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

BMC Genomics

Research Article

Leticia López-Varas¹  Gúmer Pérez¹  Raúl Castanera¹  Antonio G. Pisabarro¹  Lucía Ramírez¹  Sajeet Haridas²  Kerrie Barry²  Anna Lipzen²  Kurt LaButti²  Igor V. Grigoriev²  Vasanth Singan²  Joëlle Amselem³ 

[1] Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, 31006, Pamplona, Navarre, Spain;U.S.Department of Energy Joint Genome Institute, 94598, Walnut Creek, CA, USA;URGI, INRA, Université Paris-Saclay, 78026, Versailles, France;

关键词: Boletales;    Brown-rot;    Basidiomycete;    Genome;    Annotation;    Transposable elements;    Retrotransposon;   

DOI  :  10.1186/s12864-017-4243-z

 received in 2017-06-23, accepted in 2017-10-31,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundConiophora 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.ResultsIn 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.ConclusionsConiophora 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.

【 授权许可】

CC BY   
© The Author(s). 2017