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ARS Home » Plains Area » Manhattan, Kansas » Center for Grain and Animal Health Research » Hard Winter Wheat Genetics Research » Research » Publications at this Location » Publication #295192

Research Project: Genetic Improvement of Hard Winter Wheat to Biotic and Abiotic Stresses

Location: Hard Winter Wheat Genetics Research

Title: SNPMeta: SNP annotation and SNP metadata collection without a reference genome

item KONO, THOMAS - University Of Minnesota
item KIRAN, SETH - University Of Minnesota
item Poland, Jesse
item MORRELL, PETER - University Of Minnesota

Submitted to: Molecular Ecology Resources
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/9/2013
Publication Date: 11/16/2013
Publication URL:
Citation: Kono, T., Kiran, S., Poland, J.A., Morrell, P. 2013. SNPMeta: SNP annotation and SNP metadata collection without a reference genome. Molecular Ecology Resources. 14, 419-425.

Interpretive Summary: To utilize genome sequence information to make inference to biological traits' it is important to have genes annotated in sequence databases. For model organisms (i.e. mouse, fly, rice) this is readily accomplished through large efforts centered on the reference genome sequence. For other species that do not have sufficient reference genome resources this approach is limited. Further, the increasing availability for low-cost DNA sequencing is making new datasets readily available. To fully leverage these sequence dataset it is important to have user-friendly tools available for annotation. Here we present a bioinformatics tool SNPMeta that gathers information about DNA polymorphisms found in sequencing datasets and compares these sequences to reference databases for characterization and annotation.

Technical Abstract: The increase in availability of resequencing data is greatly accelerating SNP discovery and has facilitated the development of SNP genotyping assays. This, in turn, is increasing interest in annotation of individual SNPs. Currently, these data are only available through curation, or comparison to a reference genome. However, some organisms serve as important genetic models despite the lack of a reference genome. For these species, it is possible to annotate SNPs through comparison to cDNA, or data from well annotated genes in public repositories. We present a tool, SNPMeta, which gathers information about SNPs by comparison to sequences present in GenBank databases. Because SNPMeta sources information from GenBank, it can be used to annotate SNPs in non-model species, or species that lack a reference genome.