Next-generation sequence databases: RNA and genomic informatics resources for plants

Mayumi Nakano, Kevin McCormick, Caghan Demirci, Feray Demirci, Sai Guna Ranjan Gurazada, Deepti Ramachandruni, Ayush Dusia, Joshua A. Rothhaupt, Blake C. Meyers

Research output: Contribution to journalArticlepeer-review

16 Scopus citations

Abstract

We developed public web sites and resources for data access, display, and analysis of plant small RNAs. These web sites are interconnected with related data types. The current generation of these informatics tools was developed for Illumina data, evolving over more than 15 years of improvements. Our online databases have customized web interfaces to uniquely handle and display RNA-derived data from diverse plant species, ranging from Arabidopsis (Arabidopsis thaliana) to wheat (Triticum spp.), including many crop and model species. The web interface displays the abundance and genomic context of data for small RNAs, parallel analysis of RNA ends/degradome reads, RNA sequencing, and even chromatin immunoprecipitation sequencing data; it also provides information about potentially novel transcripts (antisense transcripts, alternative splice isoforms, and regulatory intergenic transcripts). Numerous options are included for downloading data as tables or via web services. Interpretation of these data is facilitated by the inclusion of extensive repeat or transposon data in our genome viewer. We have developed graphical and analytical tools, including a new viewer and a query page for the analysis of phased small RNAs; these are particularly useful for understanding the complex small RNA pathways of plants. These public databases are accessible at https://mpss.danforthcenter.org.

Original languageEnglish
Pages (from-to)136-146
Number of pages11
JournalPlant Physiology
Volume182
Issue number1
DOIs
StatePublished - Jan 2020

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