11 research outputs found
Transposable elements versus the fungal genome: impact on whole-genome architecture and transcriptional profiles
Incluye 10 ficheros de datosTransposable elements (TEs) are exceptional contributors to eukaryotic genome diversity.
Their ubiquitous presence impacts the genomes of nearly all species and mediates genome
evolution by causing mutations and chromosomal rearrangements and by modulating gene
expression. We performed an exhaustive analysis of the TE content in 18 fungal genomes,
including strains of the same species and species of the same genera. Our results depicted
a scenario of exceptional variability, with species having 0.02 to 29.8% of their genome consisting
of transposable elements. A detailed analysis performed on two strains of Pleurotus
ostreatus uncovered a genome that is populated mainly by Class I elements, especially
LTR-retrotransposons amplified in recent bursts from 0 to 2 million years (My) ago. The preferential
accumulation of TEs in clusters led to the presence of genomic regions that lacked
intra- and inter-specific conservation. In addition, we investigated the effect of TE insertions
on the expression of their nearby upstream and downstream genes. Our results showed
that an important number of genes under TE influence are significantly repressed, with
stronger repression when genes are localized within transposon clusters. Our transcriptional
analysis performed in four additional fungal models revealed that this TE-mediated
silencing was present only in species with active cytosine methylation machinery. We
hypothesize that this phenomenon is related to epigenetic defense mechanisms that are
aimed to suppress TE expression and control their proliferation.This work was supported by Spanish
National Research Plan (Projects AGL2011-30495
and AGL2014-55971-R) and FEDER funds; Public
University of Navarre; U.S.
Department of Energy Joint Genome Institute; and
Office of Science of the U.S. Department of Energy
under Contract No. DE-AC02-05CH11231.
Comparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletales
Background: Coniophora olivacea is a basidiomycete fungus belonging to the order Boletales that produces brown-rot decay on dead wood of conifers. The Boletales order comprises a diverse group of species including saprotrophs and ectomycorrhizal fungi that show important differences in genome size. [br/]
Results: In this study we report the 39.07-megabase (Mb) draft genome assembly and annotation of C. olivacea. A total of 14,928 genes were annotated, including 470 putatively secreted proteins enriched in functions involved in lignocellulose degradation. Using similarity clustering and protein structure prediction we identified a new family of 10 putative lytic polysaccharide monooxygenase genes. This family is conserved in basidiomycota and lacks of previous functional annotation. Further analyses showed that C. olivacea has a low repetitive genome, with 2.91% of repeats and a restrained content of transposable elements (TEs). The annotation of TEs in four related Boletales yielded important differences in repeat content, ranging from 3.94 to 41.17% of the genome size. The distribution of insertion ages of LTR-retrotransposons showed that differential expansions of these repetitive elements have shaped the genome architecture of Boletales over the last 60 million years. [br/]
Conclusions: Coniophora olivacea has a small, compact genome that shows macrosynteny with Coniophora puteana. The functional annotation revealed the enzymatic signature of a canonical brown-rot. The annotation and comparative genomics of transposable elements uncovered their particular contraction in the Coniophora genera, highlighting their role in the differential genome expansions found in Boletales species