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
Vvi18g1120 Blo01g01600 . Bda01g00481 . Bpe02g00345 . . Bma01g02370 . . Cma01g01976 . Car01g01547 . . Cpe06g00065 . . . . . . . . . . . . . . . Cone4ag1973 Cone7ag1890 . . Lsi04g01750 Csa03g04285 Chy04g00412 . . . . . . . . . Sed13g1566 Cmo01g02034 . . . . Car09g00091 . Cpe02g00067 Bhi09g02082 Tan01g5023 Cmetu04g1950 . Hepe01g1610 Mch11g0111 . Cla05g01865 Cam05g1994 Cec05g2006 Cco05g2064 Clacu05g1986 Cmu05g1867 Cre05g1991 . . . Cme04g00463
Vvi18g1121 Blo01g01601 . Bda01g00480 . Bpe02g00344 . . Bma01g02371 . . . Cma09g00101 . . . Cpe06g00063 . . . . . . . . . . . . . . . Cone4ag1974 Cone7ag1892 . . . Csa03g04286 Chy04g00411 . . . . . . . . . Sed08g0779 . Cmo09g00097 . . . Car09g00089 . . Bhi09g02080 Tan01g5029 Cmetu02g0590 . Hepe01g1609 Mch11g0110 . . . . . . . . . . . Cme04g00462
Vvi18g1122 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1123 Blo01g01602 . Bda01g00479 Bda03g00293 Bpe02g00621 Bpe04g00249 . Bma01g02372 Cmo05g00313 Cmo12g00356 . . . Car12g00382 Sed11g1091 . Cpe07g00361 Bhi04g00143 Tan02g2080 Cmetu03g0952 . Hepe10g0159 . Lcy13g1908 Cla08g01418 Cam08g1897 Cec08g1474 Cco08g1607 Clacu08g1589 . Cre08g1373 Cone4ag1976 Cone7ag1894 Cone17ag1409 Cone20ag0074 . . . Cme03g01874 . Blo18g00778 . . Bpe02g01728 Bpe05g00141 Bma01g00884 Bma05g00166 . . . Cma12g00405 Cma05g00311 Car05g00258 . Cpe11g00259 . . . . . . . . . . . . . . . Lsi08g01313 Csa02g02139 Chy03g01380 .
Vvi18g1124 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1125 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1126 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone20ag0073 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1127 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1128 . . . . . . . Bma01g02373 . . . Cma09g00099 . . . Cpe06g00062 . . . . . . . . . . . . . . . Cone4ag1977 Cone7ag1895 . . Lsi04g01753 Csa03g04287 Chy04g00410 . . . . . . . . . Sed01g2480 . Cmo09g00096 . . . Car09g00087 . . Bhi09g02078 Tan01g5032 Cmetu04g0766 . . . . Cla05g01864 Cam05g1993 Cec05g2005 Cco05g2063 Clacu05g1985 Cmu05g1866 Cre05g1990 . . . Cme04g00461
Vvi18g1129 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 31867966 31869992 - Bda002482.3 Bda01g00479 479
1 31873021 31878915 + Bda002483.1 Bda01g00480 480
1 31883003 31886077 + Bda002484.2 Bda01g00481 481
3 2581692 2588729 + Bda033480 Bda03g00293 293
4 3473228 3477932 - XM_039030232.1 Bhi04g00143 143
9 59364645 59368998 - XM_039041086.1 Bhi09g02078 2078
9 59435059 59442626 + XM_039041062.1 Bhi09g02080 2080
9 59444876 59449072 + XM_039041064.1 Bhi09g02082 2082
1 55853460 55856231 - BLOR01600 Blo01g01600 1600
1 55876436 55882485 - BLOR01601 Blo01g01601 1601
1 55882562 55890185 + BLOR01602 Blo01g01602 1602
18 22223253 22225726 - BLOR09266 Blo18g00778 778
1 8311886 8314864 + Bma001108.1 Bma01g00884 884
1 81356555 81360036 - Bma003241.1 Bma01g02370 2370
1 81364659 81370559 - Bma003242.2 Bma01g02371 2371
1 81374562 81377363 + Bma003243.1 Bma01g02372 2372
1 81380123 81382226 + Bma003244.1 Bma01g02373 2373
5 4755146 4757583 + Bma020882.1 Bma05g00166 166
2 2266431 2272302 + Bpe008186.1 Bpe02g00344 344
2 2277671 2280833 + Bpe008187.1 Bpe02g00345 345
2 4043353 4052428 + Bpe008462.1 Bpe02g00621 621
2 19732269 19737713 + Bpe009559.2 Bpe02g01728 1728
4 1669228 1671469 + Bpe014962.1 Bpe04g00249 249
5 3607634 3610122 + Bpe017526.1 Bpe05g00141 141
5 28737478 28740254 - CaPI482276_05g019930.1 Cam05g1993 1993
5 28744062 28753099 + CaPI482276_05g019940.1 Cam05g1994 1994
8 24953660 24957528 - CaPI482276_08g018970.1 Cam08g1897 1897
1 12949296 12952735 - Carg17202-RA Car01g01547 1547
5 1434807 1438871 + Carg09401-RA Car05g00258 258
9 440062 443506 - Carg08671-RA Car09g00087 87
9 444952 451561 + Carg08673-RA Car09g00089 89
9 456813 458816 + Carg08675-RA Car09g00091 91
12 2443121 2447979 - Carg03989-RA Car12g00382 382
5 29673659 29676438 - CcPI632755_05g020630.1 Cco05g2063 2063
5 29682104 29686813 + CcPI632755_05g020640.1 Cco05g2064 2064
8 27618829 27623197 - CcPI632755_08g016070.1 Cco08g1607 1607
5 32036693 32039458 - CePI673135_05g020050.1 Cec05g2005 2005
5 32045939 32052169 + CePI673135_05g020060.1 Cec05g2006 2006
8 26482237 26486577 - CePI673135_08g014740.1 Cec08g1474 1474
3 16615658 16619077 - Chy3G063600.1 Chy03g01380 1380
4 3663288 3665509 - Chy4G071280.1 Chy04g00410 410
4 3669453 3676388 + Chy4G071290.1 Chy04g00411 411
4 3678132 3682515 + Chy4G071300.1 Chy04g00412 412
5 28939610 28942388 - ClG42_05g0198500.10 Clacu05g1985 1985
5 28946153 28954326 + ClG42_05g0198600.10 Clacu05g1986 1986
8 25699258 25703623 - ClG42_08g0158900.10 Clacu08g1589 1589
5 30519628 30522998 - ClCG05G018220.2 Cla05g01864 1864
5 30528552 30533636 + ClCG05G018230.2 Cla05g01865 1865
8 27055310 27060695 - ClCG08G014250.2 Cla08g01418 1418
1 12723897 12728947 - CmaCh01G019760.1 Cma01g01976 1976
5 1344169 1350371 + CmaCh05G003110.1 Cma05g00311 311
9 440576 443672 - CmaCh09G000990.1 Cma09g00099 99
9 445158 451921 + CmaCh09G001010.1 Cma09g00101 101
12 2098984 2103912 - CmaCh12G004050.1 Cma12g00405 405
3 26964459 26967975 - MELO3C011017.2.1 Cme03g01874 1874
4 3678999 3682995 - MELO3C003746.2.1 Cme04g00461 461
4 3688393 3696094 + MELO3C003747.2.1 Cme04g00462 462
4 3697290 3701786 + MELO3C030484.2.1 Cme04g00463 463
2 14916948 14922457 - PI0026852.2 Cmetu02g0590 590
3 2408490 2412027 + PI0026179.1 Cmetu03g0952 952
4 29686133 29690007 + PI0021492.2 Cmetu04g0766 766
4 29667693 29672785 - PI0015243.1 Cmetu04g1950 1950
1 14263120 14267809 - CmoCh01G020340.1 Cmo01g02034 2034
5 1386253 1389695 + CmoCh05G003130.1 Cmo05g00313 313
9 459987 463372 - CmoCh09G000960.1 Cmo09g00096 96
9 464854 471559 + CmoCh09G000970.1 Cmo09g00097 97
12 2209108 2215620 - CmoCh12G003560.1 Cmo12g00356 356
5 28665165 28667943 - CmPI595203_05g018660.1 Cmu05g1866 1866
5 28671925 28680097 + CmPI595203_05g018670.1 Cmu05g1867 1867
4 13856873 13861098 - Conep04aG0203500.1 Cone4ag1973 1973
4 13862254 13868452 - Conep04aG0203800.1 Cone4ag1974 1974
4 13872273 13875036 + Conep04aG0204000.1 Cone4ag1976 1976
4 13875861 13877610 + Conep04aG0204100.1 Cone4ag1977 1977
7 12149614 12150398 - Conep07aG0194500.1 Cone7ag1890 1890
7 12152344 12158563 - Conep07aG0194900.1 Cone7ag1892 1892
7 12160606 12162624 + Conep07aG0195100.1 Cone7ag1894 1894
7 12163079 12165136 + Conep07aG0195200.1 Cone7ag1895 1895
17 9682270 9685052 + Conep17aG0144500.1 Cone17ag1409 1409
20 351980 352621 - Conep20aG0007500.1 Cone20ag0073 73
20 354864 358346 - Conep20aG0007700.1 Cone20ag0074 74
2 353458 358576 + Cp4.1LG02g08070.1 Cpe02g00067 67
6 317071 320446 - Cp4.1LG06g00680.1 Cpe06g00062 62
6 321822 328301 + Cp4.1LG06g00600.1 Cpe06g00063 63
6 330594 333193 + Cp4.1LG06g00640.1 Cpe06g00065 65
7 2334513 2340336 - Cp4.1LG07g03730.1 Cpe07g00361 361
11 1400064 1405755 + Cp4.1LG11g02610.1 Cpe11g00259 259
5 31979464 31982837 - CrPI670011_05g019900.1 Cre05g1990 1990
5 31989586 31995797 + CrPI670011_05g019910.1 Cre05g1991 1991
8 26758689 26763059 - CrPI670011_08g013730.1 Cre08g1373 1373
2 19366107 19370963 + CsaV3_2G029580.1 Csa02g02139 2139
3 37515538 37519888 - CsaV3_3G045910.1 Csa03g04285 4285
3 37521661 37528639 - CsaV3_3G045920.1 Csa03g04286 4286
3 37532685 37536959 + CsaV3_3G045930.1 Csa03g04287 4287
1 81363005 81369425 + Hsped.01g16090.1 Hepe01g1609 1609
1 81372124 81377347 + Hsped.01g16100.1 Hepe01g1610 1610
10 1624043 1628368 + Hsped.10g01590.1 Hepe10g0159 159
13 38032780 38037743 - Maker00033617 Lcy13g1908 1908
4 24768232 24781888 - Lsi04G017500.1 Lsi04g01750 1750
4 24785649 24789548 + Lsi04G017530.1 Lsi04g01753 1753
8 21494700 21499419 - Lsi08G013130.1 Lsi08g01313 1313
11 729513 737438 + MC11g0098 Mch11g0110 110
11 738176 744494 + MC11g0099 Mch11g0111 111
1 18552440 18556241 + Sed0023128.1 Sed01g2480 2480
8 6004469 6014483 + Sed0019774.1 Sed08g0779 779
11 26574465 26578285 + Sed0028113.2 Sed11g1091 1091
13 20838547 20845572 + Sed0018359.1 Sed13g1566 1566
1 115887773 115892091 - Tan0017098.1 Tan01g5023 5023
1 115895073 115901053 - Tan0011794.6 Tan01g5029 5029
1 115904055 115907791 + Tan0010727.3 Tan01g5032 5032
2 90304572 90310160 + Tan0010498.1 Tan02g2080 2080
18 12343091 12350591 - Vvi18g1120 Vvi18g1120 1120
18 12363303 12376914 - Vvi18g1121 Vvi18g1121 1121
18 12377349 12378164 + Vvi18g1122 Vvi18g1122 1122
18 12383517 12402372 + Vvi18g1123 Vvi18g1123 1123
18 12403267 12404134 + Vvi18g1124 Vvi18g1124 1124
18 12431385 12431715 + Vvi18g1125 Vvi18g1125 1125
18 12432434 12439491 + Vvi18g1126 Vvi18g1126 1126
18 12453623 12456717 + Vvi18g1127 Vvi18g1127 1127
18 12457244 12463240 + Vvi18g1128 Vvi18g1128 1128
18 12465256 12466480 + Vvi18g1129 Vvi18g1129 1129
       

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