PGSB PlantsDB: updates to the database framework for comparative plant genome research.

Manuel Spannagl,Klaus F.X Mayer,Karl G Kugler,Michael Seidel,Thomas Nussbaumer,Kai C Bader,Mihaela M Martis,Heidrun Gundlach

doi:10.1093/nar/gkv1130

Manuel Spannagl, Klaus F.X Mayer + Show 6 more

Open Access

https://doi.org/10.1093/nar/gkv1130

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Abstract

PGSB (Plant Genome and Systems Biology: formerly MIPS) PlantsDB (http://pgsb.helmholtz-muenchen.de/plant/index.jsp) is a database framework for the comparative analysis and visualization of plant genome data. The resource has been updated with new data sets and types as well as specialized tools and interfaces to address user demands for intuitive access to complex plant genome data. In its latest incarnation, we have re-worked both the layout and navigation structure and implemented new keyword search options and a new BLAST sequence search functionality. Actively involved in corresponding sequencing consortia, PlantsDB has dedicated special efforts to the integration and visualization of complex triticeae genome data, especially for barley, wheat and rye. We enhanced CrowsNest, a tool to visualize syntenic relationships between genomes, with data from the wheat sub-genome progenitor Aegilops tauschii and added functionality to the PGSB RNASeqExpressionBrowser. GenomeZipper results were integrated for the genomes of barley, rye, wheat and perennial ryegrass and interactive access is granted through PlantsDB interfaces. Data exchange and cross-linking between PlantsDB and other plant genome databases is stimulated by the transPLANT project (http://transplantdb.eu/).

Highlights

With the availability of efficient next-generation sequencing technologies as well as novel bioinformatic assembly and analysis strategies, plant genome sequencing has entered a new era
GenomeZipper results were integrated for the genomes of barley, rye, wheat and perennial ryegrass and interactive access is granted through PlantsDB interfaces
GenomeZippers have been constructed for barley [17], bread wheat [3], rye [4] and perennial ryegrass [18] so far and all data including raw sequences have been integrated into PlantsDB along with dedicated visualization interfaces and search options

Summary

Introduction

With the availability of (cost-) efficient next-generation sequencing technologies as well as novel bioinformatic assembly and analysis strategies, plant genome sequencing has entered a new era. The resource has been updated with new data sets and types as well as specialized tools and interfaces to address user demands for intuitive access to complex plant genome data. Involved in corresponding sequencing consortia, PlantsDB has dedicated special efforts to the integration and visualization of complex triticeae genome data, especially for barley, wheat and rye.

Results

Conclusion