Filamentous ascomycete genomes provide insights into Copia retrotransposon diversity in fungi

BMC Genomics

Research Article

Mathieu Piednoël¹  Dominique Higuet²  Éric Bonnivard²  Tifenn Donnart² 

[1] Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829, Cologne, Germany;Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), 75005, Paris, France;

关键词: Comparative genomic;    Fungi Copia retrotransposons;    GalEa elements;    Conserved Hairpin Site;   

DOI  :  10.1186/s12864-017-3795-2

 received in 2016-11-10, accepted in 2017-05-16,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundThe relative scarcity of Copia retrotransposons has been recently characterized in metazoans in comparison with the other superfamilies of LTR elements. Furthermore, Copia retrotransposons have often a particular dynamics that results in a highly predominant single clade of elements within a large host taxon, such as the GalEa-like retrotransposons in crustaceans. Taking advantage of the skyrocketing amount of genomic data available for fungi, we carried out the first large-scale comparative genomic analysis of the Copia clades in filamentous ascomycetes.ResultsScreening 30 completely sequenced genomes allowed us to identify more than 2500 Copia copies with conserved LTR, which are distributed in 138 families. Their characterization revealed that fungal Copia diversity is much broader than previously thought with at least 27 clades, 23 of which likely correspond to new ones. While the Copia copy number is low in most species, the two clades GalEa and FunCo1 are widely distributed and highly dominate Copia content as they both account for 80% of the detected sequences.ConclusionsIn Fungi, GalEa retrotransposons are restricted to Pezizomycotina in which they can make up an outstandingly high proportion of the genome (up to 10% in Cenococcum geophilum). At last, we revealed that fungal GalEa elements structurally differ from all other Copia elements with an absence of Primer Binding Site. These elements however harbor a Conserved Hairpin Site which is probably essential for their transposition.

【 授权许可】

CC BY   
© The Author(s). 2017