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.
Highlights
MATERIALS AND METHODSCitrus Black Spot (CBS), caused by Phyllosticta citricarpa, is an important disease of citrus, it can affect almost all grown citrus cultivars, including sweet orange (Citrus sinensis), mandarin (C. reticulata and C. unshiu), lime (C. aurantium) and lemon (C. limon) (Wang et al, 2012; Guarnaccia et al, 2019)
We assembled the genome of P. citriasiana using a combination of Illumina and PacBio reads with ∼250 fold of sequence depth
The assembly of P. citricarpa and P. capitalensis possess a large number of contigs, the BUSCO results showed that they are around 95% completeness, suggesting that these genomes are reliable for the downstream analyses (Table 1)
Summary
Citrus Black Spot (CBS), caused by Phyllosticta citricarpa, is an important disease of citrus, it can affect almost all grown citrus cultivars, including sweet orange (Citrus sinensis), mandarin (C. reticulata and C. unshiu), lime (C. aurantium) and lemon (C. limon) (Wang et al, 2012; Guarnaccia et al, 2019). We sequenced the genome of P. citriasiana, generating a high-quality reference genome assembly and provide an overview of the genome structure of this important pathogen; we compared its genome with other two closely related Phyllosticta species associated with citrus, i.e., P. citricarpa and P. capitalensis to provide insight into their evolutionary conservation and diversification. The resulting codon alignment was entered into PAML to calculate the Ka and Ks value with the Yang and Nielsen method (Yang and Nielsen, 2000; Yang, 2007)
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
