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
Vvi18g20 . Blo12g00837 . Bda03g00338 . Bpe04g00298 Bma04g00307 Bma01g02430 . . Cma01g02054 . Car01g01618 . . . . . . . . . . . . . . . . . . . . . . Lsi04g02439 Csa04g02753 . . . . . . . . . . . Cmo01g02110 . . . . . . Cpe02g00004 . . . . . . . Cla11g01865 Cam11g1935 Cec11g1960 Cco11g1974 Clacu11g2100 Cmu11g1902 Cre11g2310 . . Chy07g00441 Cme07g00009
Vvi18g21 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g22 Blo01g01661 . . . Bpe02g00283 . . Bma01g02429 . . . . Car01g01617 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo01g02109 . . . . . . Cpe02g00005 . . . . . . . . . . . . . . . . . .
Vvi18g23 Blo01g01659 . . . Bpe02g00284 . . . . . . Cma09g00008 . . . . . . . . . . . . . . . . . . . . . . . Lsi04g02438 Csa04g02751 . . . . . . . . . . . . Cmo09g00009 . . . Car09g00008 . . . . . . . . . Cla11g01864 Cam11g1933 Cec11g1958 Cco11g1972 Clacu11g2098 Cmu11g1900 Cre11g2309 . . Chy07g00440 Cme07g00010
Vvi18g24 . . . . . . . . . . Cma01g02053 Cma09g00010 . . . . . . . . . . . . . . . . . . . . . . . Lsi04g02436 Csa04g02750 . . Blo17g00912 . . . . . . . . Cmo01g02108 Cmo09g00010 . . . Car09g00010 . Cpe02g00006 . . . . . . . Cla11g01862 Cam11g1930 Cec11g1956 Cco11g1969 Clacu11g2095 Cmu11g1897 Cre11g2307 . . Chy07g00438 Cme07g00013
Vvi18g25 Blo01g01657 . . . Bpe02g00286 . . . . . Cma01g02052 Cma09g00011 Car01g01616 . . . . . . . . . . . . . . . . . . . . . . Lsi04g02435 Csa04g02749 . . . . . . . . . . . Cmo01g02107 Cmo09g00011 . . . . . Cpe02g00007 . . . . . . . . . . . . . . . . Chy07g00437 Cme07g00014
Vvi18g26 . . . . . . . . . . . Cma09g00012 . . . . . . . . . . . . . . . . . . . . . . . Lsi04g02433 Csa04g02748 . . . . . . . . . . . . Cmo09g00013 . . . Car09g00012 . . . . . . . . . Cla11g01861 Cam11g1928 Cec11g1955 Cco11g1967 Clacu11g2093 Cmu11g1896 Cre11g2304 . . Chy07g00436 Cme07g00015
Vvi18g27 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g28 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g29 Blo01g01656 . . . Bpe02g00287 . . Bma01g02426 . . . . Car01g01614 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe02g00009 . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 2867681 2868274 + Bda016299.1 Bda03g00338 338
1 56330111 56330509 + BLOR01656 Blo01g01656 1656
1 56335294 56340633 + BLOR01657 Blo01g01657 1657
1 56346984 56348386 - BLOR01659 Blo01g01659 1659
1 56358241 56359831 + BLOR01661 Blo01g01661 1661
12 26668131 26672910 - BLOR04856 Blo12g00837 837
17 29965441 29970110 + BLOR08458 Blo17g00912 912
1 81889037 81889294 + Bma003297.1 Bma01g02426 2426
1 81957026 81958570 + Bma003300.1 Bma01g02429 2429
1 81959335 81959946 + Bma003301.1 Bma01g02430 2430
4 2437814 2438395 + Bma018761.1 Bma04g00307 307
2 1889149 1890719 - Bpe008127.1 Bpe02g00283 283
2 1893031 1894280 + Bpe008128.1 Bpe02g00284 284
2 1898531 1902790 - Bpe008130.1 Bpe02g00286 286
2 1906609 1906866 - Bpe008131.1 Bpe02g00287 287
4 1909201 1909809 + Bpe015000.1 Bpe04g00298 298
11 31668378 31688542 + CaPI482276_11g019280.1 Cam11g1928 1928
11 31693150 31697802 + CaPI482276_11g019300.1 Cam11g1930 1930
11 31707283 31708264 - CaPI482276_11g019330.1 Cam11g1933 1933
11 31718038 31735392 + CaPI482276_11g019350.1 Cam11g1935 1935
1 13238522 13238947 + Carg21341-RA Car01g01614 1614
1 13252764 13265095 + Carg21339-RA Car01g01616 1616
1 13267083 13269255 + Carg21338-RA Car01g01617 1617
1 13269989 13270567 + Carg21337-RA Car01g01618 1618
9 58477 59544 + Carg08591-RA Car09g00008 8
9 62352 67358 - Carg08593-RA Car09g00010 10
9 69627 82837 - Carg08595-RA Car09g00012 12
11 32142907 32164348 + CcPI632755_11g019670.1 Cco11g1967 1967
11 32168942 32173528 + CcPI632755_11g019690.1 Cco11g1969 1969
11 32183121 32184218 - CcPI632755_11g019720.1 Cco11g1972 1972
11 32190486 32190788 + CcPI632755_11g019740.1 Cco11g1974 1974
11 33598804 33619084 + CePI673135_11g019550.1 Cec11g1955 1955
11 33619435 33628071 + CePI673135_11g019560.1 Cec11g1956 1956
11 33637050 33638032 - CePI673135_11g019580.1 Cec11g1958 1958
11 33647732 33657264 + CePI673135_11g019600.1 Cec11g1960 1960
7 3342271 3342974 + Chy7G132660.1 Chy07g00436 436
7 3346960 3352668 + Chy7G132670.1 Chy07g00437 437
7 3355994 3360743 + Chy7G132680.1 Chy07g00438 438
7 3364654 3366669 - Chy7G132700.1 Chy07g00440 440
7 3372965 3385806 + Chy7G132710.1 Chy07g00441 441
11 31705853 31726004 + ClG42_11g0209300.10 Clacu11g2093 2093
11 31730563 31735187 + ClG42_11g0209500.10 Clacu11g2095 2095
11 31746225 31747206 - ClG42_11g0209800.10 Clacu11g2098 2098
11 31756839 31774170 + ClG42_11g0210000.10 Clacu11g2100 2100
11 32115231 32125998 + ClCG11G019140.1 Cla11g01861 1861
11 32143312 32148593 + ClCG11G019160.1 Cla11g01862 1862
11 32159136 32160513 - ClCG11G019180.1 Cla11g01864 1864
11 32166491 32188464 + ClCG11G019190.2 Cla11g01865 1865
1 13030257 13036061 + CmaCh01G020520.1 Cma01g02052 2052
1 13036777 13043554 + CmaCh01G020530.1 Cma01g02053 2053
1 13045384 13049037 + CmaCh01G020540.1 Cma01g02054 2054
9 62206 63606 + CmaCh09G000080.1 Cma09g00008 8
9 66151 71352 - CmaCh09G000100.1 Cma09g00010 10
9 73155 80646 - CmaCh09G000110.1 Cma09g00011 11
9 81081 86559 - CmaCh09G000120.1 Cma09g00012 12
7 116503 117840 - MELO3C017072.2.1 Cme07g00009 9
7 123638 125187 + MELO3C017071.2.1 Cme07g00010 10
7 129531 135641 - MELO3C017069.2.1 Cme07g00013 13
7 137989 144537 - MELO3C017068.2.1 Cme07g00014 14
7 145825 158101 - MELO3C017067.2.1 Cme07g00015 15
1 14578096 14584353 + CmoCh01G021070.1 Cmo01g02107 2107
1 14584798 14590701 + CmoCh01G021080.1 Cmo01g02108 2108
1 14593232 14595615 + CmoCh01G021090.1 Cmo01g02109 2109
1 14596135 14596713 + CmoCh01G021100.1 Cmo01g02110 2110
9 61426 63098 + CmoCh09G000090.1 Cmo09g00009 9
9 64679 70512 - CmoCh09G000100.1 Cmo09g00010 10
9 72544 78415 - CmoCh09G000110.1 Cmo09g00011 11
9 80869 86905 - CmoCh09G000130.1 Cmo09g00013 13
11 30955298 30969629 + CmPI595203_11g018960.1 Cmu11g1896 1896
11 30975879 30984642 + CmPI595203_11g018970.1 Cmu11g1897 1897
11 30995666 30996647 - CmPI595203_11g019000.1 Cmu11g1900 1900
11 31006288 31023624 + CmPI595203_11g019020.1 Cmu11g1902 1902
2 35980 36558 - Cp4.1LG02g08650.1 Cpe02g00004 4
2 37010 39589 - Cp4.1LG02g08580.1 Cpe02g00005 5
2 41059 46659 - Cp4.1LG02g08560.1 Cpe02g00006 6
2 47394 54188 - Cp4.1LG02g08540.1 Cpe02g00007 7
2 71688 72113 - Cp4.1LG02g08630.1 Cpe02g00009 9
11 34640981 34650975 + CrPI670011_11g023040.1 Cre11g2304 2304
11 34665818 34670402 + CrPI670011_11g023070.1 Cre11g2307 2307
11 34679935 34681030 - CrPI670011_11g023090.1 Cre11g2309 2309
11 34687897 34707847 + CrPI670011_11g023100.1 Cre11g2310 2310
4 26342869 26346713 + CsaV3_4G037740.1 Csa04g02748 2748
4 26350177 26358269 + CsaV3_4G037750.1 Csa04g02749 2749
4 26359110 26365159 + CsaV3_4G037760.1 Csa04g02750 2750
4 26364874 26370906 - CsaV3_4G037770.1 Csa04g02751 2751
4 26375809 26377780 + CsaV3_4G037790.1 Csa04g02753 2753
4 31387743 31397272 + Lsi04G024330.1 Lsi04g02433 2433
4 31404230 31411495 + Lsi04G024350.1 Lsi04g02435 2435
4 31413790 31419326 + Lsi04G024360.1 Lsi04g02436 2436
4 31425665 31427387 - Lsi04G024380.1 Lsi04g02438 2438
4 31446365 31472402 + Lsi04G024390.1 Lsi04g02439 2439
18 314470 315046 - Vvi18g20 Vvi18g20 20
18 320108 322487 - Vvi18g21 Vvi18g21 21
18 325070 327505 - Vvi18g22 Vvi18g22 22
18 331413 338450 + Vvi18g23 Vvi18g23 23
18 347644 353985 - Vvi18g24 Vvi18g24 24
18 368568 375676 - Vvi18g25 Vvi18g25 25
18 381744 387296 - Vvi18g26 Vvi18g26 26
18 389001 390745 - Vvi18g27 Vvi18g27 27
18 393143 395658 + Vvi18g28 Vvi18g28 28
18 397215 398057 - Vvi18g29 Vvi18g29 29
       

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