Abstract
BackgroundThe publicly available Laccaria bicolor genome sequence has provided a considerable genomic resource allowing systematic identification of transposable elements (TEs) in this symbiotic ectomycorrhizal fungus. Using a TE-specific annotation pipeline we have characterized and analyzed TEs in the L. bicolor S238N-H82 genome.Methodology/Principal FindingsTEs occupy 24% of the 60 Mb L. bicolor genome and represent 25,787 full-length and partial copy elements distributed within 171 families. The most abundant elements were the Copia-like. TEs are not randomly distributed across the genome, but are tightly nested or clustered. The majority of TEs exhibits signs of ancient transposition except some intact copies of terminal inverted repeats (TIRS), long terminal repeats (LTRs) and a large retrotransposon derivative (LARD) element. There were three main periods of TE expansion in L. bicolor: the first from 57 to 10 Mya, the second from 5 to 1 Mya and the most recent from 0.5 Mya ago until now. LTR retrotransposons are closely related to retrotransposons found in another basidiomycete, Coprinopsis cinerea.ConclusionsThis analysis 1) represents an initial characterization of TEs in the L. bicolor genome, 2) contributes to improve genome annotation and a greater understanding of the role TEs played in genome organization and evolution and 3) provides a valuable resource for future research on the genome evolution within the Laccaria genus.
Highlights
This analysis 1) represents an initial characterization of transposable elements (TEs) in the L. bicolor genome, 2) contributes to improve genome annotation and a greater understanding of the role TEs played in genome organization and evolution and 3) provides a valuable resource for future research on the genome evolution within the Laccaria genus
From the 171 consensus sequences obtained by the RMBLR procedure, excluding 56 TE fragments, we identified 115 families of TEs in L. bicolor containing 930 full-length copies and 13,787 incomplete copies
We identified two Tad, one Deceiver, one L1, five LINEs, four MITEs, three large retrotransposon derivatives (LARD), one ERV, one DIRS, and one Helitron
Summary
L. bicolor is characterized by its ubiquitous geographical distribution and lack of strict host specificity. This habit has been associated with its relatively large genome, containing the largest fungal gene repertoire and an abundance of multiple gene families relative to other ectomycorrhizal fungi, which in turn facilitates its adaptation to and interaction with various hosts [2]. The whole-genome sequence (WGS) of L. bicolor S238N-H82 provided the first ectomycorrhizal symbiont blueprint, fostering new insights into the nature of the genome of one of the largest groups of fungi [2]. The publicly available Laccaria bicolor genome sequence has provided a considerable genomic resource allowing systematic identification of transposable elements (TEs) in this symbiotic ectomycorrhizal fungus. Using a TEspecific annotation pipeline we have characterized and analyzed TEs in the L. bicolor S238N-H82 genome
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