AUTHOR=Bahri Bochra Amina , Parvathaneni Rajiv Krishna , Spratling Willis Turner , Saxena Harshita , Sapkota Suraj , Raymer Paul L. , Martinez-Espinoza Alfredo D. 

TITLE=Whole genome sequencing of Clarireedia aff. paspali reveals potential pathogenesis factors in Clarireedia species, causal agents of dollar spot in turfgrass

JOURNAL=Frontiers in Genetics

VOLUME=13

YEAR=2023

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.1033437

DOI=10.3389/fgene.2022.1033437

ISSN=1664-8021

ABSTRACT=<p>Dollar spot is one of the most damaging diseases in turfgrass, reducing its quality and playability. Two species, <italic>Clarireedia monteithiana</italic> and <italic>C. jacksonii</italic> (formerly <italic>Sclerotinia homoeocarpa</italic>) have been reported so far in the United States To study the <italic>Clarireedia</italic> genome, two isolates H2 and H3, sampled from seashore paspalum in Hawaii in 2019 were sequenced <italic>via</italic> Illumina paired-end sequencing by synthesis technology and PacBio SMRT sequencing. Both isolates were identified as <italic>C</italic>. aff. <italic>paspali</italic>, a novel species in the United States Using short and long reads, <italic>C</italic>. aff. <italic>paspali</italic> H3 contained 193 contigs with 48.6 Mbp and presented the most completed assembly and annotation among <italic>Clarireedia</italic> species. Out of the 13,428 protein models from AUGUSTUS, 349 cytoplasmic effectors and 13 apoplastic effectors were identified by EffectorP. To further decipher <italic>Clarireedia</italic> pathogenicity, <italic>C</italic>. aff. <italic>paspali</italic> genomes (H2 and H3), as well as available <italic>C. jacksonii</italic> (LWC-10 and HRI11), <italic>C. monteithiana</italic> (DRR09 and RB-19) genomes were screened for fifty-four pathogenesis determinants, previously identified in <italic>S. sclerotiorum</italic>. Seventeen orthologs of pathogenicity genes have been identified in <italic>Clarireedia</italic> species involved in oxalic acid production (<italic>pac1</italic>, <italic>nox1</italic>), mitogen-activated protein kinase cascade (<italic>pka1</italic>, <italic>smk3</italic>, <italic>ste12</italic>), appressorium formation (<italic>caf1</italic>, <italic>pks13</italic>, <italic>ams2</italic>, <italic>rgb1</italic>, <italic>rhs1</italic>) and glycolytic pathway (<italic>gpd</italic>). Within these genes, 366 species-specific SNPs were recorded between <italic>Clarireedia</italic> species; twenty-eight were non-synonymous and non-conservative. The predicted protein structure of six of these genes showed superimposition of the models among <italic>Clarireedia</italic> spp. The genomic variations revealed here could potentially lead to differences in pathogenesis and other physiological functions among <italic>Clarireedia</italic> species.</p>