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Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

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CSRDB: a small RNA integrated database and browser resource for cereals.

Cameron Johnson¹, Lewis Bowman, Alex T Adai

¹Section of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA. camjohnson@ucdavis.edu

Nucleic Acids Research

|December 16, 2006

Summary

The Cereal Small RNA Database (CSRDB) offers extensive maize and rice small RNA (smRNA) sequence data. This resource aids research into epigenetic processes and gene networks in plants, linking smRNAs to their predicted targets.

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Area of Science:

Plant molecular biology
Bioinformatics
Genomics

Background:

Plant small RNAs (smRNAs), including microRNAs (miRNAs), short interfering RNAs (siRNAs), and trans-acting siRNAs (ta-siRNAs), play crucial roles in epigenetic regulation and gene networks governing plant development and homeostasis.
Understanding these smRNAs is vital for advancing plant science and crop improvement.

Purpose of the Study:

To establish a comprehensive bioinformatics resource, the Cereal Small RNA Database (CSRDB), for cereal crops.
To integrate and provide access to large-scale datasets of maize and rice smRNA sequences and their predicted targets.

Main Methods:

High-throughput pyrosequencing was employed to generate extensive smRNA sequence datasets for maize and rice.
smRNA sequences were mapped to the respective rice and maize genomes using the Generic Genome Browser.
Potential RNA targets for smRNAs were predicted and stored in a MySQL-based relational database.

Main Results:

The CSRDB provides mapped smRNA sequences for rice and maize, accessible via genome browsers.
A relational database links smRNAs to their predicted RNA targets, facilitating integrated analysis.
The resource features extensive data linking and integration, with both internal and external connectivity.

Conclusions:

The CSRDB serves as a valuable, integrated bioinformatics resource for researchers studying small RNAs in cereal crops.
This database facilitates the exploration of smRNA functions in plant epigenetic processes and gene regulatory networks.
The resource is publicly available and will be continuously updated with new sequence data.