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
Vvi3g766 Blo02g00919 . . . . . Bma05g00641 . . . . . . . . . . . . . . . . . Cla10g00963 Cam10g0986 Cec10g1017 . Clacu10g1008 Cmu10g1791 Cre10g1164 . . . Cone10ag1060 . . . . . . . . . Bpe05g00462 . . Sed07g1144 Cmo04g00464 . . . . . . Cpe01g00389 Bhi11g01104 Tan01g0607 Cmetu07g1105 . . Mch10g0410 . . . . . . . . Lsi03g01008 . . Cme07g02209
Vvi3g767 Blo02g00918 . . . . . . . . . . . . . . . . . . . . . . . Cla10g00962 Cam10g0985 Cec10g1016 . Clacu10g1007 Cmu10g1790 Cre10g1163 . . Cone3ag1045 Cone10ag1061 . . . . . . . . . . . . Sed07g1148 Cmo04g00463 Cmo16g00325 . . . . Cpe14g00254 . Bhi11g01103 Tan01g0606 Cmetu07g0362 . . Mch10g0409 . . . . . . . . Lsi03g01007 . . Cme07g02210
Vvi3g768 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g769 . . . . . . . . Cmo19g00554 Cmo11g01428 . . . . . Cpe04g00334 Cpe15g00429 . . . . . . . Cla02g00697 Cam02g0730 Cec02g0745 Cco02g0769 Clacu02g0741 Cmu02g0736 Cre02g1049 . . Cone3ag1046 Cone10ag1062 Lsi03g00599 Csa07g00670 . Cme01g00134 . . . . . . . . . . . Cma11g01692 Cma19g00540 Car11g01151 Car19g00397 . . . . . . . . . . . . . . . . . . Chy01g00145 .
Vvi3g770 Blo02g00917 Blo03g00060 Bda06g01159 . Bpe07g00293 . . Bma12g00302 Cmo19g00553 Cmo11g01429 . . . . . Cpe04g00335 Cpe15g00428 . . . . . . . Cla02g00698 Cam02g0731 Cec02g0746 Cco02g0770 Clacu02g0742 Cmu02g0737 Cre02g1050 . . . . Lsi03g00600 Csa07g00669 . Cme01g00135 . . . . . . . . Sed07g1149 Cmo04g00462 Cmo16g00324 Cma11g01691 Cma19g00539 Car11g01152 Car19g00396 Cpe14g00253 Cpe01g00388 Bhi11g01102 Tan01g0605 Cmetu08g1396 . Hepe07g0394 Mch10g0408 . . . . . . . . Lsi03g01006 . Chy01g00146 Cme07g02211
Vvi3g771 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g772 Blo02g00916 Blo03g00059 . Bda08g00688 Bpe07g00294 . . Bma12g00304 . . . . . . . . . . . . . . . . Cla10g00960 Cam10g0983 Cec10g1014 Cco10g0978 Clacu10g1005 Cmu10g1788 Cre10g1161 . . Cone3ag1048 Cone10ag1064 . . . . . . . . . . . . . Cmo04g00461 Cmo16g00323 . . . . Cpe14g00252 Cpe01g00387 Bhi11g01101 Tan01g0604 . . . Mch10g0407 . . . . . . . . Lsi03g01005 . . Cme07g02212
Vvi3g773 . . . . . . . . . . . . . . . . . . . . . . . . Cla10g00959 Cam10g0982 Cec10g1013 . Clacu10g1004 Cmu10g1787 Cre10g1160 . . . . . . . . . . . . . . . . Sed13g0418 Cmo04g00460 Cmo16g00321 . . . . Cpe14g00251 Cpe01g00386 Bhi11g01099 Tan01g0602 Cmetu07g0067 . . Mch10g0406 . . . . . . . . Lsi03g01004 . . Cme07g02213
Vvi3g774 . . . . . Bpe12g00734 . . Cmo19g00552 . . . . . . . Cpe15g00427 Bhi05g01001 . . . . . . Cla02g00700 Cam02g0733 Cec02g0747 Cco02g0772 Clacu02g0744 Cmu02g0739 Cre02g1052 Cone12ag1029 . . . Lsi03g00601 Csa07g00668 . Cme01g00136 . Blo13g00276 Bda15g00469 . . . . Bma08g00017 . . . . Cma19g00538 . Car19g00395 . . . . . . . . . . . . . . . . . . Chy01g00147 .
Vvi3g775 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 40816780 40818971 - Bda033724 Bda06g01159 1159
8 7309156 7310579 + Bda029144.1 Bda08g00688 688
15 7812978 7886798 - Bda012299.1 Bda15g00469 469
5 35368617 35370495 - XM_039031609.1 Bhi05g01001 1001
11 32465261 32469670 + XM_039049971.1 Bhi11g01099 1099
11 32488086 32494046 + XM_039049139.1 Bhi11g01101 1101
11 32503004 32505616 - XM_039048170.1 Bhi11g01102 1102
11 32509400 32511608 - XM_039049451.1 Bhi11g01103 1103
11 32517440 32522628 - XM_039049304.1 Bhi11g01104 1104
2 35353864 35356076 + BLOR10646 Blo02g00916 916
2 35356766 35359019 - BLOR10647 Blo02g00917 917
2 35391448 35392989 - BLOR10648 Blo02g00918 918
2 35409416 35412804 - BLOR10649 Blo02g00919 919
3 2206831 2213329 + BLOR11240 Blo03g00059 59
3 2213716 2219029 - BLOR11241 Blo03g00060 60
13 14232045 14238486 + BLOR05557 Blo13g00276 276
5 37776157 37779665 + Bma021677.1 Bma05g00641 641
8 310211 368454 - Bma027008.1 Bma08g00017 17
12 4252155 4254373 + Bma007209.1 Bma12g00302 302
12 4279837 4281761 - Bma007210.1 Bma12g00304 304
5 18974271 18977600 + Bpe017881.1 Bpe05g00462 462
7 2116573 2118831 + Bpe021103.1 Bpe07g00293 293
7 2119229 2120583 - Bpe021104.1 Bpe07g00294 294
12 12824294 12875611 + Bpe005995.1 Bpe12g00734 734
2 8830857 8835011 + CaPI482276_02g007300.1 Cam02g0730 730
2 8842635 8845189 + CaPI482276_02g007310.1 Cam02g0731 731
2 8854585 8910661 - CaPI482276_02g007330.1 Cam02g0733 733
10 21937554 21941296 + CaPI482276_10g009820.1 Cam10g0982 982
10 21943557 21948626 + CaPI482276_10g009830.1 Cam10g0983 983
10 21958680 21960197 - CaPI482276_10g009850.1 Cam10g0985 985
10 21964948 21969290 - CaPI482276_10g009860.1 Cam10g0986 986
11 9224634 9229343 + Carg23045-RA Car11g01151 1151
11 9230767 9233111 + Carg23046-RA Car11g01152 1152
19 5844487 5886794 + Carg16316-RA Car19g00395 395
19 5886840 5889442 - Carg16317-RA Car19g00396 396
19 5890572 5894420 - Carg16318-RA Car19g00397 397
2 8137199 8139954 + CcPI632755_02g007690.1 Cco02g0769 769
2 8153298 8155853 + CcPI632755_02g007700.1 Cco02g0770 770
2 8190413 8235974 - CcPI632755_02g007720.1 Cco02g0772 772
10 21149542 21154592 - CcPI632755_10g009780.1 Cco10g0978 978
2 8099926 8102673 + CePI673135_02g007450.1 Cec02g0745 745
2 8110606 8113163 + CePI673135_02g007460.1 Cec02g0746 746
2 8120541 8179120 - CePI673135_02g007470.1 Cec02g0747 747
10 22812391 22816131 + CePI673135_10g010130.1 Cec10g1013 1013
10 22818423 22823475 + CePI673135_10g010140.1 Cec10g1014 1014
10 22833385 22834902 - CePI673135_10g010160.1 Cec10g1016 1016
10 22839577 22843883 - CePI673135_10g010170.1 Cec10g1017 1017
1 976279 979522 + Chy1G001450.1 Chy01g00145 145
1 982143 984398 + Chy1G001460.1 Chy01g00146 146
1 985513 1025023 - Chy1G001470.1 Chy01g00147 147
2 7834944 7837533 + ClG42_02g0074100.10 Clacu02g0741 741
2 7844710 7847267 + ClG42_02g0074200.10 Clacu02g0742 742
2 7856853 7912294 - ClG42_02g0074400.10 Clacu02g0744 744
10 21594722 21598465 + ClG42_10g0100400.10 Clacu10g1004 1004
10 21600737 21605832 + ClG42_10g0100500.10 Clacu10g1005 1005
10 21615764 21617281 - ClG42_10g0100700.10 Clacu10g1007 1007
10 21621968 21626284 - ClG42_10g0100800.10 Clacu10g1008 1008
2 8198909 8203001 + ClCG02G007130.2 Cla02g00697 697
2 8209788 8212961 + ClCG02G007140.2 Cla02g00698 698
2 8223309 8279713 - ClCG02G007160.1 Cla02g00700 700
10 22590990 22595132 + ClCG10G009990.1 Cla10g00959 959
10 22597177 22602274 + ClCG10G010000.2 Cla10g00960 960
10 22612204 22613721 - ClCG10G010030.1 Cla10g00962 962
10 22618130 22624082 - ClCG10G010040.1 Cla10g00963 963
11 11163077 11166196 - CmaCh11G016910.1 Cma11g01691 1691
11 11169779 11174802 - CmaCh11G016920.1 Cma11g01692 1692
19 6177231 6217155 + CmaCh19G005380.1 Cma19g00538 538
19 6218313 6221043 - CmaCh19G005390.1 Cma19g00539 539
19 6222179 6225860 - CmaCh19G005400.1 Cma19g00540 540
1 961486 962730 + MELO3C018531.2.1 Cme01g00134 134
1 968040 970751 + MELO3C018532.2.1 Cme01g00135 135
1 971766 1010422 - MELO3C018533.2.1 Cme01g00136 136
7 26324798 26328146 + MELO3C018023.2.1 Cme07g02209 2209
7 26328550 26330660 + MELO3C018024.2.1 Cme07g02210 2210
7 26332840 26335862 + MELO3C018025.2.1 Cme07g02211 2211
7 26337218 26342367 - MELO3C018026.2.1 Cme07g02212 2212
7 26343709 26348662 - MELO3C018027.2.1 Cme07g02213 2213
7 249047 253431 + PI0013825.1 Cmetu07g0067 67
7 266951 268952 - PI0016177.1 Cmetu07g0362 362
7 271186 275532 - PI0017626.1 Cmetu07g1105 1105
8 20552692 20555730 - PI0013003.1 Cmetu08g1396 1396
4 2287623 2292560 + CmoCh04G004600.1 Cmo04g00460 460
4 2293636 2298023 + CmoCh04G004610.1 Cmo04g00461 461
4 2299963 2302764 - CmoCh04G004620.1 Cmo04g00462 462
4 2304252 2305622 - CmoCh04G004630.1 Cmo04g00463 463
4 2305945 2309759 - CmoCh04G004640.1 Cmo04g00464 464
11 10055199 10059434 + CmoCh11G014280.1 Cmo11g01428 1428
11 10061219 10063750 + CmoCh11G014290.1 Cmo11g01429 1429
16 1468814 1473014 + CmoCh16G003210.1 Cmo16g00321 321
16 1476243 1479201 + CmoCh16G003230.1 Cmo16g00323 323
16 1479900 1482967 - CmoCh16G003240.1 Cmo16g00324 324
16 1485072 1486562 - CmoCh16G003250.1 Cmo16g00325 325
19 6341570 6383718 + CmoCh19G005520.1 Cmo19g00552 552
19 6385113 6387929 - CmoCh19G005530.1 Cmo19g00553 553
19 6388975 6393012 - CmoCh19G005540.1 Cmo19g00554 554
2 7741703 7745736 + CmPI595203_02g007360.1 Cmu02g0736 736
2 7752954 7755509 + CmPI595203_02g007370.1 Cmu02g0737 737
2 7765088 7820569 - CmPI595203_02g007390.1 Cmu02g0739 739
10 22204910 22208653 + CmPI595203_10g017870.1 Cmu10g1787 1787
10 22210924 22216021 + CmPI595203_10g017880.1 Cmu10g1788 1788
10 22225953 22227470 - CmPI595203_10g017900.1 Cmu10g1790 1790
10 22232181 22236466 - CmPI595203_10g017910.1 Cmu10g1791 1791
3 29237063 29238985 + Conep03aG0154600.1 Cone3ag1045 1045
3 29239761 29242079 + Conep03aG0154700.1 Cone3ag1046 1046
3 29246285 29248555 - Conep03aG0154900.1 Cone3ag1048 1048
10 7384804 7388111 + Conep10aG0108700.1 Cone10ag1060 1060
10 7388600 7390314 + Conep10aG0108800.1 Cone10ag1061 1061
10 7390734 7392359 + Conep10aG0108900.1 Cone10ag1062 1062
10 7397836 7400397 - Conep10aG0109100.1 Cone10ag1064 1064
12 8614500 8636185 + Conep12aG0105800.1 Cone12ag1029 1029
1 2225815 2231107 + Cp4.1LG01g02840.1 Cpe01g00386 386
1 2232145 2236770 + Cp4.1LG01g02810.1 Cpe01g00387 387
1 2236951 2240695 - Cp4.1LG01g02730.1 Cpe01g00388 388
1 2242006 2247559 - Cp4.1LG01g02760.1 Cpe01g00389 389
4 4082695 4088446 + Cp4.1LG04g07520.1 Cpe04g00334 334
4 4088544 4091527 + Cp4.1LG04g07530.1 Cpe04g00335 335
14 1454729 1459322 + Cp4.1LG14g04760.1 Cpe14g00251 251
14 1459828 1465819 + Cp4.1LG14g04600.1 Cpe14g00252 252
14 1466626 1469794 - Cp4.1LG14g04530.1 Cpe14g00253 253
14 1471091 1472581 - Cp4.1LG14g04500.1 Cpe14g00254 254
15 5394635 5433752 + Cp4.1LG15g04270.1 Cpe15g00427 427
15 5435065 5437820 - Cp4.1LG15g04300.1 Cpe15g00428 428
15 5438837 5442617 - Cp4.1LG15g04310.1 Cpe15g00429 429
2 8376915 8379668 + CrPI670011_02g010490.1 Cre02g1049 1049
2 8386678 8389266 + CrPI670011_02g010500.1 Cre02g1050 1050
2 8395109 8451226 - CrPI670011_02g010520.1 Cre02g1052 1052
10 23871355 23875098 + CrPI670011_10g011600.1 Cre10g1160 1160
10 23877350 23882422 + CrPI670011_10g011610.1 Cre10g1161 1161
10 23892460 23893977 - CrPI670011_10g011630.1 Cre10g1163 1163
10 23898693 23903022 - CrPI670011_10g011640.1 Cre10g1164 1164
7 4752118 4788391 + CsaV3_7G007670.1 Csa07g00668 668
7 4789600 4791820 - CsaV3_7G007680.1 Csa07g00669 669
7 4793882 4797182 - CsaV3_7G007690.1 Csa07g00670 670
7 4007560 4010323 - Hsped.07g03940.1 Hepe07g0394 394
3 7455464 7463616 + Lsi03G005990.1 Lsi03g00599 599
3 7466185 7469161 + Lsi03G006000.1 Lsi03g00600 600
3 7471777 7480578 - Lsi03G006010.1 Lsi03g00601 601
3 19328922 19333284 + Lsi03G010040.1 Lsi03g01004 1004
3 19337640 19344867 + Lsi03G010050.1 Lsi03g01005 1005
3 19348856 19352076 - Lsi03G010060.1 Lsi03g01006 1006
3 19356886 19358406 - Lsi03G010070.1 Lsi03g01007 1007
3 19361234 19365789 - Lsi03G010080.1 Lsi03g01008 1008
10 2680845 2684287 + MC10g0333 Mch10g0406 406
10 2685959 2694207 + MC10g0334 Mch10g0407 407
10 2691236 2693571 - MC10g0335 Mch10g0408 408
10 2695471 2697000 - MC10g0336 Mch10g0409 409
10 2697632 2701821 - MC10g0337 Mch10g0410 410
7 8594488 8599886 + Sed0021356.1 Sed07g1144 1144
7 8612040 8612824 + Sed0009840.1 Sed07g1148 1148
7 8614869 8617937 + Sed0004020.1 Sed07g1149 1149
13 2756284 2761632 + Sed0007460.1 Sed13g0418 418
1 5518187 5522593 + Tan0014014.1 Tan01g0602 602
1 5529298 5535135 + Tan0012376.2 Tan01g0604 604
1 5536007 5538895 - Tan0018234.1 Tan01g0605 605
1 5544006 5546385 - Tan0011859.1 Tan01g0606 606
1 5547166 5552363 - Tan0020820.1 Tan01g0607 607
3 8343092 8347919 + Vvi3g766 Vvi3g766 766
3 8350297 8352225 + Vvi3g767 Vvi3g767 767
3 8375210 8376359 + Vvi3g768 Vvi3g768 768
3 8403057 8408354 + Vvi3g769 Vvi3g769 769
3 8411914 8414726 + Vvi3g770 Vvi3g770 770
3 8416041 8423780 - Vvi3g771 Vvi3g771 771
3 8426970 8430834 - Vvi3g772 Vvi3g772 772
3 8431960 8436443 - Vvi3g773 Vvi3g773 773
3 8486712 8618755 - Vvi3g774 Vvi3g774 774
3 8654172 8655019 - Vvi3g775 Vvi3g775 775
       

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