Deep RNA-Seq profile reveals biodiversity, plant-microbe interactions and a large family of NBS-LRR resistance genes in walnut (Juglans regia) tissues.

Sandeep Chakraborty,P J Martínez-García,Abhaya M Dandekar,Monica Britton

doi:10.1186/s13568-016-0182-3

Sandeep Chakraborty, P J Martínez-García + Show 2 more

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https://doi.org/10.1186/s13568-016-0182-3

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Abstract

Deep RNA-Seq profiling, a revolutionary method used for quantifying transcriptional levels, often includes non-specific transcripts from other co-existing organisms in spite of stringent protocols. Using the recently published walnut genome sequence as a filter, we present a broad analysis of the RNA-Seq derived transcriptome profiles obtained from twenty different tissues to extract the biodiversity and possible plant–microbe interactions in the walnut ecosystem in California. Since the residual nature of the transcripts being analyzed does not provide sufficient information to identify the exact strain, inferences made are constrained to the genus level. The presence of the pathogenic oomycete Phytophthora was detected in the root through the presence of a glyceraldehyde-3-phosphate dehydrogenase. Cryptococcus, the causal agent of cryptococcosis, was found in the catkins and vegetative buds, corroborating previous work indicating that the plant surface supported the sexual cycle of this human pathogen. The RNA-Seq profile revealed several species of the endophytic nitrogen fixing Actinobacteria. Another bacterial species implicated in aerobic biodegradation of methyl tert-butyl ether (Methylibium petroleiphilum) is also found in the root. RNA encoding proteins from the pea aphid were found in the leaves and vegetative buds, while a serine protease from mosquito with significant homology to a female reproductive tract protease from Drosophila mojavensis in the vegetative bud suggests egg-laying activities. The comprehensive analysis of RNA-seq data present also unraveled detailed, tissue-specific information of ~400 transcripts encoded by the largest family of resistance (R) genes (NBS-LRR), which possibly rationalizes the resistance of the specific walnut plant to the pathogens detected. Thus, we elucidate the biodiversity and possible plant–microbe interactions in several walnut (Juglans regia) tissues in California using deep RNA-Seq profiling.

Highlights

Rapid detection of pathogens in plants is becoming increasingly necessary to prevent loss of productivity and quality (Dandekar et al 2010; Fletcher et al 2006)
RNA-Seq derived transcriptome with a selection protocol for polyadenylated mRNA from an organism with known genome enables detection of mRNA from extraneous eukaryotes like fungi and pests
We have recently used a RNA-Seq methodology to derive the transcriptome of walnut (Juglans regia) from twenty different tissues types with selection for polyadenylated mRNA in the course of obtaining the walnut genome sequence (WGS)

Summary

Introduction

Rapid detection of pathogens in plants is becoming increasingly necessary to prevent loss of productivity and quality (Dandekar et al 2010; Fletcher et al 2006). RNA-Seq derived transcriptome with a selection protocol for polyadenylated mRNA from an organism with known genome enables detection of mRNA from extraneous eukaryotes like fungi and pests. Certain RNASeq protocols ensure that only polyadenylated mRNA is being analyzed, yet some bacterial mRNA does leak through in the analysis. This presents an unbiased method of diagnosing the presence of wide range of prokaryotic and eukaryotic organisms (Moretti et al 2007; Janse 2010). Such a study can guide downstream PCR diagnostics to determine the exact species/ strain of a pathogen. The detection of these pathogenic agents in an otherwise healthy plant can be ascribed to the presence and activity of resistance (R) genes that recognize pathogens, which contain complementary avirulence genes (Staskawicz 2001)

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