Laccaria amethystina LaAM-08-1 v2.0
Laccaria amethystina
Gregarious, deep purple, mushrooms of L. amethystina that grow among moss and leaf litter under spruce trees (© F Martin).

Within the framework of the JGI Mycorrhizal Genomics Initiative, we are sequencing a phylogenetically and ecologically diverse suite of mycorrhizal fungi (Basidiomycota and Ascomycota), which include the major clades of symbiotic species associating with trees and woody shrubs. Analyses of these genomes will provide insight into the diversity of mechanisms for the mycorrhizal symbiosis, including endo- and ectomycorrhiza.

The Laccaria Pan-Genome

Laccaria Berkeley and Broome is a cosmopolitan genus of mushrooms (Agaricales) collected frequently throughout North America and Eurasia. Its taxa make up a sizeable part of the basidiomycetous ECM species and have been reported from every continent except Antarctica. Because of the relative ease with which some species of Laccaria can be manipulated in the laboratory, several taxa including L. bicolor (Maire) Orton, L. laccata (Scop.: Fr.) Cooke and L. proxima (Boud.) Pat. are widely used in applied and basic research on ECM fungi, whereas L. amethystina ecology has been investigated in many ecosystems. Therefore, evolutionary genomics of Laccaria would have applied implications because of the ecological and potential economic importance of many of its taxa in addition to adding to our basic knowledge of fungi which form symbiosis.

To fully apply comparative, evolutionary genomics to symbiotic fungi, intragenus and population genome samples are needed. Here, we propose to resequence by Illumina GA the genome of 20 Laccaria strains including (1) three Laccaria species (L. laccata, L. proxima, L. tortilis) and (2) 17 strains of L. bicolor and L. amethystina of different geographic locations. These sequences will be mapped to the v2.0 of the reference L. bicolor genome (Martin et al., 2008).

A population genomic analysis of L. bicolor and L. amethystina which are closely related and split from the outgroup species, L. laccata and L. proxima, several million years ago will be carried out. The vast majority of L. amethystina DNA is readily aligned to L. bicolor (Martin, unpublished results), which permits direct use of L. bicolor annotation for investigation of polymorphism and divergence and allows reliable inference of L. bicolor/L. amethystina ancestral states over much of the genome. The analysis will use the JGI reference genome v2.0 of L. bicolor, an INRA draft version of L. amethystina genome assembly (Martin, unpublished results) and a set of light-coverage, whole-genome Illumina resequencing data from 17 American, European, and Japanese strains of L. amethystina and L. bicolor.

Such large sampling from populations in America and Eurasia will give a complete view of genomic variation in this species including vast numbers of rare variants of many different kinds (e.g. structural variants) throughout the genome. The goal here is to identify genomic regions that are candidates for selective adaptation. The main impact of this resource will be detailed annotation of the L. bicolor genome and the fostering of experimental population genomic approaches to the systematic identification of adaptations. This would allow mycologists to extract the most information about adaptive mutations that are most likely to be important to symbiosis in a well-investigated symbiotic clade.

Genome Reference(s)