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
Vvi5g129 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g130 . . . . . Bpe14g01110 . . . . Cma06g01546 Cma14g01615 Car06g01312 Car14g01434 . Cpe08g00178 Cpe03g01356 Bhi01g01055 Tan10g1044 . . . . . . . . . . . . . . Cone7ag0125 . . . . . Blo02g00490 Blo07g00162 Bda11g00515 Bda13g00204 . Bpe13g00679 . Bma06g01485 . . Cmo14g01652 . . . . . . . . . . . . . Cla05g00677 Cam05g0744 Cec05g0750 Cco05g0750 Clacu05g0736 Cmu05g0701 Cre05g0775 . Csa03g01495 . .
Vvi5g131 . . . . . . . . Cmo08g01221 . . . . . . . . . . . . . . . Cla06g00453 Cam06g0483 Cec06g0487 Cco06g0486 Clacu06g0470 Cmu06g0470 Cre06g1244 . . . . . Csa06g01770 Chy11g01541 . . . . . . . . . . . . Cma08g01250 . Car08g01123 . . Cpe17g00044 Bhi12g02020 . . . Hepe03g0074 . . . . . . . . . Lsi09g01461 . . Cme11g02049
Vvi5g132 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g133 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g134 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone11ag0132 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g135 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g136 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g137 . . . . . Bpe14g01111 . Bma05g01033 . . Cma06g01545 Cma14g01605 . Car14g01423 . Cpe08g00168 Cpe03g01347 . . . . . . . . . . . . . . Cone14ag0743 . . . . . . . Blo02g00491 Blo07g00163 Bda11g00516 . Bpe05g00834 Bpe13g00678 Bma02g00919 Bma06g01486 . . Cmo14g01640 . . . . . . . . . . . . . Cla05g00676 Cam05g0743 Cec05g0749 Cco05g0749 Clacu05g0735 Cmu05g0700 Cre05g0774 . Csa03g01494 Chy06g00732 .
Vvi5g138 . . . . . . . . Cmo08g01220 . . . . . . . . . . . . . . . Cla06g00454 Cam06g0484 Cec06g0488 Cco06g0487 Clacu06g0471 Cmu06g0472 Cre06g1245 . . . . . Csa06g01771 Chy11g01540 . . Blo07g00164 . . . Bpe13g00677 . Bma06g01487 . . . Cma08g01249 . Car08g01122 . . Cpe17g00043 Bhi12g02022 Tan06g2715 . . Hepe03g0075 . . . . . . . . . Lsi09g01460 . . Cme11g02048
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 5460591 5461665 + Bda005251.1 Bda11g00515 515
11 5462310 5464018 - Bda033041 Bda11g00516 516
13 2624088 2624775 - Bda001077.1 Bda13g00204 204
1 19539147 19541354 - XM_039025678.1 Bhi01g01055 1055
12 63344312 63350866 - XM_039020307.1 Bhi12g02020 2020
12 63354426 63360305 + XM_039020354.1 Bhi12g02022 2022
2 7315880 7316805 + BLOR10220 Blo02g00490 490
2 7330550 7333112 - BLOR10221 Blo02g00491 491
7 2093301 2094342 + BLOR18094 Blo07g00162 162
7 2098065 2102123 - BLOR18095 Blo07g00163 163
7 2107884 2114658 + BLOR18096 Blo07g00164 164
2 48387996 48389789 + Bma015700.1 Bma02g00919 919
5 48887080 48888135 - Bma022191.2 Bma05g01033 1033
6 51418306 51421402 + Bma024597.1 Bma06g01485 1485
6 51422801 51424806 - Bma024598.1 Bma06g01486 1486
6 51427151 51432660 + Bma024599.1 Bma06g01487 1487
5 21587325 21588380 - Bpe018247.1 Bpe05g00834 834
13 13482814 13488354 - Bpe010378.2 Bpe13g00677 677
13 13494026 13495734 + Bpe010379.1 Bpe13g00678 678
13 13496332 13497247 - Bpe010380.2 Bpe13g00679 679
14 8291035 8291974 + Bpe014485.1 Bpe14g01110 1110
14 8293859 8309309 - Bpe014486.1 Bpe14g01111 1111
5 6453566 6456687 + CaPI482276_05g007430.1 Cam05g0743 743
5 6458214 6459542 - CaPI482276_05g007440.1 Cam05g0744 744
6 6941392 6946606 - CaPI482276_06g004830.1 Cam06g0483 483
6 6949299 6955173 + CaPI482276_06g004840.1 Cam06g0484 484
6 9392080 9393464 - Carg23750-RA Car06g01312 1312
8 7597127 7602437 - Carg18864-RA Car08g01122 1122
8 7603435 7608148 + Carg18865-RA Car08g01123 1123
14 11934562 11939390 - Carg19645-RA Car14g01423 1423
14 11991093 11992187 - Carg19656-RA Car14g01434 1434
5 6152252 6155342 + CcPI632755_05g007490.1 Cco05g0749 749
5 6156859 6158192 - CcPI632755_05g007500.1 Cco05g0750 750
6 5339706 5344894 - CcPI632755_06g004860.1 Cco06g0486 486
6 5347573 5353430 + CcPI632755_06g004870.1 Cco06g0487 487
5 6176299 6179381 + CePI673135_05g007490.1 Cec05g0749 749
5 6180903 6182206 - CePI673135_05g007500.1 Cec05g0750 750
6 5470145 5475404 - CePI673135_06g004870.1 Cec06g0487 487
6 5478093 5483959 + CePI673135_06g004880.1 Cec06g0488 488
6 4989298 4992446 + Chy6G112600.1 Chy06g00732 732
11 21967637 21972755 - Chy11G201200.1 Chy11g01540 1540
11 21973529 21980846 + Chy11G201210.1 Chy11g01541 1541
5 6175643 6178715 + ClG42_05g0073500.10 Clacu05g0735 735
5 6180219 6181520 - ClG42_05g0073600.10 Clacu05g0736 736
6 5475975 5481194 - ClG42_06g0047000.10 Clacu06g0470 470
6 5483843 5489690 + ClG42_06g0047100.10 Clacu06g0471 471
5 6287019 6294332 + ClCG05G006310.2 Cla05g00676 676
5 6292422 6294241 - ClCG05G006320.1 Cla05g00677 677
6 5523478 5529553 - ClCG06G004860.2 Cla06g00453 453
6 5529991 5537659 + ClCG06G004870.2 Cla06g00454 454
6 9681315 9689722 + CmaCh06G015450.1 Cma06g01545 1545
6 9688535 9690178 - CmaCh06G015460.1 Cma06g01546 1546
8 7630189 7636159 - CmaCh08G012490.1 Cma08g01249 1249
8 7637609 7642381 + CmaCh08G012500.1 Cma08g01250 1250
14 12059052 12069216 - CmaCh14G016050.1 Cma14g01605 1605
14 12125704 12136301 + CmaCh14G016150.1 Cma14g01615 1615
11 28251794 28257335 - MELO3C021296.2.1 Cme11g02048 2048
11 28259132 28265189 + MELO3C021295.2.1 Cme11g02049 2049
8 7744913 7751526 - CmoCh08G012200.1 Cmo08g01220 1220
8 7751356 7756166 + CmoCh08G012210.1 Cmo08g01221 1221
14 12998686 13003026 - CmoCh14G016400.1 Cmo14g01640 1640
14 13057918 13059006 - CmoCh14G016520.1 Cmo14g01652 1652
5 6019019 6022104 + CmPI595203_05g007000.1 Cmu05g0700 700
5 6023606 6024907 - CmPI595203_05g007010.1 Cmu05g0701 701
6 5278491 5283712 - CmPI595203_06g004700.1 Cmu06g0470 470
6 5286364 5292220 + CmPI595203_06g004720.1 Cmu06g0472 472
7 528147 529597 + Conep07aG0012600.1 Cone7ag0125 125
11 595732 597767 + Conep11aG0013500.1 Cone11ag0132 132
14 4151159 4153796 - Conep14aG0076000.1 Cone14ag0743 743
3 10916869 10922986 - Cp4.1LG03g11580.1 Cpe03g01347 1347
3 10976477 10977571 - Cp4.1LG03g11540.1 Cpe03g01356 1356
8 1083263 1087086 - Cp4.1LG08g05090.1 Cpe08g00168 168
8 1225704 1226855 - Cp4.1LG08g04880.1 Cpe08g00178 178
17 281014 286336 - Cp4.1LG17g00380.1 Cpe17g00043 43
17 287381 292179 + Cp4.1LG17g00500.1 Cpe17g00044 44
5 6820242 6823367 + CrPI670011_05g007740.1 Cre05g0774 774
5 6824902 6826244 - CrPI670011_05g007750.1 Cre05g0775 775
6 6343454 6348679 - CrPI670011_06g012440.1 Cre06g1244 1244
6 6351399 6357289 + CrPI670011_06g012450.1 Cre06g1245 1245
3 11083694 11087130 + CsaV3_3G014940.1 Csa03g01494 1494
3 11087652 11089434 - CsaV3_3G014950.1 Csa03g01495 1495
6 15561497 15573395 - CsaV3_6G022650.1 Csa06g01770 1770
6 15574574 15581430 + CsaV3_6G022660.1 Csa06g01771 1771
3 871363 877507 - Hsped.03g00740.1 Hepe03g0074 74
3 880687 887855 + Hsped.03g00750.1 Hepe03g0075 75
9 22589088 22597217 - Lsi09G014600.1 Lsi09g01460 1460
9 22598316 22604776 + Lsi09G014610.1 Lsi09g01461 1461
6 79536918 79543994 - Tan0017531.1 Tan06g2715 2715
10 9319015 9322357 - Tan0004806.2 Tan10g1044 1044
5 1307368 1308279 + Vvi5g129 Vvi5g129 129
5 1312474 1313977 + Vvi5g130 Vvi5g130 130
5 1314895 1338433 - Vvi5g131 Vvi5g131 131
5 1343316 1345600 + Vvi5g132 Vvi5g132 132
5 1354933 1357002 + Vvi5g133 Vvi5g133 133
5 1363012 1369931 + Vvi5g134 Vvi5g134 134
5 1371011 1377054 - Vvi5g135 Vvi5g135 135
5 1377517 1379954 + Vvi5g136 Vvi5g136 136
5 1380483 1388778 - Vvi5g137 Vvi5g137 137
5 1400041 1407785 + Vvi5g138 Vvi5g138 138
       

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