Genomic Sequencing of Phyllosticta citriasiana Provides Insight Into Its Conservation and Diversification With Two Closely Related Phyllosticta Species Associated With Citrus

Abstract

Phyllosticta capitalensis, Phyllosticta citricarpa, and Phyllosticta citriasiana are three very important Phyllosticta species associated with citrus. P. capitalensis is an endophyte fungus of citrus while P. citricarpa can cause black spot of citrus (e.g., oranges and mandarins). P. citriasiana was identified recently which is the causal agent of the pomelo tan spot. Here, we present the ∼34 Mb genome of P. citriasiana. The genome is organized in 92 contigs, encompassing 9202 predicted genes. Comparative genomic analyses with two other Phyllosticta species (P. citricarpa and P. capitalensis) associated with citrus was conducted to understand their evolutionary conservation and diversification. Pair-wise genome alignments revealed that these species are highly syntenic. All species encode similar numbers of CAZymes and secreted proteins. However, the molecular functions of the secretome showed that each species contains some enzymes with distinct activities. The three Phyllosticta species investigated shared a core set of 7261 protein families. P. capitalensis had the largest set of orphan genes (1991), in complete contrast to that of P. citriasiana (364) and P. citricarpa (262). Most of the orphan genes are functionally unknown, but they contain a certain number of species-specific secreted proteins. A total of 23 secondary metabolites biosynthesis clusters were identified in the three Phyllosticta species, 21 of them being highly conserved among these species while the remaining two showed whole cluster gain and loss polymorphisms or gene content polymorphisms. Taken together, our study reveals insights into the genetic mechanisms of host adaptation of three species of Phyllosticta associated with citrus and paves the way to identify effectors that function in infection of citrus plants.

Differential Expression of Fungal Genes Determines the Lifestyle of Plectosphaerella Strains During Arabidopsis thaliana Colonization

“…While nutrient acquisition of necrotrophic and hemibiotrophic fungi is based on killing the host cell at the last stage of infection, biotrophic fungi absorb nutrients from living cells (Laluk and Mengiste 2010;Oliver and Ipcho 2004). The genomes of the three Plectosphaerella strains studied here harbor similar numbers of CAZymes (Table 2), also in line with those found in other necrotrophic and hemibiotrophic phytopathogenic fungi of dicots (Gazis et al 2016;Knapp et al 2018;Wang et al 2020;Xu et al 2014). However, the numbers of GT, CE, GH, and PL CAZymes in Plectosphaerella genomes are higher than in other phytopathogenic fungi, except for some Colletotrichum and Fusarium species (Hacquard et al 2016).…”

“…Plant-fungus interactions are diverse and largely dependent on the genetic determinants of fungus and host and on the environmental conditions (Brader et al 2017;Rai and Agarkar 2016;Zeilinger et al 2016). Comparing closely related fungal species with different abilities to cause disease in different hosts can provide novel cues about the specific genetic determinants of pathogenesis (Hacquard et al 2016;Seidl et al 2015;Wang et al 2020;Xu et al 2014). In this work, we have compared the initial colonization steps of three strains of the genus Plectosphaerella on wild-type and immunocompromised Arabidopsis genotypes, and we have sequenced and annotated the genomes and studied the transcriptional responses of these fungi upon plant colonization.…”

Phytochemical and Therapeutic Potential of Citrus grandis (L.) Osbeck: A Review

“…It must be noted that lycopene and β-carotene found abundantly in red-fleshed ( Citrus grandis ) fruits may exert anticancer activity. 132 …”

Enemy or ally: a genomic approach to elucidate the lifestyle of Phyllosticta citrichinaensis

“…have been hampered by the quality of genomes and the availability of only a single endophyte genome (P. capitalensis), which was relatively distantly related to the species it was compared to, and consequently genomic adaptations towards these two broad lifestyles remained unclear (Wikee et al 2013b;Rodrigues et al 2019;Wang et al 2020). Therefore, a comparison of new and high-quality genomes which includes multiple species of different lifestyles could provide the necessary foundation to finally discovering the genomic underpinning for phytopathology in Phyllosticta, which is essential for the development of better disease management strategies.…”

“…Therefore, if these two species were certain to be of two different lifestyles, these species would be ideal to study pathogenicity in Phyllosticta. As the genome of P. citrichinaensis has not been included in earlier comparative work focused on lifestyle differences (Rodrigues et al 2019;Wang et al 2020), a thorough study of its genome and comparison to the genomes of the other species in this genus could provide valuable information on this species' lifestyle as well as genomic underpinning of disease mechanisms of other species in this genus. Here, we present the first comparative genomics study using multiple complete genomes of two endophytic and three phytopathogenic Phyllosticta species and established genomic differences between species of different lifestyles within this genus.…”