Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Population Genomic Differentiation of the Ectomycorrhizal Fungus Suillus pungens Along a Climate Gradient

Authors:

Jay Yeam1* (jyeam@stanford.edu), Kabir G. Peay1,2

Institutions:

1Department of Biology, Stanford University; 2Department of Earth System Science, Stanford University

Goals

This project examines genomic and functional variation among ectomycorrhizal fungi along a natural climate gradient and consequences for host adaptation and ecosystem function.

Abstract

Dispersal limitations and geographic barriers can influence microbial population structure and gene flow at the landscape level, resulting in divergent genotypes and regional endemism. However, the drivers and genetic basis of population differentiation across large spatial scales, particularly among mycorrhizal fungi, remains poorly understood. This study investigates the population structure of Suillus pungens, an ectomycorrhizal fungus endemic to the California coast and a host-specialist to Pinus muricata and Pinus radiata. The research team performed whole-genome sequencing on 70 individuals collected across a latitudinal and 4-fold precipitation gradient. The team used a combination of paired-end sequencing on the Illumina NextSeq 500 System (with a 2 x 150 base pair read length) and MiSeq (2 x 250 base pair read length) and produced a total average read depth of 6. Using an annotated reference genome, gene variant bioinformatic approaches (GATK) were employed, resulting in identification of 541,091 SNPs across these 70 individuals. Significant population genetic structure was found among Northern and Southern populations as well as highly differentiated host-associated genotypes. Of these SNPs, a strong functional signature of adaptation was identified, with southern populations enriched in genes involved in cell signaling and membrane fluidity, a potential adaptation to drought stress. These results provide some of the first genomic evidence for local adaptation within ectomycorrhizal species and show that barriers to gene flow can develop over relatively small spatial scales. Future work will explore how this degree of local adaptation by ectomycorrhizal fungi contributes to host stress tolerance or affects ecosystem function.

Funding Information

This project is funded by award DE-SC0023661 from the DOE Office of Science, BER Program.