Comparative genome analysis identifies necrosis-inducing effectors in the lentil pathogen Ascochyta lentis in isolates with distinct virulence profiles

Background Ascochyta blight of lentil is a devastating fungal disease caused by the hemibiotrophic fungal pathogen Ascochyta lentis. This disease leads to significant yield loss and reduced seed quality when not managed properly. Fungal pathogens employ a suite of effectors to manipulate their host. Here, we present telomere-to-telomere assemblies, genome annotations, and comparative genome analysis of two A. lentis isolates, Al Kewell and P94-24, with opposing virulence profiles to identify and characterise effector-like elements. Results The two genomes are highly syntenic and only contain a small number of structural variations, mostly limited to repeat-rich regions, more specifically long terminal repeat retrotransposons. Protein coding genes were ranked for their effector likelihood using Predector. The top 12 candidate effectors were characterised by agroinfiltration into Nicotiana benthamiana , of which 11 candidates induced necrotic lesions including the two candidates present only in Al Kewell. Another major difference is the presence of Penelope -like elements of type Coprina at several chromosomal ends in the genome of P94-24 and their absence in Al Kewell. Al Kewell on the other hand contains two biosynthetic gene clusters which are heavily truncated in P94-24 and are predicted to encode genes involved in the synthesis of known fungal toxins, one of which is an effector candidate that induced necrosis on N. benthamiana . Conclusions These genomic resources present new interesting effector candidates and other putative pathogenicity elements that should advance our understanding of the complex lentil-pathogen interaction.