Overview of the functional virulent genome of the coffee leaf rust pathogen Hemileia vastatrix with an emphasis on early stages of infection.

Pedro Talhinhas,Corinne Da Silva,Julie Poulain,Octã¡Vio S Paulo,Maria Do Cã©U Silva,Anne-Sophie Petitot,Dora Batista,Emmanuelle Morin,Bruno Vieira,Andreia Loureiro,Helena G Azinheira,Sã­Lvia Tavares,Sã©Bastien Duplessis,Diana Fernandez

doi:10.3389/fpls.2014.00088

Abstract

Hemileia vastatrix is the causal agent of coffee leaf rust, the most important disease of coffee Arabica. In this work, a 454-pyrosequencing transcriptome analysis of H. vastatrix germinating urediniospores (gU) and appressoria (Ap) was performed and compared to previously published in planta haustoria-rich (H) data. A total of 9234 transcripts were identified and annotated. Ca. 50% of these transcripts showed no significant homology to international databases. Only 784 sequences were shared by the three conditions, and 75% were exclusive of either gU (2146), Ap (1479) or H (3270). Relative transcript abundance and RT-qPCR analyses for a selection of genes indicated a particularly active metabolism, translational activity and production of new structures in the appressoria and intense signaling, transport, secretory activity and cellular multiplication in the germinating urediniospores, suggesting the onset of a plant-fungus dialogue as early as at the germ tube stage. Gene expression related to the production of carbohydrate-active enzymes and accumulation of glycerol in germinating urediniospores and appressoria suggests that combined lytic and physical mechanisms are involved in appressoria-mediated penetration. Besides contributing to the characterization of molecular processes leading to appressoria-mediated infection by rust fungi, these results point toward the identification of new H. vastatrix candidate virulence factors, with 516 genes predicted to encode secreted proteins.

Highlights

Rust diseases have been a long standing threat for centuries and have reshaped cultivation of crops and breeding strategies
Coffee leaf rust caused by Hemileia vastatrix Berk & Broome is the major disease of Arabica cultivated coffees (Coffea arabica L.) (Silva et al, 2006)
Complementing the knowledge gained into the in planta transcriptome of coffee rust, here we report on the in-depth transcriptome analysis of H. vastatrix by 454-based RNA-Seq during urediniospore germination and appressorium formation, two early and key stages of infection

Summary

Introduction

Rust diseases have been a long standing threat for centuries and have reshaped cultivation of crops and breeding strategies. Coffee leaf rust caused by Hemileia vastatrix Berk & Broome is the major disease of Arabica cultivated coffees (Coffea arabica L.) (Silva et al, 2006). Breeding and selection of coffee resistant genotypes to different fungal races from several parts of the world has been successful (Silva et al, 2006), but as a consequence of the high adaptive potential of the pathogen, the emergence of new rust pathotypes and the corresponding breakdown of resistance has been observed in many improved coffee varieties in several countries (Várzea and Marques, 2005; Diniz et al, 2012; Cressey, 2013). Currently coffee leaf rust still stands as the major constraint to Arabica coffee production

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