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
Vvi18g30 Blo01g01655 . . . Bpe02g00288 . . . . . Cma01g02048 . Car01g01613 . . . . . . . . . . . . . . . . . . . . . . Lsi04g02432 Csa04g02746 . . . . . . . . . . . Cmo01g02104 . . . . . . . . . . . . . . Cla11g01860 Cam11g1927 Cec11g1954 Cco11g1966 Clacu11g2092 Cmu11g1895 Cre11g2303 . . Chy07g00434 Cme07g00016
Vvi18g31 . . . Bda03g00337 . Bpe04g00296 Bma04g00306 . . . Cma01g02046 Cma09g00013 Car01g01612 . . . . . . . . . . . . . . . . . . . . . . Lsi04g02431 Csa04g02745 . . Blo17g00911 . . . . . . . . Cmo01g02103 . . . . Car09g00013 . Cpe02g00010 . . . . . . . Cla11g01859 Cam11g1926 Cec11g1953 Cco11g1965 Clacu11g2091 Cmu11g1894 Cre11g2302 . . Chy07g00433 Cme07g00017
Vvi18g32 Blo01g01654 Blo12g00839 . . Bpe02g00289 . Bma04g00305 Bma01g02425 . . . Cma09g00015 . . . . . . . . . . . . . . . . . . . . . . . Lsi04g02428 Csa04g02744 . . . . . . . . . . . . Cmo09g00014 . . . Car09g00014 . . . . . . . . . Cla11g01858 Cam11g1925 Cec11g1952 Cco11g1964 Clacu11g2090 Cmu11g1893 Cre11g2301 . . Chy07g00432 Cme07g00018
Vvi18g33 . Blo12g00840 . Bda03g00336 Bpe02g00290 Bpe04g00295 Bma04g00304 Bma01g02424 . . Cma01g02045 Cma09g00016 Car01g01611 . . . . . . . . . . . . . . . . . . . . Cone17ag1482 Cone20ag0004 Lsi04g02427 Csa04g02743 . . . . . . . . . . . Cmo01g02102 Cmo09g00015 . . . Car09g00015 . Cpe02g00011 . . . . . . . Cla11g01857 . Cec11g1951 . . Cmu11g1892 . . . Chy07g00431 Cme07g00019
Vvi18g34 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g35 . . . . . . . Bma01g02422 . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag1950 . . . Csa04g02739 . . . . . . . . . . . . . . . . . . . Bhi09g02827 . . . . Mch11g0029 . . . . . . . . . . Chy07g00426 .
Vvi18g36 . . . . . . . . . . Cma01g02043 . Car01g01610 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda01g01577 . . Bma01g00689 . . Cmo01g02101 . . . . . . Cpe02g00012 . . . . . . . . . . . . . . . . . .
Vvi18g37 Blo01g01651 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g38 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda01g01576 . . Bma01g00690 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g39 . Blo12g00841 . Bda03g00335 . Bpe04g00294 Bma04g00303 . Cmo05g00977 . . . . . . . . . . . . . . . Cla08g00920 Cam08g1367 Cec08g0950 Cco08g1068 Clacu08g1072 . Cre08g0858 . . . . . . . Cme03g01323 . . . . . . . . . . . . Cma05g00957 Car05g00840 . Cpe11g00770 . . . . . . . . . . . . . . . Lsi08g00764 . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 51588792 51590781 + Bda032959 Bda01g01576 1576
1 51590827 51596177 - Bda003844.1 Bda01g01577 1577
3 2826619 2828491 - Bda016295.1 Bda03g00335 335
3 2829858 2837952 - Bda016296.1 Bda03g00336 336
3 2851334 2852140 - Bda016297.3 Bda03g00337 337
9 74990061 74992175 - XM_039043174.1 Bhi09g02827 2827
1 56304124 56304999 - BLOR01651 Blo01g01651 1651
1 56317151 56325849 - BLOR01654 Blo01g01654 1654
1 56327145 56329852 - BLOR01655 Blo01g01655 1655
12 26691395 26693602 + BLOR04858 Blo12g00839 839
12 26694118 26701029 + BLOR04859 Blo12g00840 840
12 26702534 26704930 + BLOR04860 Blo12g00841 841
17 29959235 29961663 + BLOR08457 Blo17g00911 911
1 6328607 6337953 + Bma000899.1 Bma01g00689 689
1 6338882 6339866 - Bma030199 Bma01g00690 690
1 81851899 81853864 + Bma030303 Bma01g02422 2422
1 81871449 81882757 - Bma003295.1 Bma01g02424 2424
1 81883097 81885340 - Bma003296.1 Bma01g02425 2425
4 2402567 2404234 - Bma018757.1 Bma04g00303 303
4 2405963 2413990 - Bma018758.1 Bma04g00304 304
4 2420406 2422806 - Bma018759.1 Bma04g00305 305
4 2425618 2426436 - Bma018760.1 Bma04g00306 306
2 1907246 1910248 + Bpe008132.1 Bpe02g00288 288
2 1911395 1913619 + Bpe008133.1 Bpe02g00289 289
2 1913946 1919932 + Bpe008134.1 Bpe02g00290 290
4 1879734 1882116 - Bpe025600 Bpe04g00294 294
4 1883206 1890259 - Bpe014997.1 Bpe04g00295 295
4 1896730 1897539 - Bpe014998.1 Bpe04g00296 296
8 19999804 20009711 + CaPI482276_08g013670.1 Cam08g1367 1367
11 31646008 31655743 - CaPI482276_11g019250.1 Cam11g1925 1925
11 31658541 31659365 - CaPI482276_11g019260.1 Cam11g1926 1926
11 31660832 31663934 - CaPI482276_11g019270.1 Cam11g1927 1927
1 13223074 13226503 + Carg21345-RA Car01g01610 1610
1 13227607 13230745 - Carg21344-RA Car01g01611 1611
1 13233008 13233838 - Carg21343-RA Car01g01612 1612
1 13235394 13238217 - Carg21342-RA Car01g01613 1613
5 8300694 8304612 + Carg21899-RA Car05g00840 840
9 84063 84890 + Carg08596-RA Car09g00013 13
9 86707 90072 + Carg08597-RA Car09g00014 14
9 91120 96210 + Carg08598-RA Car09g00015 15
8 22499590 22502684 + CcPI632755_08g010680.1 Cco08g1068 1068
11 32120320 32130074 - CcPI632755_11g019640.1 Cco11g1964 1964
11 32132933 32133757 - CcPI632755_11g019650.1 Cco11g1965 1965
11 32135143 32138286 - CcPI632755_11g019660.1 Cco11g1966 1966
8 21354878 21364726 + CePI673135_08g009500.1 Cec08g0950 950
11 33568718 33573596 - CePI673135_11g019510.1 Cec11g1951 1951
11 33575105 33578344 - CePI673135_11g019520.1 Cec11g1952 1952
11 33581248 33582072 - CePI673135_11g019530.1 Cec11g1953 1953
11 33583568 33586689 - CePI673135_11g019540.1 Cec11g1954 1954
7 3293583 3295352 + Chy7G132560.1 Chy07g00426 426
7 3315598 3320280 - Chy7G132610.1 Chy07g00431 431
7 3321628 3325132 - Chy7G132620.1 Chy07g00432 432
7 3327414 3328244 - Chy7G132630.1 Chy07g00433 433
7 3329233 3332053 - Chy7G132640.1 Chy07g00434 434
8 20769321 20772826 + ClG42_08g0107200.10 Clacu08g1072 1072
11 31683445 31693094 - ClG42_11g0209000.10 Clacu11g2090 2090
11 31695938 31696762 - ClG42_11g0209100.10 Clacu11g2091 2091
11 31698221 31701323 - ClG42_11g0209200.10 Clacu11g2092 2092
8 21763385 21767205 + ClCG08G009150.1 Cla08g00920 920
11 32092127 32102487 - ClCG11G019100.2 Cla11g01857 1857
11 32098545 32102375 - ClCG11G019110.1 Cla11g01858 1858
11 32105065 32105889 - ClCG11G019120.1 Cla11g01859 1859
11 32107042 32110998 - ClCG11G019130.2 Cla11g01860 1860
1 12993973 12997984 + CmaCh01G020430.1 Cma01g02043 2043
1 12998834 13004372 - CmaCh01G020450.1 Cma01g02045 2045
1 13006431 13007261 - CmaCh01G020460.1 Cma01g02046 2046
1 13007954 13011090 - CmaCh01G020480.1 Cma01g02048 2048
5 7741094 7744994 + CmaCh05G009570.1 Cma05g00957 957
9 87546 88304 + CmaCh09G000130.1 Cma09g00013 13
9 90333 93982 + CmaCh09G000150.1 Cma09g00015 15
9 94539 101005 + CmaCh09G000160.1 Cma09g00016 16
3 22778878 22782838 + MELO3C026512.2.1 Cme03g01323 1323
7 158722 161902 + MELO3C017066.2.1 Cme07g00016 16
7 163633 165344 + MELO3C017065.2.1 Cme07g00017 17
7 167310 171145 + MELO3C017064.2.1 Cme07g00018 18
7 171917 176877 + MELO3C017063.2.1 Cme07g00019 19
1 14542120 14547272 + CmoCh01G021010.1 Cmo01g02101 2101
1 14547451 14553007 - CmoCh01G021020.1 Cmo01g02102 2102
1 14553947 14556073 - CmoCh01G021030.1 Cmo01g02103 2103
1 14558352 14561302 - CmoCh01G021040.1 Cmo01g02104 2104
5 7874902 7878813 + CmoCh05G009770.1 Cmo05g00977 977
9 90019 94450 + CmoCh09G000140.1 Cmo09g00014 14
9 95007 101274 + CmoCh09G000150.1 Cmo09g00015 15
11 30932982 30937798 - CmPI595203_11g018920.1 Cmu11g1892 1892
11 30939024 30942639 - CmPI595203_11g018930.1 Cmu11g1893 1893
11 30945484 30946308 - CmPI595203_11g018940.1 Cmu11g1894 1894
11 30947767 30950864 - CmPI595203_11g018950.1 Cmu11g1895 1895
7 12440276 12442062 + Conep07aG0200800.1 Cone7ag1950 1950
17 9987181 9993801 - Conep17aG0152300.1 Cone17ag1482 1482
20 44293 50454 + Conep20aG0000400.1 Cone20ag0004 4
2 76608 78361 + Cp4.1LG02g08720.1 Cpe02g00010 10
2 79743 85342 + Cp4.1LG02g08700.1 Cpe02g00011 11
2 85595 90936 - Cp4.1LG02g08500.1 Cpe02g00012 12
11 6228477 6231884 + Cp4.1LG11g07670.1 Cpe11g00770 770
8 21739290 21742400 + CrPI670011_08g008580.1 Cre08g0858 858
11 34618518 34628147 - CrPI670011_11g023010.1 Cre11g2301 2301
11 34630894 34631718 - CrPI670011_11g023020.1 Cre11g2302 2302
11 34633201 34636303 - CrPI670011_11g023030.1 Cre11g2303 2303
4 26301211 26303097 + CsaV3_4G037650.1 Csa04g02739 2739
4 26318564 26323607 - CsaV3_4G037690.1 Csa04g02743 2743
4 26323657 26328097 - CsaV3_4G037700.1 Csa04g02744 2744
4 26330449 26331279 - CsaV3_4G037710.1 Csa04g02745 2745
4 26332210 26335040 - CsaV3_4G037720.1 Csa04g02746 2746
4 31365489 31370787 - Lsi04G024270.1 Lsi04g02427 2427
4 31372866 31375476 - Lsi04G024280.1 Lsi04g02428 2428
4 31381633 31382457 - Lsi04G024310.1 Lsi04g02431 2431
4 31383605 31388189 - Lsi04G024320.1 Lsi04g02432 2432
8 16044530 16048807 + Lsi08G007640.1 Lsi08g00764 764
11 216462 220004 - MC11g0025 Mch11g0029 29
18 399143 410940 + Vvi18g30 Vvi18g30 30
18 411860 416076 + Vvi18g31 Vvi18g31 31
18 420615 423710 + Vvi18g32 Vvi18g32 32
18 425429 432998 + Vvi18g33 Vvi18g33 33
18 438421 443080 + Vvi18g34 Vvi18g34 34
18 444049 446447 + Vvi18g35 Vvi18g35 35
18 447135 470607 + Vvi18g36 Vvi18g36 36
18 474842 476501 - Vvi18g37 Vvi18g37 37
18 492064 492984 - Vvi18g38 Vvi18g38 38
18 494022 498427 - Vvi18g39 Vvi18g39 39
       

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