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

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 the Nicotiana attenuata Data Hub (NaDH) as a centralized platform for integrating and visualizing genomic, phylogenomic, transcriptomic and metabolomic data in N. attenuata. The NaDH currently hosts collections of predicted protein coding sequences of 11 plant species, including two recently sequenced Nicotiana 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, the NaDH 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 factor NaMYB8 as an example, we illustrate that the tools and data in NaDH can facilitate identification of candidate genes involved in the biosynthesis of specialized metabolites.

Conclusion: The NaDH provides interactive visualization and data analysis tools that integrate the expression and evolutionary history of genes in Nicotiana, which can facilitate rapid gene discovery and comparative genomic analysis. Because N. attenuata shares many genome-wide features with other Nicotiana species including cultivated tobacco, and hence NaDH can be a resource for exploring the function and evolution of genes in Nicotiana species in general. The NaDH can be accessed at: http://nadh.ice.mpg.de/ .

Keywords: Co-expression analysis; Metabolomics; Nicotiana attenuata; Phylogenomics; Transcriptomics; genomics.

Fig. 1

Overview of data structure and utilities in the NaDH. The NaDH consists of 10 major utilities, which can be accessed by either gene ID or metabolite spectrum ID

Fig. 2

Examples of visualization on co-expressed genes and metabolites. a Genes that are co-expressed with a transcription factor (TF) NaMYB8 (NIATv7_g41919) (red). Each node represents a co-expressed gene, radiating position of the node represents the most recent duplication events it has experienced and clock-wise position of the node represents the highest expression among four tissues and relative tissue specificity. b Metabolite spectra that are co-expressed with NaAT1 (NIATv7_g11614), a gene from phenolamides pathway. Color indicate different functional classes of metabolite spectra: dark green: phenolamides; pink: different 17-hydrogeranyllinalool diterpene glycosides; blue: quinate conjugates; grey: not annotated metabolite spectra. Node number shows the m/z value of the metabolite spectrum and letters refers to different isotopes. Edges indicate structure similarities among metabolite spectra: yellow: NDP based similarity, red: NL based similarity. NDP was calculated based on shared fragments and NL was calculated based on shared neutral losses

Fig. 3

Example of visualizing gene expression and evolution. a Expression of NaDH29 (NIATv7_g06682) in leaves and roots of control or wounding or M. sexta oral secretion induced plants. b Presence and absence of N’,N”-dicaffeoylspermidine (DCS) [m/z: 470.2284287, retention time: 395.616992] different N. attenuata tissues. c Phylogenetic tree of 4CL gene family visualized using iTOL. Gene structure of each gene is shown on the right side. Colors refer to different species

Fig. 4

Co-expressed genes and metabolite spectra of the phenolamides pathway. a Genes co-expressed with NaMYB8 (NIATv7_g41919). Each circle indicates one gene and the tree structure visualizes their phylogenetic history and the age of the duplication events: N: Nicotiana specific; S: Solanaceae specific; O: older duplication. The red color indicates that the gene is correlated with NaMYB8. The thickness of the black lines connecting NaMYB8 with other genes indicates the expression correlation coefficient. PAL: Phenylalanine ammonia-lyase; C4H: cinnamate-4-hydroxylase; C3H: coumarate-3-hydroxylase; 4CL: 4-coumarate coenzyme A ligase. b Co-expression of metabolites and genes from the phenolamides pathway. CP: N-caffeoylputrescine, CoP: N-coumaroylputrescine, MCoS: N-coumarylspermidine, MCS: N-caffeoylspermidine, CoCS: N-coumaryl, caffeoyl spermidine, DCS: N’,N”-dicaffeoylspermidine, DFS: N’,N”-di-feruloyl-spermidine, dashed line: unknown reaction, dashed box: metabolite not measurable with used mass spectrometry method. Red lines indicate correlation coefficient higher than 0.6