NDLI: Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers

Content Provider	Springer Nature Link
Author	Labbé, Jessy Murat, Claude Morin, Emmanuelle Tacon, François Martin, Francis
Copyright Year	2010
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.
Starting Page	75
Ending Page	88
Page Count	14
File Format	PDF
ISSN	01728083
Journal	Current Genetics
Volume Number	57
Issue Number	2
e-ISSN	14320983
Language	English
Publisher	Springer-Verlag
Publisher Date	2010-12-04
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Simple sequence repeat Microsatellites Laccaria bicolor Ectomycorrhizal fungus Microbial Genetics and Genomics Microbiology Cell Biology Proteomics Plant Sciences Biochemistry
Content Type	Text
Resource Type	Article
Subject	Genetics Medicine

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