Nicotiana attenuata Data Hub (NaDH): an integrative platform for exploring genomic, transcriptomic and metabolomic data in wild tobacco. (December 2017)

• Record Type: Journal Article
• Authors: Brockmöller, Thomas; Ling, Zhihao; Li, Dapeng; Gaquerel, Emmanuel; Baldwin, Ian; Xu, Shuqing
• Is Part Of: BMC genomics. Volume 18:Number 1(2017)
• Page Start: 1
• Page End: 11
• Publication Date: 2017-12
• Subjects: Nicotiana attenuata -- Phylogenomics -- Transcriptomics -- genomics -- Metabolomics -- Co-expression analysis; Genomes -- Periodicals; Gene mapping -- Periodicals; Genomics -- Periodicals; Base Sequence -- Periodicals; Chromosome Mapping -- Periodicals; Genetic Techniques -- Periodicals; Sequence Analysis, DNA -- Periodicals; 572.8605
• DOI: 10.1186/s12864-016-3465-9
• Languages: English
• ISSNs: 1471-2164

Abstract

Abstract Background Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now. Description We present theNicotiana attenuata Data Hub (Na DH) as a centralized platform for integrating and visualizing genomic, phylogenomic, transcriptomic and metabolomic data inN. attenuata . TheNa DH currently hosts collections of predicted protein coding sequences of 11 plant species, including two recently sequencedNicotiana species, and their functional annotations, 222 microarray datasets from 10 different experiments, a transcriptomic atlas based on 20 RNA-seq expression profiles and a metabolomic atlas based on 895 metabolite spectra analyzed by mass spectrometry. We implemented several visualization tools, including a modified version of the Electronic Fluorescent Pictograph (eFP) browser, co-expression networks and the Interactive Tree Of Life (iTOL) for studying gene expression divergence among duplicated homologous. In addition, theNa DH allows researchers to query phylogenetic trees of 16, 305 gene families and provides tools for analyzing their evolutionary history. Furthermore, we also implemented tools to identify co-expressed genes and metabolites, which can be used for predicting the functions of genes. Using the transcription factorNaMYB8 as an example, we illustrate that the tools and data inNa DH can facilitate identification of candidate genes involved in the biosynthesis of specialized metabolites. Conclusion TheNa DH provides interactive visualization and data analysis tools that integrate the expression and evolutionary history of genes inNicotiana, which can facilitate rapid gene discovery and comparative genomic analysis. BecauseN. attenuata shares many genome-wide features with otherNicotiana species including cultivated tobacco, and henceNa DH can be a resource for exploring the function and evolution of genes inNicotiana species in general. TheNa DH can be accessed at:http://nadh.ice.mpg.de/ .