Population Genomics Reveals Population Structure and Mating-Type Loci in Marssonina brunnea .

Marssonina brunnea is an important fungal pathogen of poplar trees. We collected 32 M. brunnea f.sp. multigermtubi ( MbMu ) and three M. brunnea f.sp. monogermtubi ( MbMo ) isolates from four poplar species in three Chinese regions and performed genome resequencing. An annotation of SNPs of MbMu indicated that the SNPs potentially have a functional effect on 69.2% of the predicted genes. Using the SNP dataset of nonredundant isolates, a structure and principal component analysis revealed that MbMu and MbMo belong to two genetically distinct populations. By contrast, subpopulation structures could not be found among MbMu isolates. A neighbor-net analysis and a homoplasy index test provided evidence of recombination among MbMu isolates. The short distance (109-174 bp) of linkage disequilibrium half-decay supported the presence of a high level of recombination in the MbMu population. The genetic architectures of the MAT loci of MbMu and MbMo were revealed by searching genome assemblies or by homology-based cloning, and a BLAST search verified each isolate carrying one of the two opposite MAT loci. This study revealed that the MbMu population contains a wide range of functional variants, shows high-frequency recombination, and exhibits heterothallic mating systems, indicating high evolutionary potential and a resultant threat to poplar plantations.