Combating a Global Threat to a Clonal Crop: Banana Black Sigatoka Pathogen Pseudocercospora fijiensis (Synonym Mycosphaerella fijiensis) Genomes Reveal Clues for Disease Control

Abstract

Black Sigatoka or black leaf streak disease, caused by the Dothideomycete fungus Pseudocercospora fijiensis (previously: Mycosphaerella fijiensis), is the most significant foliar disease of banana worldwide. Due to the lack of effective host resistance, management of this disease requires frequent fungicide applications, which greatly increase the economic and environmental costs to produce banana. Weekly applications in most banana plantations lead to rapid evolution of fungicide-resistant strains within populations causing disease-control failures throughout the world. Given its extremely high economic importance, two strains of P. fijiensis were sequenced and assembled with the aid of a new genetic linkage map. The 74-Mb genome of P. fijiensis is massively expanded by LTR retrotransposons, making it the largest genome within the Dothideomycetes. Melting-curve assays suggest that the genomes of two closely related members of the Sigatoka disease complex, P. eumusae and P. musae, also are expanded. Electrophoretic karyotyping and analyses of molecular markers in P. fijiensis field populations showed chromosome-length polymorphisms and high genetic diversity. Genetic differentiation was also detected using neutral markers, suggesting strong selection with limited gene flow at the studied geographic scale. Frequencies of fungicide resistance in fungicide-treated plantations were much higher than those in untreated wild-type P. fijiensis populations. A homologue of the Cladosporium fulvum Avr4 effector, PfAvr4, was identified in the P. fijiensis genome. Infiltration of the purified PfAVR4 protein into leaves of the resistant banana variety Calcutta 4 resulted in a hypersensitive-like response. This result suggests that Calcutta 4 could carry an unknown resistance gene recognizing PfAVR4. Besides adding to our understanding of the overall Dothideomycete genome structures, the P. fijiensis genome will aid in developing fungicide treatment schedules to combat this pathogen and in improving the efficiency of banana breeding programs.

Progress in understanding Pseudocercospora banana pathogens and the development of resistant Musa germplasm

“…An analysis of several isolates of P. fijiensis has also revealed allelic variation in some of the effector‐coding sequences (Stergiopoulos et al ., ). These findings further strengthen the radiative evolution theory for the Pseudocercospora banana pathogens (Arango‐Isaza et al ., ). With this information and knowledge of gene expansions in these pathogens, gene validation studies could be further intensified to gain more insight on gene function in the Pseudocercospora banana pathogens (Santana et al ., ).…”

“…These efforts have resulted in the identification of gene homologues associated with P. fijiensis virulence (Cho et al ., ; De Wit et al ., ; Stergiopoulos et al ., ). Later, the genomes of P. fijiensis isolates CIRAD86 and CIRAD139 were sequenced using Sanger and Illumina Hi Seq technologies, and have provided more detailed information on genomic structure and content, as well as the functionality of several genes in the pathogen (Ohm et al ., ; Arango‐Isaza et al ., ). These studies have clearly demonstrated genome expansion in P. fijiensis by the presence of repetitive sequences; such expansion may possibly be a result of horizontal gene transfer from banana or from other fungi colonizing banana (Friesen et al ., ; Arzanlou et al ., ; Ma et al ., ; Santana et al ., ; Czislowski et al ., ).…”

“…These studies have clearly demonstrated genome expansion in P. fijiensis by the presence of repetitive sequences; such expansion may possibly be a result of horizontal gene transfer from banana or from other fungi colonizing banana (Friesen et al ., ; Arzanlou et al ., ; Ma et al ., ; Santana et al ., ; Czislowski et al ., ). Comparative genomic analysis between P. fijiensis and P. eumusae has led to the suggestion that the two pathogens share a common ancestor and could have possibly emerged as a result of radiative evolution (Arango‐Isaza et al ., ). More importantly, these studies have determined that the gene content of virulent P. fijiensis and P. eumusae display complementary expansions and contractions in gene families involved in metabolism and enzymatic degradation (Chang et al ., ).…”

“…The genomes of these three pathogens have lineage‐specific transposable element expansions that may have played an important role during species divergence. Furthermore, it may be useful to apply reverse genetic studies to elucidate gene function in the Pseudocercospora banana pathogens; this may reveal new factors that are important for the virulence of the pathogens when colonizing banana (Arango‐Isaza et al ., ; Chang et al ., ).…”

“…Plant pathogens secrete a wide range of small molecules (microRNAs, metabolites and toxins) and proteins referred to as effectors that, depending on the host lifestyle, result in triggered resistance or susceptibility responses (Weiberg et al ., ; Vleeshouwers & Oliver, ; Arango‐Isaza et al ., ). Effector‐triggered immunity is a result of interaction between pathogen virulence factors and their cognate resistance genes in the host (Vleeshouwers & Oliver, ).…”