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
Vvi17g816 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g817 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone16ag0073 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g818 . . . . . . . . . Cmo18g00151 . . . . . . . . . . . . . . . . . . . . . Cone2ag0931 . . . Lsi02g00412 Csa01g00881 Chy12g01241 Cme12g01664 . . . . . . . . . . . . Cma18g00190 . Car18g00182 Cpe09g01005 . Bhi08g01658 Tan05g1972 . . . . . Cla01g01329 Cam01g1399 Cec01g1431 Cco01g1492 Clacu01g1396 Cmu01g1304 Cre01g1237 . . . .
Vvi17g819 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g820 . . Bda06g00618 Bda15g00540 . . . Bma12g01054 . . Cma10g00093 Cma11g00070 Car10g00082 Car11g00062 Sed08g0451 . Cpe04g01581 Bhi02g00603 Tan09g2304 Cmetu05g0163 . . . . Cla06g01699 Cam06g1886 Cec06g1935 Cco06g1939 Clacu06g1842 Cmu06g1784 . . . Cone13ag0167 Cone19ag0164 . . . . Blo13g00144 Blo15g00251 . . Bpe07g00858 . . Bma08g00083 . Cmo10g00097 Cmo11g00072 . . . . . Cpe18g00869 . . . . . . . . . . . . . . . . . .
Vvi17g821 . . . . . Bpe13g00264 . . . . . . . . . . . Bhi02g00602 . . . . . . Cla06g01700 Cam06g1888 Cec06g1937 Cco06g1941 Clacu06g1844 Cmu06g1785 Cre06g2600 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa01g00103 . .
Vvi17g822 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g823 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g824 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g825 . . . . . . . . . . . Cma11g00069 . . . . Cpe04g01582 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma03g01307 . . . Cmo11g00070 . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 8452801 8455097 + Bda023889.1 Bda06g00618 618
15 8473381 8475741 - Bda012373.1 Bda15g00540 540
2 11440480 11445316 - XM_039024208.1 Bhi02g00602 602
2 11446485 11451711 - XM_039023782.1 Bhi02g00603 603
8 46726197 46731925 + XM_039039595.1 Bhi08g01658 1658
13 4553508 4555857 + BLOR05425 Blo13g00144 144
15 2597508 2600080 - BLOR06645 Blo15g00251 251
3 25709937 25715639 + Bma017809.1 Bma03g01307 1307
8 978383 980761 - Bma027082.1 Bma08g00083 83
12 42635482 42637847 + Bma008403.1 Bma12g01054 1054
7 14725572 14728058 + Bpe021701.1 Bpe07g00858 858
13 10581403 10590211 - Bpe006387.1 Bpe13g00264 264
1 27543794 27547677 - CaPI482276_01g013990.1 Cam01g1399 1399
6 29905239 29908253 + CaPI482276_06g018860.1 Cam06g1886 1886
6 29918182 29918580 + CaPI482276_06g018880.1 Cam06g1888 1888
10 369743 373371 - Carg10314-RA Car10g00082 82
11 338012 343894 - Carg20200-RA Car11g00062 62
18 1003443 1008722 + Carg06749-RA Car18g00182 182
1 26691100 26695584 + CcPI632755_01g014920.1 Cco01g1492 1492
6 29638039 29641021 + CcPI632755_06g019390.1 Cco06g1939 1939
6 29651355 29651741 + CcPI632755_06g019410.1 Cco06g1941 1941
1 28967099 28972740 - CePI673135_01g014310.1 Cec01g1431 1431
6 32712064 32715074 + CePI673135_06g019350.1 Cec06g1935 1935
6 32725314 32725712 + CePI673135_06g019370.1 Cec06g1937 1937
12 17070905 17075415 - Chy12G218410.1 Chy12g01241 1241
1 25266087 25270567 + ClG42_01g0139600.10 Clacu01g1396 1396
6 28956135 28959149 + ClG42_06g0184200.10 Clacu06g1842 1842
6 28969060 28969458 + ClG42_06g0184400.10 Clacu06g1844 1844
1 26644749 26651255 + ClCG01G013470.2 Cla01g01329 1329
6 30581440 30584882 + ClCG06G017390.2 Cla06g01699 1699
6 30585642 30594988 + ClCG06G017400.2 Cla06g01700 1700
10 377698 381636 - CmaCh10G000930.1 Cma10g00093 93
11 339242 342183 - CmaCh11G000690.1 Cma11g00069 69
11 342282 345428 - CmaCh11G000700.1 Cma11g00070 70
18 982858 988938 + CmaCh18G001900.1 Cma18g00190 190
12 23658277 23664463 - MELO3C002296.2.1 Cme12g01664 1664
5 6463156 6467230 + PI0022107.1 Cmetu05g0163 163
10 414401 418783 - CmoCh10G000970.1 Cmo10g00097 97
11 326270 328845 - CmoCh11G000700.1 Cmo11g00070 70
11 331889 333357 - CmoCh11G000720.1 Cmo11g00072 72
18 1056034 1061232 + CmoCh18G001510.1 Cmo18g00151 151
1 25608585 25609113 + CmPI595203_01g013040.1 Cmu01g1304 1304
6 28861206 28871775 + CmPI595203_06g017840.1 Cmu06g1784 1784
6 28874286 28874684 + CmPI595203_06g017850.1 Cmu06g1785 1785
2 35062258 35066861 + Conep02aG0196500.1 Cone2ag0931 931
13 1042578 1045746 + Conep13aG0017200.1 Cone13ag0167 167
16 365823 367638 + Conep16aG0007400.1 Cone16ag0073 73
19 936595 939205 + Conep19aG0017000.1 Cone19ag0164 164
4 12352525 12356164 + Cp4.1LG04g15680.1 Cpe04g01581 1581
4 12356978 12360881 + Cp4.1LG04g15710.1 Cpe04g01582 1582
9 8897627 8903785 - Cp4.1LG09g10120.1 Cpe09g01005 1005
18 7958982 7963076 + Cp4.1LG18g08600.1 Cpe18g00869 869
1 25572027 25576521 - CrPI670011_01g012370.1 Cre01g1237 1237
6 33685921 33698749 + CrPI670011_06g026000.1 Cre06g2600 2600
1 600864 602205 + CsaV3_1G001030.1 Csa01g00103 103
1 5498721 5506226 + CsaV3_1G008820.1 Csa01g00881 881
2 3446359 3456445 + Lsi02G004120.1 Lsi02g00412 412
8 2794300 2800730 - Sed0020380.1 Sed08g0451 451
5 69332505 69337988 - Tan0019848.2 Tan05g1972 1972
9 72951311 72956301 + Tan0003198.1 Tan09g2304 2304
17 10769896 10770858 + Vvi17g816 Vvi17g816 816
17 10773203 10775493 - Vvi17g817 Vvi17g817 817
17 10796673 10803874 + Vvi17g818 Vvi17g818 818
17 10807097 10814954 + Vvi17g819 Vvi17g819 819
17 10820977 10825022 + Vvi17g820 Vvi17g820 820
17 10831350 10834156 + Vvi17g821 Vvi17g821 821
17 10834157 10834817 + Vvi17g822 Vvi17g822 822
17 10834908 10835557 + Vvi17g823 Vvi17g823 823
17 10852794 10853467 + Vvi17g824 Vvi17g824 824
17 10859610 10862639 + Vvi17g825 Vvi17g825 825
       

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