Genome-wide differentiation and mating-type gene variation distinguish life cycle forms of the Scots pine blister rust fungus Cronartium pini
Rust fungi have complex life-cycles, producing distinct spore stages and infecting one host species or two unrelated hosts. How mating-type (MAT) genes vary between contrasting life-cycles remains poorly understood. Cronartium pini provides a system to compare MAT genes within a species because it occurs as two life-cycle forms: a heteroecious form alternating between two hosts and producing five spore stages, and an autoecious form infecting one host and producing two spore stages. We generated genome assemblies for 18 isolates representing the two forms, and combined genome-wide SNP analyses with MAT gene read-depth estimates and phylogenetic reconstruction to compare their MAT gene variation. Genome-wide SNPs separated the forms, with heteroecious isolates showing high heterozygous SNP proportions and autoecious isolates showing low heterozygosity. MAT gene analyses showed that heteroecious isolates carried more MAT homologs and greater MAT sequence variation than autoecious isolates, with reduced read depth consistent with divergent homologs represented separately in the dikaryotic genome. Autoecious isolates carried fewer MAT homologs with read depth close to the genome-wide average, consistent with highly similar or identical MAT sequences in the two nuclei. However, a subset of autoecious isolates showed a distinct MATprofile with additional homologs. At the species level, C.pini showed tetrapolar MAT architecture. HD phylogenies were compatible with a multiallelic locus, whereas the P/R locus could not be resolved. These findings show that MAT gene variation is structured by life-cycle form and reveal unexpected heterogeneity within the autoecious form, providing a framework for future functional studies of mating compatibility in C.pini.
Rust fungi have complex life-cycles, producing distinct spore stages and infecting one host species or two unrelated hosts. How mating-type (MAT) genes vary between contrasting life-cycles remains poorly understood. Cronartium pini provides a system to compare MAT genes within a species because it occurs as two life-cycle forms: a heteroecious form alternating between two hosts and producing five spore stages, and an autoecious form infecting one host and producing two spore stages. We generated genome assemblies for 18 isolates representing the two forms, and combined genome-wide SNP analyses with MAT gene read-depth estimates and phylogenetic reconstruction to compare their MAT gene variation. Genome-wide SNPs separated the forms, with heteroecious isolates showing high heterozygous SNP proportions and autoecious isolates showing low heterozygosity. MAT gene analyses showed that heteroecious isolates carried more MAT homologs and greater MAT sequence variation than autoecious isolates, with reduced read depth consistent with divergent homologs represented separately in the dikaryotic genome. Autoecious isolates carried fewer MAT homologs with read depth close to the genome-wide average, consistent with highly similar or identical MAT sequences in the two nuclei. However, a subset of autoecious isolates showed a distinct MATprofile with additional homologs. At the species level, C.pini showed tetrapolar MAT architecture. HD phylogenies were compatible with a multiallelic locus, whereas the P/R locus could not be resolved. These findings show that MAT gene variation is structured by life-cycle form and reveal unexpected heterogeneity within the autoecious form, providing a framework for future functional studies of mating compatibility in C.pini.
Swedish University of Agricultural Sciences