2025/07/16 by Ying Tan, Ziying Ma, Xuefan Hua +8 · 1 voice
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #Mycorrhizal Fungi and Plant Interactions #Plant Pathogens and Fungal Diseases #Yeasts and Rust Fungi Studies
paper · doi:10.1094/phyto-07-24-0239-sc
openalex publication_date 2025/07/16 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01
species complex (CGSC), comprising more than 50 closely related species, constitutes a globally significant phytopathogenic group. Current species delimitation within this complex predominantly relies on multilocus phylogeny, an approach that is time-consuming and technically demanding. To address these limitations, we screened for novel high-resolution markers by performing comparative analyses of public CGSC genomes. Candidate loci being universally present across the CGSC and showing a clock-like evolutionary rate and rapid sequence divergence were further evaluated based on characteristics of the DNA barcoding gap, gene tree-species tree concordance, and phylogenetic topological support. This multi-criteria screening pipeline identified a 3,111-bp locus (M28), which encodes a PMS1 homolog in the DNA mismatch repair pathway with good potential. In phylogenetic reconstruction using 103 representative isolates spanning 41 validated CGSC species, single-locus M28 phylogeny showed high topological congruence with genome-based phylogeny and demonstrated good species-level discrimination capacity, except for very shallow phylogenetic nodes. Consequently, a degenerate primer pair targeting the M28 locus was designed, which demonstrated high PCR amplification efficiency. Together, this study establishes M28 as an efficient species discrimination barcode for cost-effective, high-throughput species diversity assessments in the CGSC.