Profiling mRNAs of two Cuscuta species reveals possible candidate transcripts shared by parasitic plants.

Linjian Jiang,Martina Fraga,Saranga Wijeratne,Feng Qu,Zhaohu Li,Tea Meulia,Doug Doohan,Asela J Wijeratne

doi:10.1371/journal.pone.0081389

Linjian Jiang, Martina Fraga + Show 6 more

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https://doi.org/10.1371/journal.pone.0081389

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Abstract

Dodders are among the most important parasitic plants that cause serious yield losses in crop plants. In this report, we sought to unveil the genetic basis of dodder parasitism by profiling the trancriptomes of Cuscuta pentagona and C. suaveolens, two of the most common dodder species using a next-generation RNA sequencing platform. De novo assembly of the sequence reads resulted in more than 46,000 isotigs and contigs (collectively referred to as expressed sequence tags or ESTs) for each species, with more than half of them predicted to encode proteins that share significant sequence similarities with known proteins of non-parasitic plants. Comparing our datasets with transcriptomes of 12 other fully sequenced plant species confirmed a close evolutionary relationship between dodder and tomato. Using a rigorous set of filtering parameters, we were able to identify seven pairs of ESTs that appear to be shared exclusively by parasitic plants, thus providing targets for tailored management approaches. In addition, we also discovered ESTs with sequences similarities to known plant viruses, including cryptic viruses, in the dodder sequence assemblies. Together this study represents the first comprehensive transcriptome profiling of parasitic plants in the Cuscuta genus, and is expected to contribute to our understanding of the molecular mechanisms of parasitic plant-host plant interactions.

Highlights

Parasitic plants receive part or all of the nutrients, including photosynthate, nitrogen, minerals, as well as water, from their host plants, inflicting physiological stresses to the latter, leading to stunting, loss of productivity, and sometimes death, of the host crops [1;2]
Initial de novo assembly of raw reads using the Newbler 2.5 software showed that a substantial proportion of reads of both species could be assembled into large isotigs of 1,000 nucleotides or longer, resulting in 18,150 and 20,510 isotigs for C. pentagona and C. suaveolens, respectively
The raw sequence data of C. pentagona and C. suaveolens have been deposited in GenBank with the accession numbers SRA071492 and SRA071493; and their assembled expressed sequence tags (ESTs) were deposited in GenBank’s TSA database with the accession numbers SUB373257 and SUB357373

Summary

Introduction

Parasitic plants receive part or all of the nutrients, including photosynthate, nitrogen, minerals, as well as water, from their host plants, inflicting physiological stresses to the latter, leading to stunting, loss of productivity, and sometimes death, of the host crops [1;2]. Recent studies suggest that host plants respond to initial invasion by parasitic plants with defense responses that share similar features with anti-microbial defenses [5;6]. It remains to be resolved how parasitic plants overcome these defense responses to establish successful parasitism. Understanding the molecular basis of parasitic plant-host interactions is of critical importance to crop production as many staple crops, including maize, tomato, alfalfa, and soybean, are known to suffer from infestation by parasitic plants, leading to significant yield losses [1;2]

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