In-Depth Transcriptome Sequencing of Mexican Lime Trees Infected with Candidatus Phytoplasma aurantifolia.

Mohsen Mardi,Javad Gharechahi,Ghasem Hosseini Salekdeh,Laleh Karimi Farsad,Chih-Horng Kuo

doi:10.1371/journal.pone.0130425

Abstract

Witches’ broom disease of acid lime greatly affects the production of Mexican lime in Iran. It is caused by a phytoplasma (Candidatus Phytoplasma aurantifolia). However, the molecular mechanisms that underlie phytoplasma pathogenicity and the mode of interactions with host plants are largely unknown. Here, high-throughput transcriptome sequencing was conducted to explore gene expression signatures associated with phytoplasma infection in Mexican lime trees. We assembled 78,185 unique transcript sequences (unigenes) with an average length of 530 nt. Of these, 41,805 (53.4%) were annotated against the NCBI non-redundant (nr) protein database using a BLASTx search (e-value ≤ 1e-5). When the abundances of unigenes in healthy and infected plants were compared, 2,805 transcripts showed significant differences (false discovery rate ≤ 0.001 and log2 ratio ≥ 1.5). These differentially expressed genes (DEGs) were significantly enriched in 43 KEGG metabolic and regulatory pathways. The up-regulated DEGs were mainly categorized into pathways with possible implication in plant-pathogen interaction, including cell wall biogenesis and degradation, sucrose metabolism, secondary metabolism, hormone biosynthesis and signalling, amino acid and lipid metabolism, while down-regulated DEGs were predominantly enriched in ubiquitin proteolysis and oxidative phosphorylation pathways. Our analysis provides novel insight into the molecular pathways that are deregulated during the host-pathogen interaction in Mexican lime trees infected by phytoplasma. The findings can be valuable for unravelling the molecular mechanisms of plant-phytoplasma interactions and can pave the way for engineering lime trees with resistance to witches’ broom disease.

Highlights

Mexican lime (Citrus aurantifolia L.) is one of the most economically important citrus trees grown in the south of Iran
This result confirmed that the 16S rRNA gene sequence detected in the infected plants was amplified from a variant of 16SrII-B, which was mostly related to Ca
Using next-generation sequencing (NGS) we sequenced the transcriptome of Mexican lime trees infected with Ca

Summary

Introduction

Mexican lime (Citrus aurantifolia L.) is one of the most economically important citrus trees grown in the south of Iran. The production of its fruit has been markedly reduced by a severe epidemic of the devastating witches’ broom disease of lime (WBDL) in Iran and adjoining. A candidatus phytoplasma (Candidatus phytoplasma aurantifolia) has been identified as the causative agent of WBDL [10]. It is an obligate biotrophic mycoplasma-like organism that completely depends on living host cells for its nutritional requirements. There are major obstacles to the detailed characterisation of phytoplasmas and identification of the molecular mechanisms behind their pathogenicity and mode of interaction with host plants owing to the inability to culture them in vitro and their inaccessibility in host plants [11,12]

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