A Large Family of AvrLm6-like Genes in the Apple and Pear Scab Pathogens, Venturia inaequalis and Venturia pirina

Abstract

Venturia inaequalis and V. pirina are Dothideomycete fungi that cause apple scab and pear scab disease, respectively. Whole genome sequencing of V. inaequalis and V. pirina isolates has revealed predicted proteins with sequence similarity to AvrLm6, a Leptosphaeria maculans effector that triggers a resistance response in Brassica napus and B. juncea carrying the resistance gene, Rlm6. AvrLm6-like genes are present as large families (>15 members) in all sequenced strains of V. inaequalis and V. pirina, while in L. maculans, only AvrLm6 and a single paralog have been identified. The Venturia AvrLm6-like genes are located in gene-poor regions of the genomes, and mostly in close proximity to transposable elements, which may explain the expansion of these gene families. An AvrLm6-like gene from V. inaequalis with the highest sequence identity to AvrLm6 was unable to trigger a resistance response in Rlm6-carrying B. juncea. RNA-seq and qRT-PCR gene expression analyses, of in planta- and in vitro-grown V. inaequalis, has revealed that many of the AvrLm6-like genes are expressed during infection. An AvrLm6 homolog from V. inaequalis that is up-regulated during infection was shown (using an eYFP-fusion protein construct) to be localized to the sub-cuticular stroma during biotrophic infection of apple hypocotyls.

Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range

“…The parameters (default) used were those that resulted in the AvrLm6-like proteins forming a cluster with the same members as when clustered manually [45]. The clusters were manually inspected and those members with a similar cysteine pattern retained.…”

Population genome sequencing of the scab fungal speciesVenturia inaequalis,Venturia pirina,Venturia aucupariaeandVenturia asperata

“…Other scab fungi are pathogenic on various tree hosts, including Fusicladium effusum on pecan, F. oleaginum on olive, V. populina on poplar, V. saliciperda on willow and V. fraxini on ash, among many others (Sivanesan, 1977;Zhang et al, 2011;Young et al, 2018). Despite being economically important pathogens, the genetic basis of the interactions between scab fungi and their respective hosts remains poorly understood (Singh et al, 2005;Steiner and Oerke, 2007;Kucheryava et al, 2008;Bowen et al, 2009;Mesarich et al, 2012;Cooke et al, 2014;Shiller et al, 2015;Deng et al, 2017).…”

“…pomi, V. inaequalis f. sp. eriobotrya, V. pirina and F. effusum, and they revealed that V. inaequalis strains tend to have a higher repeat content compared to other species, with up to 47% of their genome sequence covered by repetitive elements (Shiller et al 2015;Bock et al, 2016;Deng et al, 2017 ;Passey et al, 2018). These studies highlighted in Venturia genomes the expansion of putative effector gene families, genes that are known to determine plantfungus interactions (Shiller et al, 2015;Deng et al, 2017).…”

“…eriobotrya, V. pirina and F. effusum, and they revealed that V. inaequalis strains tend to have a higher repeat content compared to other species, with up to 47% of their genome sequence covered by repetitive elements (Shiller et al 2015;Bock et al, 2016;Deng et al, 2017 ;Passey et al, 2018). These studies highlighted in Venturia genomes the expansion of putative effector gene families, genes that are known to determine plantfungus interactions (Shiller et al, 2015;Deng et al, 2017). The high repeat content and the employed Illumina sequencing strategy resulted in assemblies with between 1,012 and 1,680 scaffolds (Shiller et al 2015;Deng et al, 2017) and up to 231 contigs using the PacBio technology (Passey et al, 2018).…”

“…These studies highlighted in Venturia genomes the expansion of putative effector gene families, genes that are known to determine plantfungus interactions (Shiller et al, 2015;Deng et al, 2017). The high repeat content and the employed Illumina sequencing strategy resulted in assemblies with between 1,012 and 1,680 scaffolds (Shiller et al 2015;Deng et al, 2017) and up to 231 contigs using the PacBio technology (Passey et al, 2018). Genetic studies need higher quality genome assemblies and genomic population studies require re-sequencing of many strains from diverse populations.…”