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United States Department of Agriculture

Agricultural Research Service

Research Project: MOLECULAR GENETIC TOOLS FOR POTATO AND FRUIT TREE IMPROVEMENT

Location: Crop Improvement & Utilization Research

Title: USDA Potato Small Rna Database

Author
item McCue, Kent

Submitted to: World Wide Web
Publication Type: Other
Publication Acceptance Date: August 13, 2010
Publication Date: August 13, 2010
Citation: Mc Cue, K.F. 2010. USDA Potato Small RNA Database. Available:http://avena.pw.usda.gov/potato.

Interpretive Summary: Small RNAs (sRNAs) are short (19-24) nucleic acid sequences tat are present in plants and animals. These small nucleic acid sequences affect gene regulation by limiting gene expression or by turning off genes after expression. This regulation may be involved in various cellular processes including growth, development, adaptation, and defense. Using high throughput sequencing (HTS) a tremendous amount of sequence data for sRNA can be generated. We have created a database of the sRNA sequences from a potato leaf using HTS. The database is presented on a publicly available website at http://avena.pw.usda.gov/potato/ that can be searched using known genes or nucleic acid sequences to determine whether there are sRNA related to the query sequence. This database is available to researchers and scientists in government, academia and industry who are interested in the roles sRNA play in the regulation of biological functions in the potato and related plants.

Technical Abstract: Small RNAs (sRNAs) are now understood to be involved in gene regulation, function and development. High throughput sequencing (HTS) of sRNAs generates large data sets for analyzing the abundance, source and roles for specific sRNAs. These sRNAs result from transcript degradation as well as specific regulatory micro RNA (miRNA) and small inhibitory RNAs (siRNA) involved in gene regulation. We have isolated and sequenced the sRNA population from the potato leaf using the Genome Analyzer IIx. The 10,000 most abundant transcripts were filtered for redundancy resulting in a data set of 9,727 unique sequences used to create a searchable database of potato leaf sRNA. The data set includes sRNAs for the degradation products of chlorplastic and ribosomal RNA as well as representatives of known miRNA families. Many of these sRNA are related to sRNA observed in other plants such as tomato differing by single nucleotide polymorphism. The majority of sRNAs present in leaves were 24 nucleotides long (58%) sRNAs from 20 to 21 nucleotides long represented an additional 28% of the abundant sRNA. Less than 10% of the abundant sRNA were attributable to chloroplast, ribosomal RNA or mitochondrial RNA in origin. This data set is now available using a BLAST search tool to identify sRNA specific to query sequences at http://avena.pw.usda.gov/potato/.

Last Modified: 8/2/2014
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