Genome Comparison Reveals a High-Resolution DNA Marker for Phylogenetic Discrimination Within the Colletotrichum gloeosporioides Species Complex

This is the authors' abstract. We don't add key points for this paper.

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.