02467 2467
12 77617319 77621541 + XM_039019470.1 Bhi12g02468 2468
1 2457985 2459463 + BLOR00181 Blo01g00181 181
12 16483486 16484412 + BLOR04291 Blo12g00272 272
12 16484620 16486137 - BLOR04292 Blo12g00273 273
12 16515526 16516071 + BLOR04293 Blo12g00274 274
12 16552268 16554712 + BLOR04294 Blo12g00275 275
4 10829575 10831652 - Bma019401.1 Bma04g00856 856
4 10845691 10846488 - Bma019403.2 Bma04g00857 857
5 50559260 50560487 + Bma022343.1 Bma05g01153 1153
4 5949504 5951846 - Bpe015552.1 Bpe04g00888 888
4 5955631 5956905 - Bpe015553.1 Bpe04g00889 889
4 5959421 5960983 + Bpe015554.1 Bpe04g00890 890
4 5961235 5962014 - Bpe025667 Bpe04g00891 891
5 22506237 22507504 + Bpe018375.1 Bpe05g00963 963
14 5967434 5971169 - Bpe014165.1 Bpe14g00787 787
14 5980428 5981990 + Bpe014167.1 Bpe14g00789 789
14 5984718 5995159 - Bpe014168.1 Bpe14g00790 790
14 6004095 6006098 + Bpe014169.1 Bpe14g00791 791
14 6008693 6010654 + Bpe014170.1 Bpe14g00792 792
6 3076655 3082472 - CaPI482276_06g001110.1 Cam06g0111 111
6 3090165 3092235 - CaPI482276_06g001120.1 Cam06g0112 112
6 3105623 3109048 + CaPI482276_06g001130.1 Cam06g0113 113
6 10174160 10178188 - Carg15448-RA Car06g01427 1427
6 10181699 10190105 - Carg15447-RA Car06g01428 1428
6 10216151 10220100 - Carg15441-RA Car06g01434 1434
8 1020766 1025722 - Carg05012-RA Car08g00167 167
8 1031739 1034657 + Carg05014-RA Car08g00169 169
14 10879778 10885277 + Carg06587-RA Car14g01266 1266
17 5561534 5565591 - Carg18916-RA Car17g00583 583
6 1044114 1047508 - CcPI632755_06g001130.1 Cco06g0113 113
6 1059448 1065229 + CcPI632755_06g001140.1 Cco06g0114 114
6 1071576 1077572 + CcPI632755_06g001150.1 Cco06g0115 115
6 1065074 1068467 - CePI673135_06g001140.1 Cec06g0114 114
6 1100929 1102985 + CePI673135_06g001150.1 Cec06g0115 115
6 1110601 1116364 + CePI673135_06g001160.1 Cec06g0116 116
6 1231980 1235383 - ClG42_06g0011500.10 Clacu06g0115 115
6 1246807 1248892 + ClG42_06g0011600.10 Clacu06g0116 116
6 1258933 1264908 + ClG42_06g0011700.10 Clacu06g0117 117
6 1065956 1071133 - ClCG06G001100.1 Cla06g00102 102
6 1083940 1089986 + ClCG06G001110.2 Cla06g00103 103
6 1096044 1101982 + ClCG06G001120.1 Cla06g00104 104
6 10407698 10409967 - CmaCh06G016920.1 Cma06g01692 1692
6 10413182 10418601 - CmaCh06G016930.1 Cma06g01693 1693
14 11018138 11024076 + CmaCh14G014380.1 Cma14g01438 1438
17 5260023 5264076 - CmaCh17G006180.1 Cma17g00618 618
7 24617306 24621118 - MELO3C017768.2.1 Cme07g01945 1945
7 24633580 24638797 - MELO3C017769.2.1 Cme07g01946 1946
11 31128618 31132792 - MELO3C022423.2.1 Cme11g02434 2434
11 31143799 31147162 + MELO3C022425.2.1 Cme11g02436 2436
11 877816 880364 + PI0003184.1 Cmetu11g0399 399
11 885017 891011 + PI0005622.1 Cmetu11g0606 606
11 868766 872348 - PI0013887.1 Cmetu11g1399 1399
6 11584546 11588341 - CmoCh06G016750.1 Cmo06g01675 1675
6 11592268 11600588 - CmoCh06G016770.1 Cmo06g01677 1677
6 11624509 11632359 - CmoCh06G016840.1 Cmo06g01684 1684
8 1097864 1102974 - CmoCh08G001880.1 Cmo08g00188 188
8 1105441 1107052 - CmoCh08G001890.1 Cmo08g00189 189
8 1109272 1112210 + CmoCh08G001900.1 Cmo08g00190 190
14 11917002 11921469 + CmoCh14G014740.1 Cmo14g01474 1474
17 6383272 6386627 - CmoCh17G006020.1 Cmo17g00602 602
6 1027361 1030764 - CmPI595203_06g001130.1 Cmu06g0113 113
6 1042157 1044252 + CmPI595203_06g001140.1 Cmu06g0114 114
6 1054277 1060228 + CmPI595203_06g001150.1 Cmu06g0115 115
11 4526688 4552905 + Conep11aG0069100.1 Cone11ag0673 673
11 4562692 4566657 + Conep11aG0069200.1 Cone11ag0674 674
14 3079979 3083328 - Conep14aG0063000.1 Cone14ag0616 616
14 3088582 3090882 - Conep14aG0063100.1 Cone14ag0617 617
14 3097886 3099879 + Conep14aG0063200.1 Cone14ag0618 618
14 3104329 3106400 + Conep14aG0063300.1 Cone14ag0619 619
14 3115120 3116558 - Conep14aG0063500.1 Cone14ag0621 621
15 3250281 3253252 - Conep15aG0063600.1 Cone15ag0623 623
15 3263714 3265613 - Conep15aG0063700.1 Cone15ag0624 624
15 3270649 3281146 + Conep15aG0063800.1 Cone15ag0625 625
15 3285003 3287342 + Conep15aG0064000.1 Cone15ag0627 627
15 3296109 3298023 - Conep15aG0064200.1 Cone15ag0629 629
17 8183951 8188430 - Cp4.1LG17g10800.1 Cpe17g01077 1077
17 8190891 8191451 - Cp4.1LG17g10850.1 Cpe17g01078 1078
17 8194948 8197842 + Cp4.1LG17g10790.1 Cpe17g01079 1079
6 2123059 2126458 - CrPI670011_06g008830.1 Cre06g0883 883
6 2138969 2141048 + CrPI670011_06g008840.1 Cre06g0884 884
6 2148734 2154511 + CrPI670011_06g008850.1 Cre06g0885 885
3 62020017 62024062 - Hsped.03g11000.1 Hepe03g1100 1100
3 62104595 62107367 + Hsped.03g11010.1 Hepe03g1101 1101
7 840990 846204 + Sed0019824.1 Sed07g0076 76
9 3678160 3680773 - Sed0003072.1 Sed09g0393 393
9 3695483 3710017 + Sed0015541.1 Sed09g0394 394
6 22056702 22069291 - Tan0007098.1 Tan06g1528 1528
6 22092782 22095516 - Tan0013613.1 Tan06g1529 1529
6 22118353 22122556 + Tan0001905.1 Tan06g1530 1530
10 19448017 19452765 + Tan0002497.2 Tan10g1432 1432
5 23788469 23793486 - Vvi5g1319 Vvi5g1319 1319
5 23799540 23804603 + Vvi5g1320 Vvi5g1320 1320
5 23815689 23820063 + Vvi5g1321 Vvi5g1321 1321
5 23820101 23824960 - Vvi5g1322 Vvi5g1322 1322
5 23827251 23863361 - Vvi5g1323 Vvi5g1323 1323
5 23866669 23876835 + Vvi5g1324 Vvi5g1324 1324
5 23880483 23883402 + Vvi5g1325 Vvi5g1325 1325
5 23888939 23891150 + Vvi5g1326 Vvi5g1326 1326
5 23891151 23894151 + Vvi5g1327 Vvi5g1327 1327
5 23897673 23899101 + Vvi5g1328 Vvi5g1328 1328
       

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