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Comparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletales.

Authors :
Castanera, Raúl
Pérez, Gúmer
López-Varas, Leticia
Amselem, Joëlle
LaButti, Kurt
Singan, Vasanth
Lipzen, Anna
Haridas, Sajeet
Barry, Kerrie
Grigoriev, Igor V.
Pisabarro, Antonio G.
Ramírez, Lucía
Source :
BMC Genomics. 11/16/2017, Vol. 18, p1-14. 14p. 2 Diagrams, 4 Charts, 4 Graphs.
Publication Year :
2017

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 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. [ABSTRACT FROM AUTHOR]

Details

Language :
English
ISSN :
14712164
Volume :
18
Database :
Academic Search Index
Journal :
BMC Genomics
Publication Type :
Academic Journal
Accession number :
126278801
Full Text :
https://doi.org/10.1186/s12864-017-4243-z