Genome-wide identification and annotation of microsatellite markers in white truffle (Tuber magnatum)

The white truffle Tuber magnatum Pico is an ectomycorrhizal fungus, which produces the most economically valuable edible ascomata, referred to as truffles. Highly appreciated sensory properties and exceptional market prices make truffle fungi an important focus of research. Accordingly, there is increasing interest to characterize truffle aroma volatiles, fully understand their reproduction and, characterize their genomes, analyze their population structure and molecular genetic diversity. While production of truffle species was confined before to natural woodlands, development of host seedling inoculation protocols in 1970s established truffle production as a managed agricultural activity. On the other hand, T. magnatum inoculated seedling production was achieved only recently, since morphological criteria were insufficient for the precise identification of T. magnatum mycorrhizas without DNA-based identification protocols. The present research describes the development and functional annotation of novel microsatellite markers in T. magnatum genome. A bioinformatics workflow was applied in order to mine for microsatellite sequences in T. magnatum genome assembly, convert the loci to PCR markers, map marker amplification on genomic sequences and calculate allele sizes. As a result, 11 189 microsatellite markers specific to T. magnatum were developed. Annotation analysis was performed for marker sequences, resulting in 3377 marker loci matching with T. magnatum proteins. Thus, these markers have high potential to tag genes of interest in functional genomic analyses. As a result of the present work, a large database of T. magnatum specific DNA markers was introduced as a useful genomic resource for the valuable ectomycorrhizal fungus species