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
Vvi19g524 . Blo03g01455 Bda07g00368 . . . . . . Cmo04g01038 . . . . . . . . . . . . . . Cla10g00496 Cam10g0488 Cec10g0506 Cco10g0491 Clacu10g0508 Cmu10g1335 Cre10g0740 . . Cone14ag1150 Cone15ag1166 . Csa03g00502 . Cme06g02240 . . . . Bpe11g00553 . . . Sed04g0718 . . Cma04g00962 . Car04g00903 . . Cpe01g00875 Bhi11g00603 Tan01g1718 Cmetu06g2809 . . . . . . . . . . . Lsi05g00584 . Chy06g01824 .
Vvi19g525 . . . . Bpe09g00171 . Bma10g00551 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone15ag1167 . . . . Blo07g00902 . Bda05g00718 Bda12g00912 . Bpe03g00790 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g526 . . . . . . Bma10g00552 . . Cmo04g01039 . . . . . . . . . . . . . . Cla10g00495 . . . . . . . . Cone14ag1151 Cone15ag1168 . Csa03g00501 . Cme06g02238 . . Bda05g00717 Bda12g00913 . . . . . . . Cma04g00963 . Car04g00904 . . . . . . . . . . . . . . . . . Lsi05g00583 . Chy06g01825 .
Vvi19g527 . . . . Bpe09g00169 . . . . . Cma01g01124 . Car01g00998 Car09g00874 Sed04g3216 Cpe06g00774 Cpe02g00777 Bhi09g01656 Tan01g4563 Cmetu01g2650 . Hepe01g1265 Mch11g1197 . . . . . . . . . . Cone14ag1152 Cone15ag1169 Lsi02g01898 Csa07g01101 . . Blo07g00901 . Bda05g00716 Bda12g00914 . Bpe03g00789 . . . Cmo01g01175 Cmo09g00956 . . . . . . . . . . . . . Cla09g01015 Cam09g1072 Cec09g1072 Cco09g1090 . . Cre09g1036 . . . Cme01g01024
Vvi19g528 . . . . . . Bma10g00553 Bma13g01065 . . . Cma09g00958 Car01g00997 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme01g01022
Vvi19g529 . . . . . Bpe08g01118 . . . . Cma01g01123 . Car01g00996 . Sed04g3221 . Cpe02g00778 Bhi09g01657 Tan01g4565 Cmetu01g0146 . Hepe01g1264 Mch11g1198 . . . . . . . . . Cone9ag0064 . . Lsi02g01897 Csa07g01102 . . . . . . . . Bma07g01289 . . Cmo01g01174 . . . . . . . . . . . . . . Cla09g01016 Cam09g1073 Cec09g1073 Cco09g1092 . . Cre09g1038 . . . Cme01g01020
Vvi19g530 . . . . . . . . . . . . . . . . . . . . . . . . Cla10g00494 Cam10g0486 Cec10g0504 Cco10g0489 Clacu10g0505 Cmu10g1332 Cre10g0735 . . . . . Csa03g00500 . Cme06g02233 . . . . . . . . Sed04g0721 . . . Cma16g00898 . Car16g00874 . . Bhi11g00600 Tan01g1721 Cmetu06g0380 . Hepe07g1266 . . . . . . . . . . . Chy06g01826 .
Vvi19g531 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g532 . . . . Bpe09g00168 . Bma10g00554 Bma13g01066 Cmo16g00933 . . . . . . . . . . . . . . . Cla10g00493 Cam10g0485 Cec10g0503 . Clacu10g0504 Cmu10g1331 Cre10g0734 . . . Cone15ag1171 . Csa03g00499 . Cme06g02863 Blo07g00900 Blo10g00840 Bda05g00715 Bda12g00919 . Bpe03g00788 . . . . . . Cma16g00899 . Car16g00875 . . Bhi11g00599 . . . . Mch10g1293 . . . . . . . . Lsi05g00582 . Chy06g01827 .
Vvi19g533 . . . . . . Bma10g00555 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1154 . . . . . Blo07g00899 . Bda05g00714 . . Bpe03g00787 . . . . . . . . . Cpe14g00746 . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 55539164 55548825 + Bda021856.1 Bda05g00714 714
5 55549808 55552822 - Bda021857.1 Bda05g00715 715
5 55556696 55561417 + Bda021858.1 Bda05g00716 716
5 55574676 55576373 + Bda021859.1 Bda05g00717 717
5 55584316 55585503 - Bda021860.1 Bda05g00718 718
7 4677337 4678079 + Bda025454.1 Bda07g00368 368
12 39837480 39838651 + Bda009449.1 Bda12g00912 912
12 39840717 39842256 - Bda009450.1 Bda12g00913 913
12 39847068 39851656 - Bda009451.1 Bda12g00914 914
12 40216284 40218595 + Bda009463.1 Bda12g00919 919
9 44571579 44577551 - XM_039041405.1 Bhi09g01656 1656
9 44666973 44670649 + XM_039040417.1 Bhi09g01657 1657
11 13799800 13826970 + XM_039047838.1 Bhi11g00599 599
11 13833771 13840010 + XM_039047371.1 Bhi11g00600 600
11 13927769 13929901 - XM_039047803.1 Bhi11g00603 603
3 41166973 41176660 + BLOR12636 Blo03g01455 1455
7 27868387 27879999 + BLOR18831 Blo07g00899 899
7 27881029 27883934 - BLOR18832 Blo07g00900 900
7 27906524 27911276 + BLOR18833 Blo07g00901 901
7 27953782 27958306 - BLOR18834 Blo07g00902 902
10 26745384 26747819 + BLOR02630 Blo10g00840 840
7 48519709 48522598 - Bma026561.1 Bma07g01289 1289
10 6668874 6669510 + Bma004251.1 Bma10g00551 551
10 6671703 6673383 - Bma004252.2 Bma10g00552 552
10 6691174 6695477 - Bma004254.1 Bma10g00553 553
10 6700803 6703557 + Bma004255.1 Bma10g00554 554
10 6704544 6714241 - Bma030359 Bma10g00555 555
13 43360999 43364193 - Bma010185.1 Bma13g01065 1065
13 43387452 43389081 + Bma010186.1 Bma13g01066 1066
3 27842371 27851944 + Bpe012699.1 Bpe03g00787 787
3 27852924 27855752 - Bpe012700.1 Bpe03g00788 788
3 27858339 27863105 + Bpe012701.1 Bpe03g00789 789
3 27875410 27876607 - Bpe012702.1 Bpe03g00790 790
8 13165953 13168963 - Bpe023244.1 Bpe08g01118 1118
9 1155497 1157842 - Bpe023840.1 Bpe09g00168 168
9 1164103 1168735 + Bpe023841.1 Bpe09g00169 169
9 1183041 1183690 - Bpe026208 Bpe09g00171 171
11 4242700 4243443 + Bpe003920.1 Bpe11g00553 553
9 11075783 11081015 - CaPI482276_09g010720.1 Cam09g1072 1072
9 11090468 11105735 + CaPI482276_09g010730.1 Cam09g1073 1073
10 7275996 7286358 + CaPI482276_10g004850.1 Cam10g0485 485
10 7287970 7296872 + CaPI482276_10g004860.1 Cam10g0486 486
10 7333735 7335050 - CaPI482276_10g004880.1 Cam10g0488 488
1 9438321 9442217 - Carg22366-RA Car01g00996 996
1 9445024 9446456 + Carg22365-RA Car01g00997 997
1 9447600 9450200 + Carg22364-RA Car01g00998 998
4 5162611 5163309 + Carg00078-RA Car04g00903 903
4 5164563 5166522 - Carg00079-RA Car04g00904 904
9 5335676 5340689 - Carg12828-RA Car09g00874 874
16 6589090 6591966 + Carg27295-RA Car16g00874 874
16 6628287 6632030 + Carg27294-RA Car16g00875 875
9 10406076 10411292 - CcPI632755_09g010900.1 Cco09g1090 1090
9 10421931 10436930 + CcPI632755_09g010920.1 Cco09g1092 1092
10 5833622 5854477 + CcPI632755_10g004890.1 Cco10g0489 489
10 5891351 5892730 - CcPI632755_10g004910.1 Cco10g0491 491
9 10440990 10446232 - CePI673135_09g010720.1 Cec09g1072 1072
9 10456074 10471086 + CePI673135_09g010730.1 Cec09g1073 1073
10 6045803 6056680 + CePI673135_10g005030.1 Cec10g0503 503
10 6058328 6070146 + CePI673135_10g005040.1 Cec10g0504 504
10 6098503 6099877 - CePI673135_10g005060.1 Cec10g0506 506
6 21988999 21990220 + Chy6G123520.1 Chy06g01824 1824
6 22002857 22005140 - Chy6G123530.1 Chy06g01825 1825
6 22020352 22024051 - Chy6G123540.1 Chy06g01826 1826
6 22031340 22038367 - Chy6G123550.1 Chy06g01827 1827
10 6107743 6117998 + ClG42_10g0050400.10 Clacu10g0504 504
10 6119574 6128789 + ClG42_10g0050500.10 Clacu10g0505 505
10 6167207 6168510 - ClG42_10g0050800.10 Clacu10g0508 508
9 10672357 10678699 - ClCG09G010860.2 Cla09g01015 1015
9 10689960 10705170 + ClCG09G010880.2 Cla09g01016 1016
10 6496208 6506652 + ClCG10G005280.2 Cla10g00493 493
10 6508037 6517296 + ClCG10G005290.1 Cla10g00494 494
10 6551164 6553389 + ClCG10G005300.1 Cla10g00495 495
10 6561709 6563618 - ClCG10G005310.1 Cla10g00496 496
1 8241918 8245973 - CmaCh01G011230.1 Cma01g01123 1123
1 8248303 8253251 + CmaCh01G011240.1 Cma01g01124 1124
4 4937653 4938773 + CmaCh04G009620.1 Cma04g00962 962
4 4939503 4941490 - CmaCh04G009630.1 Cma04g00963 963
9 4822916 4828886 - CmaCh09G009580.1 Cma09g00958 958
16 6565342 6570064 + CmaCh16G008980.1 Cma16g00898 898
16 6589649 6593443 + CmaCh16G008990.1 Cma16g00899 899
1 12603616 12607469 - MELO3C013155.2.1 Cme01g01020 1020
1 12616065 12617795 + MELO3C027396.2.1 Cme01g01022 1022
1 12619135 12622090 + MELO3C013156.2.1 Cme01g01024 1024
6 29254878 29259065 + MELO3C025360.2.1 Cme06g02233 2233
6 29279709 29282158 + MELO3C025362.2.1 Cme06g02238 2238
6 29312179 29313468 - MELO3C025364.2.1 Cme06g02240 2240
6 36069186 36073582 - MELO3C014197.2.1 Cme06g02863 2863
1 10988554 10992301 + PI0013245.1 Cmetu01g0146 146
1 10965997 10972127 - PI0026895.1 Cmetu01g2650 2650
6 26372477 26378067 + PI0015471.1 Cmetu06g0380 380
6 26322253 26324133 + PI0028888.1 Cmetu06g2809 2809
1 9574336 9578266 - CmoCh01G011740.1 Cmo01g01174 1174
1 9581001 9585847 + CmoCh01G011750.1 Cmo01g01175 1175
4 5180353 5181519 + CmoCh04G010380.1 Cmo04g01038 1038
4 5182482 5184444 - CmoCh04G010390.1 Cmo04g01039 1039
9 5032917 5039142 - CmoCh09G009560.1 Cmo09g00956 956
16 5805041 5809046 - CmoCh16G009330.1 Cmo16g00933 933
10 6231547 6241802 + CmPI595203_10g013310.1 Cmu10g1331 1331
10 6243380 6252583 + CmPI595203_10g013320.1 Cmu10g1332 1332
10 6291053 6292360 - CmPI595203_10g013350.1 Cmu10g1335 1335
9 304990 307891 - Conep09aG0006400.1 Cone9ag0064 64
14 9512920 9514203 + Conep14aG0117400.1 Cone14ag1150 1150
14 9514375 9517382 - Conep14aG0117500.1 Cone14ag1151 1151
14 9522833 9528035 - Conep14aG0117600.1 Cone14ag1152 1152
14 9541856 9550143 - Conep14aG0117800.1 Cone14ag1154 1154
15 9435155 9436688 + Conep15aG0119500.1 Cone15ag1166 1166
15 9437400 9438872 + Conep15aG0119600.1 Cone15ag1167 1167
15 9439397 9442463 - Conep15aG0119700.1 Cone15ag1168 1168
15 9444959 9450065 - Conep15aG0119800.1 Cone15ag1169 1169
15 9455970 9458550 + Conep15aG0120000.1 Cone15ag1171 1171
1 5147747 5148797 + Cp4.1LG01g07980.1 Cpe01g00875 875
2 4946316 4952116 - Cp4.1LG02g00890.1 Cpe02g00777 777
2 4956964 4961052 + Cp4.1LG02g00940.1 Cpe02g00778 778
6 4882970 4889140 - Cp4.1LG06g08850.1 Cpe06g00774 774
14 5682170 5693344 + Cp4.1LG14g07480.1 Cpe14g00746 746
9 10615844 10621080 - CrPI670011_09g010360.1 Cre09g1036 1036
9 10638140 10645572 + CrPI670011_09g010380.1 Cre09g1038 1038
10 7119662 7129954 + CrPI670011_10g007340.1 Cre10g0734 734
10 7131665 7140971 + CrPI670011_10g007350.1 Cre10g0735 735
10 7183949 7185326 - CrPI670011_10g007400.1 Cre10g0740 740
3 4156891 4161534 + CsaV3_3G004990.1 Csa03g00499 499
3 4161990 4165350 + CsaV3_3G005000.1 Csa03g00500 500
3 4175719 4178012 + CsaV3_3G005010.1 Csa03g00501 501
3 4185706 4187480 - CsaV3_3G005020.1 Csa03g00502 502
7 10640198 10647677 - CsaV3_7G021900.1 Csa07g01101 1101
7 10655751 10661834 + CsaV3_7G021910.1 Csa07g01102 1102
1 77927396 77936884 - Hsped.01g12640.1 Hepe01g1264 1264
1 77936887 77943029 + Hsped.01g12650.1 Hepe01g1265 1265
7 37034421 37037810 + Hsped.07g12660.1 Hepe07g1266 1266
2 24898320 24902164 - Lsi02G018970.1 Lsi02g01897 1897
2 24909436 24915497 + Lsi02G018980.1 Lsi02g01898 1898
5 7233178 7244925 + Lsi05G005820.1 Lsi05g00582 582
5 7261881 7264409 + Lsi05G005830.1 Lsi05g00583 583
5 7273115 7275568 - Lsi05G005840.1 Lsi05g00584 584
10 10799134 10803501 - MC10g1059 Mch10g1293 1293
11 8411999 8418721 - MC11g0988 Mch11g1197 1197
11 8427710 8431893 + MC11g0989 Mch11g1198 1198
4 5839792 5840985 + Sed0013637.1 Sed04g0718 718
4 5859826 5864797 - Sed0023010.2 Sed04g0721 721
4 42761102 42766810 - Sed0021197.1 Sed04g3216 3216
4 42773234 42777414 + Sed0023076.3 Sed04g3221 3221
1 18317919 18319015 - Tan0003989.2 Tan01g1718 1718
1 18395731 18398635 - Tan0020566.1 Tan01g1721 1721
1 111503038 111506925 - Tan0022695.2 Tan01g4563 4563
1 111518089 111521928 + Tan0001024.1 Tan01g4565 4565
19 6678932 6680585 + Vvi19g524 Vvi19g524 524
19 6681566 6685068 + Vvi19g525 Vvi19g525 525
19 6691783 6695136 - Vvi19g526 Vvi19g526 526
19 6697727 6702141 - Vvi19g527 Vvi19g527 527
19 6702166 6706645 - Vvi19g528 Vvi19g528 528
19 6715871 6719385 + Vvi19g529 Vvi19g529 529
19 6719842 6720919 - Vvi19g530 Vvi19g530 530
19 6722281 6722658 - Vvi19g531 Vvi19g531 531
19 6729220 6732091 + Vvi19g532 Vvi19g532 532
19 6732345 6747822 - Vvi19g533 Vvi19g533 533
       

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