Abstract
It is becoming clear that simple sequence repeats
(SSRs) play a significant role in fungal genome organization,
and they are a large source of genetic markers for population
genetics and meiotic maps. We identified SSRs in the Laccaria
bicolor genome by in silico survey and analyzed their
distribution in the different genomic regions. We also compared
the abundance and distribution of SSRs in L. bicolor
with those of the following fungal genomes: Phanerochaete
chrysosporium, Coprinopsis cinerea, Ustilago maydis,
Cryptococcus neoformans, Aspergillus nidulans, Magnaporthe
grisea, Neurospora crassa and Saccharomyces cerevisiae.
Using the MISA computer program, we detected
277,062 SSRs in the L. bicolor genome representing 8% of
the assembled genomic sequence. Among the analyzed
basidiomycetes, L. bicolor exhibited the highest SSR density
although no correlation between relative abundance and the
genome sizes was observed. In most genomes the short
motifs (mono- to trinucleotides) were more abundant than
the longer repeated SSRs. Generally, in each organism, the
occurrence, relative abundance, and relative density of SSRs
decreased as the repeat unit increased. Furthermore, each
organism had its own common and longest SSRs. In the
L. bicolor genome, most of the SSRs were located in intergenic
regions (73.3%) and the highest SSR density was
observed in transposable elements (TEs; 6,706 SSRs/Mb).
However, 81% of the protein-coding genes contained SSRs
in their exons, suggesting that SSR polymorphism may alter
gene phenotypes. Within a L. bicolor offspring, sequence
polymorphism of 78 SSRs was mainly detected in non-TE
intergenic regions. Unlike previously developed microsatellite
markers, these new ones are spread throughout the
genome; these markers could have immediate applications in
population genetics.