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
Vvi1g1031 . . . . . . Bma14g01683 . . . . . . . . . . Bhi07g00113 . . Lac13g1620 Hepe01g0410 . . . . . . . . . . . . . . . Chy10g00122 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01026 . .
Vvi1g1032 . Blo16g01069 . Bda11g01157 Bpe13g01355 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo11g00858 . Bda11g01157 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1033 . . . . . . . . . . . . . . . . Cpe01g01901 . . . . . . . . . . . . . . . . . . . . . . . . Bda07g01495 . . . . . . Cmo04g02291 Cmo15g00872 Cma04g02191 Cma15g00840 Car04g02117 Car15g00791 . . Bhi12g01045 . . . . . . Cla01g00724 Cam01g0751 Cec01g0750 Cco01g0776 Clacu01g0743 Cmu01g0712 Cre09g1794 Lsi09g00784 Csa05g01365 Chy09g00416 Cme09g01204
Vvi1g1034 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0828 Cone9ag0828 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1035 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe11g01733 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1036 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1037 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1038 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1039 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1040 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 27712934 27715192 - Bda033973 Bda07g01495 1495
11 11847769 11849928 - Bda007648.1 Bda11g01157 1157
7 6949126 6982630 - XM_039036549.1 Bhi07g00113 113
12 31938762 31943144 + XM_039050657.1 Bhi12g01045 1045
11 15957983 15958942 - BLOR03734 Blo11g00858 858
16 39243819 39249342 - BLOR21856 Blo16g01069 1069
14 35804274 35809340 + Bma012426.2 Bma14g01683 1683
11 13705780 13708309 + Bpe005049.1 Bpe11g01733 1733
13 18813046 18815226 - Bpe011017.1 Bpe13g01355 1355
1 8309955 8318552 + CaPI482276_01g007510.1 Cam01g0751 751
4 17242226 17245853 + Carg17724-RA Car04g02117 2117
15 4491605 4495847 - Carg01364-RA Car15g00791 791
1 8120344 8121144 + CcPI632755_01g007760.1 Cco01g0776 776
1 8199122 8199922 + CePI673135_01g007500.1 Cec01g0750 750
9 3651722 3657216 - Chy9G161320.1 Chy09g00416 416
10 3171248 3202220 - Chy10G173160.1 Chy10g00122 122
1 7986969 7995533 + ClG42_01g0074300.10 Clacu01g0743 743
1 8409629 8418194 + ClCG01G007400.2 Cla01g00724 724
4 15284556 15288362 + CmaCh04G021910.1 Cma04g02191 2191
15 4252449 4259080 - CmaCh15G008400.1 Cma15g00840 840
9 16947915 16952206 - MELO3C005172.2.1 Cme09g01204 1204
4 17039195 17041688 + CmoCh04G022910.1 Cmo04g02291 2291
15 4427651 4432134 - CmoCh15G008720.1 Cmo15g00872 872
1 7968276 7969076 + CmPI595203_01g007120.1 Cmu01g0712 712
6 4238018 4239940 - Conep06aG0085400.1 Cone6ag0828 828
9 4049910 4051406 - Conep09aG0084800.1 Cone9ag0828 828
1 16223035 16227073 + Cp4.1LG01g18990.1 Cpe01g01901 1901
9 36387216 36391125 - CrPI670011_09g017940.1 Cre09g1794 1794
5 9862240 9895376 - CsaV3_5G013320.1 Csa05g01026 1026
5 14365904 14370501 + CsaV3_5G018870.1 Csa05g01365 1365
1 56844870 56870832 - Hsped.01g04100.1 Hepe01g0410 410
13 17485656 17488963 + Lag0041416.1 Lac13g1620 1620
9 8908961 8913221 + Lsi09G007840.1 Lsi09g00784 784
1 16623442 16639232 - Vvi1g1031 Vvi1g1031 1031
1 16683139 16690231 - Vvi1g1032 Vvi1g1032 1032
1 16692429 16716306 - Vvi1g1033 Vvi1g1033 1033
1 16739673 16740975 - Vvi1g1034 Vvi1g1034 1034
1 16740976 16743471 - Vvi1g1035 Vvi1g1035 1035
1 16801193 16801244 - Vvi1g1036 Vvi1g1036 1036
1 16879403 16894049 + Vvi1g1037 Vvi1g1037 1037
1 16894942 16897180 + Vvi1g1038 Vvi1g1038 1038
1 16897461 16906512 - Vvi1g1039 Vvi1g1039 1039
1 16916996 16917977 - Vvi1g1040 Vvi1g1040 1040
       

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