Comparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletales
Date
2017Author
Version
Acceso abierto / Sarbide irekia
Type
Artículo / Artikulua
Version
Versión publicada / Argitaratu den bertsioa
Project Identifier
ES/1PE/AGL2014–55971-R
Impact
|
10.1186/s12864-017-4243-z
Abstract
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.
Results: In this study we report the 39.07-megabase (Mb) draft genome assembly and annotation of ...
[++]
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.
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 LTRretrotransposons
showed that differential expansions of these repetitive elements have shaped the genome architecture of
Boletales over the last 60 million years.
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. [--]
Subject
Boletales,
Brown-rot,
Basidiomycete,
Genome,
Annotation,
Transposable elements,
Retrotransposon
Publisher
BioMed Central
Published in
BMC Genomics (2017) 18:883
Departament
Universidad Pública de Navarra. Departamento de Producción Agraria /
Nafarroako Unibertsitate Publikoa. Nekazaritza Ekoizpena Saila
Publisher version
Sponsorship
This work was supported by Spanish National Research Plan (Project
AGL2014–55971-R) and FEDER funds; Public University of Navarre. The work
of RC is supported by an FPI grant from the Spanish Ministry of Economy
and Competitiveness. The work conducted by the U.S. Department of Energy
Joint Genome Institute, a DOE Office of Science User Facility, is supported by
the Office of Science of the U.S. Department of Energy under Contract No.
DE-AC02-05CH11231.
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