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SNP-Seek database of SNPs derived from 3000 rice genomes.

Alexandrov N, Tai S, Wang W, Mansueto L, Palis K, Fuentes RR, Ulat VJ, Chebotarov D, Zhang G, Li Z, Mauleon R, Hamilton RS, McNally KL - Nucleic Acids Res. (2014)

Bottom Line: We have identified about 20 million rice SNPs by aligning reads from the 3000 rice genomes project with the Nipponbare genome.SNPs can be visualized together with the gene structures in JBrowse genome browser.Evolutionary relationships between rice varieties can be explored using phylogenetic trees or multidimensional scaling plots.

View Article: PubMed Central - PubMed

Affiliation: T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines n.alexandrov@irri.org.

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Related in: MedlinePlus

Multidimensional scaling plot of the 3000 rice varieties. Ind1, ind2 and ind3 are three groups of indica rice, indx corresponds to other indica varieties, temp is temperate japonica, trop is tropical japonica, temp/trop and trop/temp are admixed temperate and tropical japonica varieties, japx is other japonica varieties, aus is aus, inax is admixed aus and indica, aro is aromatic and admix is all other unassigned varieties.
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Figure 4: Multidimensional scaling plot of the 3000 rice varieties. Ind1, ind2 and ind3 are three groups of indica rice, indx corresponds to other indica varieties, temp is temperate japonica, trop is tropical japonica, temp/trop and trop/temp are admixed temperate and tropical japonica varieties, japx is other japonica varieties, aus is aus, inax is admixed aus and indica, aro is aromatic and admix is all other unassigned varieties.

Mentions: We deployed interfaces to facilitate the following major types of queries: (i) for two varieties find all SNPs from a gene or genomic region that differentiate them; (ii) for a gene or genome region, show all SNP calls for all varieties (Supplementary Figure S1); (iii) find all sequenced varieties from a certain country or a subpopulation, which can be viewed as a phylogenetic tree, built using TreeConstructor class from BioJava (13) and rendered using jsPhyloSVG JavaScript library (14) (Supplementary Figure S2) or as a multidimensional scaling plots (Figure 4). The results of SNP search can be viewed as a table exported to text files, or visualized in JBrowse.


SNP-Seek database of SNPs derived from 3000 rice genomes.

Alexandrov N, Tai S, Wang W, Mansueto L, Palis K, Fuentes RR, Ulat VJ, Chebotarov D, Zhang G, Li Z, Mauleon R, Hamilton RS, McNally KL - Nucleic Acids Res. (2014)

Multidimensional scaling plot of the 3000 rice varieties. Ind1, ind2 and ind3 are three groups of indica rice, indx corresponds to other indica varieties, temp is temperate japonica, trop is tropical japonica, temp/trop and trop/temp are admixed temperate and tropical japonica varieties, japx is other japonica varieties, aus is aus, inax is admixed aus and indica, aro is aromatic and admix is all other unassigned varieties.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383887&req=5

Figure 4: Multidimensional scaling plot of the 3000 rice varieties. Ind1, ind2 and ind3 are three groups of indica rice, indx corresponds to other indica varieties, temp is temperate japonica, trop is tropical japonica, temp/trop and trop/temp are admixed temperate and tropical japonica varieties, japx is other japonica varieties, aus is aus, inax is admixed aus and indica, aro is aromatic and admix is all other unassigned varieties.
Mentions: We deployed interfaces to facilitate the following major types of queries: (i) for two varieties find all SNPs from a gene or genomic region that differentiate them; (ii) for a gene or genome region, show all SNP calls for all varieties (Supplementary Figure S1); (iii) find all sequenced varieties from a certain country or a subpopulation, which can be viewed as a phylogenetic tree, built using TreeConstructor class from BioJava (13) and rendered using jsPhyloSVG JavaScript library (14) (Supplementary Figure S2) or as a multidimensional scaling plots (Figure 4). The results of SNP search can be viewed as a table exported to text files, or visualized in JBrowse.

Bottom Line: We have identified about 20 million rice SNPs by aligning reads from the 3000 rice genomes project with the Nipponbare genome.SNPs can be visualized together with the gene structures in JBrowse genome browser.Evolutionary relationships between rice varieties can be explored using phylogenetic trees or multidimensional scaling plots.

View Article: PubMed Central - PubMed

Affiliation: T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines n.alexandrov@irri.org.

Show MeSH
Related in: MedlinePlus